diff --git a/reports/anvil-production/README.md b/reports/anvil-production/README.md index ae9c7c906..5d9dacf9e 100644 --- a/reports/anvil-production/README.md +++ b/reports/anvil-production/README.md @@ -13,4 +13,4 @@ After each successful deployment, automated tool tests are also run against the Latest tool tests for each chunk: -
Chunk IDTool ListLatest reportPrevious report
0ToolsetMon Dec 23 00:52:47 2024Mon Dec 16 00:56:24 2024
1ToolsetMon Dec 23 12:51:32 2024Mon Dec 16 12:56:13 2024
2ToolsetTue Dec 24 00:51:49 2024Tue Dec 17 00:54:20 2024
3ToolsetTue Dec 24 12:51:57 2024Tue Dec 17 12:55:09 2024
4ToolsetWed Dec 25 00:50:33 2024Wed Dec 18 00:53:13 2024
5ToolsetWed Dec 25 12:50:42 2024Wed Dec 18 12:54:17 2024
6ToolsetThu Dec 26 00:49:58 2024Thu Dec 19 00:52:41 2024
7ToolsetThu Dec 26 12:50:53 2024Thu Dec 19 12:53:13 2024
8ToolsetFri Dec 27 00:52:01 2024Fri Dec 20 00:50:54 2024
9ToolsetFri Dec 27 12:50:36 2024Fri Dec 20 12:50:33 2024
10ToolsetSat Dec 28 00:50:11 2024Sat Dec 21 00:51:11 2024
11ToolsetSat Dec 28 12:48:29 2024Sat Dec 21 12:49:28 2024
12ToolsetSun Dec 29 00:56:38 2024Sun Dec 22 00:55:45 2024
13ToolsetSun Dec 29 12:48:44 2024Sun Dec 22 12:48:27 2024
+
Chunk IDTool ListLatest reportPrevious report
0ToolsetMon Dec 30 00:52:50 2024Mon Dec 23 00:52:47 2024
1ToolsetMon Dec 23 12:51:32 2024Mon Dec 16 12:56:13 2024
2ToolsetTue Dec 24 00:51:49 2024Tue Dec 17 00:54:20 2024
3ToolsetTue Dec 24 12:51:57 2024Tue Dec 17 12:55:09 2024
4ToolsetWed Dec 25 00:50:33 2024Wed Dec 18 00:53:13 2024
5ToolsetWed Dec 25 12:50:42 2024Wed Dec 18 12:54:17 2024
6ToolsetThu Dec 26 00:49:58 2024Thu Dec 19 00:52:41 2024
7ToolsetThu Dec 26 12:50:53 2024Thu Dec 19 12:53:13 2024
8ToolsetFri Dec 27 00:52:01 2024Fri Dec 20 00:50:54 2024
9ToolsetFri Dec 27 12:50:36 2024Fri Dec 20 12:50:33 2024
10ToolsetSat Dec 28 00:50:11 2024Sat Dec 21 00:51:11 2024
11ToolsetSat Dec 28 12:48:29 2024Sat Dec 21 12:49:28 2024
12ToolsetSun Dec 29 00:56:38 2024Sun Dec 22 00:55:45 2024
13ToolsetSun Dec 29 12:48:44 2024Sun Dec 22 12:48:27 2024
diff --git a/reports/anvil-production/tool-tests/chunks.json b/reports/anvil-production/tool-tests/chunks.json index a1a198223..effd44b4e 100644 --- a/reports/anvil-production/tool-tests/chunks.json +++ b/reports/anvil-production/tool-tests/chunks.json @@ -84,11 +84,11 @@ "date2": "Fri Dec 20 00:50:54 2024" }, "0": { - "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-12-23-00-37-1/results.html", - "date1": "Mon Dec 23 00:52:47 2024", - "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-12-23-00-37-1/tools.yml", - "run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-12-16-00-40-1/results.html", - "date2": "Mon Dec 16 00:56:24 2024" + "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-12-30-00-37-1/results.html", + "date1": "Mon Dec 30 00:52:50 2024", + "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-12-30-00-37-1/tools.yml", + "run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-12-23-00-37-1/results.html", + "date2": "Mon Dec 23 00:52:47 2024" }, "7": { "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-12-26-12-35-1/results.html", diff --git a/reports/anvil-production/tool-tests/prod-24-12-30-00-37-1/chunk.json b/reports/anvil-production/tool-tests/prod-24-12-30-00-37-1/chunk.json new file mode 100644 index 000000000..acb43dfa7 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-12-30-00-37-1/chunk.json @@ -0,0 +1,7 @@ +{ + "0": { + "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-12-30-00-37-1/results.html", + "date1": "Mon Dec 30 00:52:50 2024", + "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-12-30-00-37-1/tools.yml" + } +} \ No newline at end of file diff --git a/reports/anvil-production/tool-tests/prod-24-12-30-00-37-1/chunk.txt b/reports/anvil-production/tool-tests/prod-24-12-30-00-37-1/chunk.txt new file mode 100644 index 000000000..4dc2f6329 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-12-30-00-37-1/chunk.txt @@ -0,0 +1,16 @@ +-t sra_tools --tool-version e08a7ad4378b +-t split_file_on_column --tool-version 37a53100b67e +-t fastq_filter --tool-version 81a9090d6df3 +-t samtools_view --tool-version b72793637686 +-t samtools_split --tool-version 135c85f4cfaf +-t sam_merge --tool-version 1977f1637890 +-t bcftools_concat --tool-version d40d4bf05718 +-t bcftools_annotate --tool-version 403553ae19f6 +-t vcffixup --tool-version 11f62f071125 +-t vcftools_annotate --tool-version 57a6550df582 +-t porechop --tool-version 93d623d9979c +-t deeptools_compute_gc_bias --tool-version 2bc10a9ca58b +-t bwa --tool-version 3fe632431b68 +-t snpsift_dbnsfp --tool-version 4e21e4f2bc48 +-t limma_voom --tool-version 0921444c832d +-t mummer_delta_filter --tool-version b3acbb3a6af0 diff --git a/reports/anvil-production/tool-tests/prod-24-12-30-00-37-1/errors/18d63872b3269485.json b/reports/anvil-production/tool-tests/prod-24-12-30-00-37-1/errors/18d63872b3269485.json new file mode 100644 index 000000000..ef32b52a8 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-12-30-00-37-1/errors/18d63872b3269485.json @@ -0,0 +1,44 @@ +{ + "model_class": "Job", + "id": "18d63872b3269485", + "state": "error", + "exit_code": null, + "update_time": "2024-12-30T01:24:07.030917", + "create_time": "2024-12-30T01:23:58.594333", + "galaxy_version": "23.1", + "command_version": null, + "copied_from_job_id": null, + "tool_id": "upload1", + "history_id": "1262154bdd2f9614", + "external_id": "gxy-bw9r7", + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/150/registry.xml' '/galaxy/server/database/jobs_directory/000/150/upload_params.json' '150:/galaxy/server/database/objects/9/2/e/dataset_92e7072c-bd26-4720-9dd9-24b19f4d0fd5_files:/galaxy/server/database/objects/9/2/e/dataset_92e7072c-bd26-4720-9dd9-24b19f4d0fd5.dat'", + "traceback": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_gm0vimvg\"", + "files_metadata": "{\"__current_case__\": 75, \"file_type\": \"fasta\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"bwa-mem-mt-genome.fa\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_yq8olrga\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"fasta\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "18d63872b3269485", + "src": "hda", + "uuid": "92e7072c-bd26-4720-9dd9-24b19f4d0fd5" + } + }, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stderr": "", + "stdout": "", + "job_messages": null, + "dependencies": [], + "user_email": "tests@fake.org", + "job_metrics": [] +} diff --git a/reports/anvil-production/tool-tests/prod-24-12-30-00-37-1/errors/196b84ddca54174e.json b/reports/anvil-production/tool-tests/prod-24-12-30-00-37-1/errors/196b84ddca54174e.json new file mode 100644 index 000000000..a4fa6c587 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-12-30-00-37-1/errors/196b84ddca54174e.json @@ -0,0 +1,47 @@ +{ + "model_class": "Job", + "id": "196b84ddca54174e", + "state": "error", + "exit_code": null, + "update_time": "2024-12-30T01:11:04.111061", + "create_time": "2024-12-30T01:10:55.277916", + "galaxy_version": "23.1", + "command_version": null, + "copied_from_job_id": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.9", + "history_id": "1262154bdd2f9614", + "external_id": "gxy-6hvzc", + "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && samtools split -f 'Read_Group_%!.bam' -u '/galaxy/server/database/objects/1/4/c/dataset_14cae4b9-035c-43dd-b791-7a371b5cb643.dat' -@ $addthreads '/galaxy/server/database/objects/1/6/c/dataset_16c65af2-71c6-444d-b73a-9dbe010b8b63.dat'", + "traceback": null, + "params": { + "__input_ext": "\"bam\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "header": null + }, + "inputs": { + "input_bam": { + "id": "274f511891181a00", + "src": "hda", + "uuid": "16c65af2-71c6-444d-b73a-9dbe010b8b63" + } + }, + "outputs": { + "output": { + "id": "196b84ddca54174e", + "src": "hda", + "uuid": "14cae4b9-035c-43dd-b791-7a371b5cb643" + } + }, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stderr": "", + "stdout": "", + "job_messages": null, + "dependencies": [], + "user_email": "tests@fake.org", + "job_metrics": [] +} diff --git a/reports/anvil-production/tool-tests/prod-24-12-30-00-37-1/errors/1bc5c07b81485c83.json b/reports/anvil-production/tool-tests/prod-24-12-30-00-37-1/errors/1bc5c07b81485c83.json new file mode 100644 index 000000000..885dbccc0 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-12-30-00-37-1/errors/1bc5c07b81485c83.json @@ -0,0 +1,44 @@ +{ + "model_class": "Job", + "id": "1bc5c07b81485c83", + "state": "error", + "exit_code": null, + "update_time": "2024-12-30T00:59:01.349179", + "create_time": "2024-12-30T00:58:52.041724", + "galaxy_version": "23.1", + "command_version": null, + "copied_from_job_id": null, + "tool_id": "upload1", + "history_id": "1262154bdd2f9614", + "external_id": "gxy-r5c47", + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/22/registry.xml' '/galaxy/server/database/jobs_directory/000/22/upload_params.json' '22:/galaxy/server/database/objects/b/6/f/dataset_b6f9f501-2b3c-44d2-893f-59e883837a99_files:/galaxy/server/database/objects/b/6/f/dataset_b6f9f501-2b3c-44d2-893f-59e883837a99.dat'", + "traceback": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_pfdgri5u\"", + "files_metadata": "{\"__current_case__\": 75, \"file_type\": \"fasta\"}", + "dbkey": "\"equCab2\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"chr_m.fasta\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_srjps2c_\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"fasta\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "1bc5c07b81485c83", + "src": "hda", + "uuid": "b6f9f501-2b3c-44d2-893f-59e883837a99" + } + }, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stderr": "", + "stdout": "", + "job_messages": null, + "dependencies": [], + "user_email": "tests@fake.org", + "job_metrics": [] +} diff --git a/reports/anvil-production/tool-tests/prod-24-12-30-00-37-1/errors/1e2ca038c6fae50b.json b/reports/anvil-production/tool-tests/prod-24-12-30-00-37-1/errors/1e2ca038c6fae50b.json new file mode 100644 index 000000000..fbd36397d --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-12-30-00-37-1/errors/1e2ca038c6fae50b.json @@ -0,0 +1,44 @@ +{ + "model_class": "Job", + "id": "1e2ca038c6fae50b", + "state": "error", + "exit_code": null, + "update_time": "2024-12-30T01:13:29.734171", + "create_time": "2024-12-30T01:13:21.747181", + "galaxy_version": "23.1", + "command_version": null, + "copied_from_job_id": null, + "tool_id": "upload1", + "history_id": "1262154bdd2f9614", + "external_id": "gxy-r69wd", + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/96/registry.xml' '/galaxy/server/database/jobs_directory/000/96/upload_params.json' '96:/galaxy/server/database/objects/4/3/6/dataset_4362608b-2033-46e3-9f03-9ae4ab2a427f_files:/galaxy/server/database/objects/4/3/6/dataset_4362608b-2033-46e3-9f03-9ae4ab2a427f.dat'", + "traceback": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_rcbypy56\"", + "files_metadata": "{\"__current_case__\": 328, \"file_type\": \"vcf\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"concat.1.a.vcf\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_xe3n0iq7\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"vcf\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "1e2ca038c6fae50b", + "src": "hda", + "uuid": "4362608b-2033-46e3-9f03-9ae4ab2a427f" + } + }, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stderr": "", + "stdout": "", + "job_messages": null, + "dependencies": [], + "user_email": "tests@fake.org", + "job_metrics": [] +} diff --git a/reports/anvil-production/tool-tests/prod-24-12-30-00-37-1/errors/8d426062260e5599.json b/reports/anvil-production/tool-tests/prod-24-12-30-00-37-1/errors/8d426062260e5599.json new file mode 100644 index 000000000..4f45d57ca --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-12-30-00-37-1/errors/8d426062260e5599.json @@ -0,0 +1,44 @@ +{ + "model_class": "Job", + "id": "8d426062260e5599", + "state": "error", + "exit_code": null, + "update_time": "2024-12-30T01:12:51.637365", + "create_time": "2024-12-30T01:12:42.076269", + "galaxy_version": "23.1", + "command_version": null, + "copied_from_job_id": null, + "tool_id": "upload1", + "history_id": "1262154bdd2f9614", + "external_id": "gxy-7lk46", + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/90/registry.xml' '/galaxy/server/database/jobs_directory/000/90/upload_params.json' '90:/galaxy/server/database/objects/c/1/1/dataset_c117bbb6-a4ec-4dc3-be7b-2cdf8c77d746_files:/galaxy/server/database/objects/c/1/1/dataset_c117bbb6-a4ec-4dc3-be7b-2cdf8c77d746.dat'", + "traceback": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_dcigc3_k\"", + "files_metadata": "{\"__current_case__\": 328, \"file_type\": \"vcf\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"concat.2.b.vcf\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_4tvyu87m\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"vcf\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "8d426062260e5599", + "src": "hda", + "uuid": "c117bbb6-a4ec-4dc3-be7b-2cdf8c77d746" + } + }, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stderr": "", + "stdout": "", + "job_messages": null, + "dependencies": [], + "user_email": "tests@fake.org", + "job_metrics": [] +} diff --git a/reports/anvil-production/tool-tests/prod-24-12-30-00-37-1/errors/9d9743b4b8ce0c75.json b/reports/anvil-production/tool-tests/prod-24-12-30-00-37-1/errors/9d9743b4b8ce0c75.json new file mode 100644 index 000000000..c07872df8 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-12-30-00-37-1/errors/9d9743b4b8ce0c75.json @@ -0,0 +1,44 @@ +{ + "model_class": "Job", + "id": "9d9743b4b8ce0c75", + "state": "error", + "exit_code": null, + "update_time": "2024-12-30T01:18:02.671700", + "create_time": "2024-12-30T01:17:54.229422", + "galaxy_version": "23.1", + "command_version": null, + "copied_from_job_id": null, + "tool_id": "upload1", + "history_id": "1262154bdd2f9614", + "external_id": "gxy-4npg9", + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/123/registry.xml' '/galaxy/server/database/jobs_directory/000/123/upload_params.json' '123:/galaxy/server/database/objects/c/a/4/dataset_ca478d32-1a6d-408d-a1b7-f0190ae03182_files:/galaxy/server/database/objects/c/a/4/dataset_ca478d32-1a6d-408d-a1b7-f0190ae03182.dat'", + "traceback": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_90jsm48h\"", + "files_metadata": "{\"__current_case__\": 328, \"file_type\": \"vcf\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"annotate3.vcf\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_eeh3mlfl\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"vcf\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "9d9743b4b8ce0c75", + "src": "hda", + "uuid": "ca478d32-1a6d-408d-a1b7-f0190ae03182" + } + }, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stderr": "", + "stdout": "", + "job_messages": null, + "dependencies": [], + "user_email": "tests@fake.org", + "job_metrics": [] +} diff --git a/reports/anvil-production/tool-tests/prod-24-12-30-00-37-1/errors/bf46a3337c78fbae.json b/reports/anvil-production/tool-tests/prod-24-12-30-00-37-1/errors/bf46a3337c78fbae.json new file mode 100644 index 000000000..dd816f24a --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-12-30-00-37-1/errors/bf46a3337c78fbae.json @@ -0,0 +1,44 @@ +{ + "model_class": "Job", + "id": "bf46a3337c78fbae", + "state": "error", + "exit_code": null, + "update_time": "2024-12-30T01:30:29.874464", + "create_time": "2024-12-30T01:30:18.785228", + "galaxy_version": "23.1", + "command_version": null, + "copied_from_job_id": null, + "tool_id": "upload1", + "history_id": "1262154bdd2f9614", + "external_id": "gxy-xsfmx", + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/177/registry.xml' '/galaxy/server/database/jobs_directory/000/177/upload_params.json' '187:/galaxy/server/database/objects/7/8/6/dataset_786d6f0f-fef3-436b-9dab-20ee29af478a_files:/galaxy/server/database/objects/7/8/6/dataset_786d6f0f-fef3-436b-9dab-20ee29af478a.dat'", + "traceback": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_sztuuv8u\"", + "files_metadata": "{\"__current_case__\": 677, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"Mut1.counts\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_z_op2nzb\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"auto\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "a5874df6dbd01444", + "src": "hda", + "uuid": "786d6f0f-fef3-436b-9dab-20ee29af478a" + } + }, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stderr": "", + "stdout": "", + "job_messages": null, + "dependencies": [], + "user_email": "tests@fake.org", + "job_metrics": [] +} diff --git a/reports/anvil-production/tool-tests/prod-24-12-30-00-37-1/errors/c932bf8ced6c313e.json b/reports/anvil-production/tool-tests/prod-24-12-30-00-37-1/errors/c932bf8ced6c313e.json new file mode 100644 index 000000000..26b82c105 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-12-30-00-37-1/errors/c932bf8ced6c313e.json @@ -0,0 +1,44 @@ +{ + "model_class": "Job", + "id": "c932bf8ced6c313e", + "state": "error", + "exit_code": null, + "update_time": "2024-12-30T01:03:31.288002", + "create_time": "2024-12-30T01:03:21.861264", + "galaxy_version": "23.1", + "command_version": null, + "copied_from_job_id": null, + "tool_id": "upload1", + "history_id": "1262154bdd2f9614", + "external_id": "gxy-7fn4f", + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/42/registry.xml' '/galaxy/server/database/jobs_directory/000/42/upload_params.json' '42:/galaxy/server/database/objects/5/b/a/dataset_5ba6f385-5fb8-4ea8-b781-f14cc4ccb78b_files:/galaxy/server/database/objects/5/b/a/dataset_5ba6f385-5fb8-4ea8-b781-f14cc4ccb78b.dat'", + "traceback": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_ywpc3_01\"", + "files_metadata": "{\"__current_case__\": 36, \"file_type\": \"bam\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"bam_to_sam_in1.bam\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_dqqyncqp\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"bam\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "c932bf8ced6c313e", + "src": "hda", + "uuid": "5ba6f385-5fb8-4ea8-b781-f14cc4ccb78b" + } + }, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stderr": "", + "stdout": "", + "job_messages": null, + "dependencies": [], + "user_email": "tests@fake.org", + "job_metrics": [] +} diff --git a/reports/anvil-production/tool-tests/prod-24-12-30-00-37-1/errors/f2cc7012ce9ef9eb.json b/reports/anvil-production/tool-tests/prod-24-12-30-00-37-1/errors/f2cc7012ce9ef9eb.json new file mode 100644 index 000000000..2c8108062 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-12-30-00-37-1/errors/f2cc7012ce9ef9eb.json @@ -0,0 +1,63 @@ +{ + "model_class": "Job", + "id": "f2cc7012ce9ef9eb", + "state": "error", + "exit_code": null, + "update_time": "2024-12-30T01:32:35.024142", + "create_time": "2024-12-30T01:32:08.640702", + "galaxy_version": "23.1", + "command_version": null, + "copied_from_job_id": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.58.1+galaxy0", + "history_id": "1262154bdd2f9614", + "external_id": "gxy-dmg8h", + "command_line": "Rscript '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/119b069fc845/limma_voom/limma_voom.R' -R '/galaxy/server/database/objects/7/0/d/dataset_70db7eb5-9187-4e8d-976c-2f85b234332d.dat' -o '/galaxy/server/database/objects/7/0/d/dataset_70db7eb5-9187-4e8d-976c-2f85b234332d_files' -m '/galaxy/server/database/objects/2/c/b/dataset_2cb770f2-6d4d-4ba6-910b-c692bc348e64.dat' -i 'Genotype::Mut,Mut,Mut,WT,WT,WT' -a '/galaxy/server/database/objects/5/3/8/dataset_53890e8f-2ca0-443f-b576-be0255b29fd3.dat' -D 'Mut-WT' -P i -l '0.0' -p '0.05' -d 'BH' -G '6' -t 3.0 -n 'TMM' -b && mkdir ./output_dir && cp '/galaxy/server/database/objects/7/0/d/dataset_70db7eb5-9187-4e8d-976c-2f85b234332d_files'/*tsv output_dir/ && cp -r ./glimma* '/galaxy/server/database/objects/7/0/d/dataset_70db7eb5-9187-4e8d-976c-2f85b234332d_files'", + "traceback": null, + "params": { + "__input_ext": "\"input\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "adv": "{\"lfc\": \"0.0\", \"normalisationOption\": \"TMM\", \"pAdjust\": \"BH\", \"pVal\": \"0.05\", \"robOption\": true, \"topgenes\": \"6\", \"treat\": false}", + "out": "{\"filtCounts\": false, \"libinfo\": false, \"normCounts\": false, \"plots\": \"i\", \"rdaOption\": false, \"rscript\": false}", + "f": "{\"filt\": {\"__current_case__\": 1, \"filt_select\": \"no\"}}", + "cont": "{\"__current_case__\": 1, \"cfile\": \"no\", 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+9927453eb3cf07d0,1262154bdd2f9614,anvil-test-2024-12-30-00-52,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +1bc5c07b81485c83,1262154bdd2f9614,anvil-test-2024-12-30-00-52,error,upload1,,,,,,,,,,, +222157f9a6d65187,1262154bdd2f9614,anvil-test-2024-12-30-00-52,ok,samtools_view/1.9+galaxy3,,,,4080.0000000,1.0000000,,,,,,0E-7 +5033959ec363fc59,1262154bdd2f9614,anvil-test-2024-12-30-00-52,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +f83dd5df92ab0095,1262154bdd2f9614,anvil-test-2024-12-30-00-52,ok,fastq_filter/1.1.5+galaxy2,,,,4080.0000000,1.0000000,,,,,,0E-7 +114c4fc9d837e2a4,1262154bdd2f9614,anvil-test-2024-12-30-00-52,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +a7423e877e245689,1262154bdd2f9614,anvil-test-2024-12-30-00-52,ok,fastq_filter/1.1.5+galaxy2,,,,4080.0000000,1.0000000,,,,,,0E-7 +c34145a5b18ac270,1262154bdd2f9614,anvil-test-2024-12-30-00-52,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +9fe808e36bac6b18,1262154bdd2f9614,anvil-test-2024-12-30-00-52,ok,fastq_filter/1.1.5+galaxy2,,,,4080.0000000,1.0000000,,,,,,0E-7 +7a2ddfbe28faee75,1262154bdd2f9614,anvil-test-2024-12-30-00-52,ok,upload1,,,,4080.0000000,1.0000000,,,,,,3.0000000 +b096be5748b51dbe,1262154bdd2f9614,anvil-test-2024-12-30-00-52,ok,fastq_filter/1.1.5+galaxy2,,,,4080.0000000,1.0000000,,,,,,0E-7 +0c0aaad32f0bd67e,1262154bdd2f9614,anvil-test-2024-12-30-00-52,ok,upload1,,,,4080.0000000,1.0000000,,,,,,3.0000000 +2e8e3dc12ae7e587,1262154bdd2f9614,anvil-test-2024-12-30-00-52,ok,fastq_filter/1.1.5+galaxy2,,,,4080.0000000,1.0000000,,,,,,0E-7 +eb7a7a25753973f3,1262154bdd2f9614,anvil-test-2024-12-30-00-52,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +b409dcdfe62a54cf,1262154bdd2f9614,anvil-test-2024-12-30-00-52,ok,fastq_filter/1.1.5+galaxy2,,,,4080.0000000,1.0000000,,,,,,1.0000000 +c22a295c0ada3a9f,1262154bdd2f9614,anvil-test-2024-12-30-00-52,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +0f853f868e941b7d,1262154bdd2f9614,anvil-test-2024-12-30-00-52,ok,fastq_filter/1.1.5+galaxy2,,,,4080.0000000,1.0000000,,,,,,0E-7 +724c2bda50d999de,1262154bdd2f9614,anvil-test-2024-12-30-00-52,ok,upload1,,,,4080.0000000,1.0000000,,,,,,5.0000000 +1f5f83989277390b,1262154bdd2f9614,anvil-test-2024-12-30-00-52,ok,fastq_filter/1.1.5+galaxy2,,,,4080.0000000,1.0000000,,,,,,0E-7 +5acef09e9d7f0e3e,1262154bdd2f9614,anvil-test-2024-12-30-00-52,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +2120c8b44284dbd0,1262154bdd2f9614,anvil-test-2024-12-30-00-52,ok,fastq_filter/1.1.5+galaxy2,,,,4080.0000000,1.0000000,,,,,,0E-7 +1262154bdd2f9614,1262154bdd2f9614,anvil-test-2024-12-30-00-52,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 diff --git a/reports/anvil-production/tool-tests/prod-24-12-30-00-37-1/job.log b/reports/anvil-production/tool-tests/prod-24-12-30-00-37-1/job.log new file mode 100644 index 000000000..faf199fc4 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-12-30-00-37-1/job.log @@ -0,0 +1,17560 @@ +DEBUG:yacman.yacman:Patching yaml loader +DEBUG:galaxy.app:python path is: /galaxy/server/scripts, /galaxy/server/lib, /galaxy/server/lib, /usr/local/lib/python310.zip, /usr/local/lib/python3.10, /usr/local/lib/python3.10/lib-dynload, /galaxy/server/.venv/lib/python3.10/site-packages +DEBUG:galaxy.config:Configuration directory is /galaxy/server/config +DEBUG:galaxy.config:Data directory is /galaxy/server/database +DEBUG:galaxy.config:Managed config directory is /galaxy/server/config +WARNING:galaxy.config:Paths for the 'interactivetools_map' option are now relative to 'data_dir', remove the leading 'database/' to suppress this warning: database/interactivetools_map.sqlite +WARNING:galaxy.config:Option master_api_key has been deprecated in favor of bootstrap_admin_api_key +WARNING:galaxy.config:Config option 'containers_resolvers_config_file' is deprecated and will be removed in a future release. Please consult the latest version of the sample configuration file. +INFO:alembic.runtime.migration:Context impl PostgresqlImpl. +INFO:alembic.runtime.migration:Will assume transactional DDL. +INFO:galaxy.model.migrations:Your galaxy database is up-to-date +INFO:alembic.runtime.migration:Context impl PostgresqlImpl. +INFO:alembic.runtime.migration:Will assume transactional DDL. +INFO:galaxy.model.migrations:Your tool shed install database is up-to-date +INFO:galaxy.app:Install database targeting Galaxy's database configuration. +DEBUG:galaxy.web_stack:WeblessApplicationStack initialized +DEBUG:galaxy.web_stack:Will attach to pool(s): job-handlers +galaxy.jobs DEBUG 2024-12-30 00:50:49,904 [pN:job_handler_0,p:8,tN:MainThread] Read job configuration from file: /galaxy/server/config/job_conf.yml +galaxy.jobs INFO 2024-12-30 00:50:49,905 [pN:job_handler_0,p:8,tN:MainThread] Job handler assignment methods set to: db-skip-locked +galaxy.jobs INFO 2024-12-30 00:50:49,905 [pN:job_handler_0,p:8,tN:MainThread] Tag [_default_] handlers: job_handler_0 +galaxy.web_stack.handlers DEBUG 2024-12-30 00:50:49,905 [pN:job_handler_0,p:8,tN:MainThread] default set to child with id or tag 'tpv_dispatcher' +galaxy.jobs DEBUG 2024-12-30 00:50:49,905 [pN:job_handler_0,p:8,tN:MainThread] Done loading job configuration +galaxy.security.vault WARNING 2024-12-30 00:50:50,206 [pN:job_handler_0,p:8,tN:MainThread] No vault configured. We recommend defining the vault_config_file setting in galaxy.yml +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,241 [pN:job_handler_0,p:8,tN:MainThread] Loading datatypes from /galaxy/server/lib/galaxy/config/sample/datatypes_conf.xml.sample +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,242 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.h. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,242 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.c. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,242 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.cpp. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,243 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.py. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,243 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.go. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,243 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.rs. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,243 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.cs. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,243 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension hep.root. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,243 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:JP2 from the datatype registry for extension jp2. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,243 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Ab1 from the datatype registry for extension ab1. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,244 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.assembly:Amos from the datatype registry for extension afg. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,245 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.goldenpath:GoldenPath from the datatype registry for extension agp. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,245 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioComposite from the datatype registry for extension anvio_cog_profile. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,245 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioComposite from the datatype registry for extension anvio_composite. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,246 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry for extension anvio_classifier. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,246 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioContigsDB from the datatype registry for extension anvio_contigs_db. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,246 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioDB from the datatype registry for extension anvio_db. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,246 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioGenomesDB from the datatype registry for extension anvio_genomes_db. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,246 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioPanDB from the datatype registry for extension anvio_pan_db. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,246 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioComposite from the datatype registry for extension anvio_pfam_profile. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,246 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioProfileDB from the datatype registry for extension anvio_profile_db. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,246 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioSamplesDB from the datatype registry for extension anvio_samples_db. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,246 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension anvio_state. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,246 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioStructureDB from the datatype registry for extension anvio_structure_db. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,246 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:TSV from the datatype registry for extension anvio_variability. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,247 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Arff from the datatype registry for extension arff. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,247 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Paf from the datatype registry for extension paf. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,247 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Gfa1 from the datatype registry for extension gfa1. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,247 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Gfa2 from the datatype registry for extension gfa2. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,247 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry for extension asn1. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,247 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry for extension asn1-binary. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,247 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Axt from the datatype registry for extension axt. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,247 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:FeatureLocationIndex from the datatype registry for extension fli. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,247 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Bam from the datatype registry for extension bam. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,248 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension bai. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,248 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:BamInputSorted from the datatype registry for extension qname_input_sorted.bam. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,248 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:BamQuerynameSorted from the datatype registry for extension qname_sorted.bam. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,248 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:BamNative from the datatype registry for extension unsorted.bam. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,248 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:ProBam from the datatype registry for extension probam. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,248 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CRAM from the datatype registry for extension cram. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,248 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:Bed from the datatype registry for extension bed. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,248 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:BedGraph from the datatype registry for extension bedgraph. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,248 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:BedStrict from the datatype registry for extension bedstrict. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,249 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:Bed6 from the datatype registry for extension bed6. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,249 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:Bed12 from the datatype registry for extension bed12. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,249 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:ProBed from the datatype registry for extension probed. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,249 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.chrominfo:ChromInfo from the datatype registry for extension len. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,249 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:DAA from the datatype registry for extension daa. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,249 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RMA6 from the datatype registry for extension rma6. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,250 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:DMND from the datatype registry for extension dmnd. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,250 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Parquet from the datatype registry for extension parquet. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,250 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Idat from the datatype registry for extension idat. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,250 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:BigBed from the datatype registry for extension bigbed. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,250 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:BigWig from the datatype registry for extension bigwig. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,250 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension cxb. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,250 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:ChromatinInteractions from the datatype registry for extension chrint. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,250 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry for extension csv. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,250 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:TSV from the datatype registry for extension tsv. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,250 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:TSV from the datatype registry for extension intermine_tabular. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,251 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:CustomTrack from the datatype registry for extension customtrack. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,251 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.ngsindex:BowtieColorIndex from the datatype registry for extension bowtie_color_index. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,251 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.ngsindex:BowtieBaseIndex from the datatype registry for extension bowtie_base_index. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,251 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:csFasta from the datatype registry for extension csfasta. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,251 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry for extension data. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,251 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension gz. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,251 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension binary. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,252 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension d3_hierarchy. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,252 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:ImgtJson from the datatype registry for extension imgt.json. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,252 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:GeoJson from the datatype registry for extension geojson. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,252 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension data_manager_json. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,252 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:DotBracket from the datatype registry for extension dbn. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,252 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension fai. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,252 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry for extension fasta. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,252 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Fastg from the datatype registry for extension fastg. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,252 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Fastq from the datatype registry for extension fastq. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,253 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:FastqSanger from the datatype registry for extension fastqsanger. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,253 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:FastqSolexa from the datatype registry for extension fastqsolexa. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,253 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:FastqCSSanger from the datatype registry for extension fastqcssanger. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,253 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:FastqIllumina from the datatype registry for extension fastqillumina. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,253 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:SequenceSplitLocations from the datatype registry for extension fqtoc. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,254 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Eland from the datatype registry for extension eland. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,254 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:ElandMulti from the datatype registry for extension elandmulti. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,254 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tracks:GeneTrack from the datatype registry for extension genetrack. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,254 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:Gff from the datatype registry for extension gff. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,254 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:Gff3 from the datatype registry for extension gff3. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,255 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Gif from the datatype registry for extension gif. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,255 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Gmaj from the datatype registry for extension gmaj.zip. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,255 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension graph_dot. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,255 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:Gtf from the datatype registry for extension gtf. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,255 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension toolshed.gz. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,255 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension hdf4. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,255 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry for extension h5. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,255 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry for extension scool. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,256 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Grib from the datatype registry for extension grib. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,256 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Loom from the datatype registry for extension loom. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,256 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Anndata from the datatype registry for extension h5ad. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,256 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Visium from the datatype registry for extension visium.tar.gz. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,256 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry for extension mz5. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,256 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension hyphy_results.json. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,256 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension hivtrace. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,256 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Cool from the datatype registry for extension cool. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,256 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:MCool from the datatype registry for extension mcool. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,256 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:H5MLM from the datatype registry for extension h5mlm. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,257 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:LudwigModel from the datatype registry for extension ludwig_model. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,257 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Html from the datatype registry for extension html. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,257 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Html from the datatype registry for extension ludwig_report.html. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,257 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:Interval from the datatype registry for extension interval. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,257 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension jellyfish. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,349 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.isa:IsaTab from the datatype registry for extension isa-tab. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,349 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.isa:IsaJson from the datatype registry for extension isa-json. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,349 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension picard_interval_list. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,350 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension gatk_interval. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,350 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension gatk_report. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,350 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension gatk_dbsnp. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,350 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension gatk_tranche. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,350 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension gatk_recal. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,350 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension hhr. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,350 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Jpg from the datatype registry for extension jpg. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,351 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension tiff. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,351 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension tf2. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,351 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension tf8. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,351 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension btf. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,351 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension tif. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,351 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension svs. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,351 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension scn. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,351 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension bif. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,351 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:OMETiff from the datatype registry for extension ome.tiff. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,352 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry for extension vms. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,352 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry for extension vmu. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,352 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry for extension ndpi. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,352 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Mirax from the datatype registry for extension mrxs. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,352 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Sakura from the datatype registry for extension svslide. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,352 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Bmp from the datatype registry for extension bmp. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,352 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Im from the datatype registry for extension im. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,352 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Pcd from the datatype registry for extension pcd. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,352 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Pcx from the datatype registry for extension pcx. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,352 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Ppm from the datatype registry for extension ppm. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,352 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Psd from the datatype registry for extension psd. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,352 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Xbm from the datatype registry for extension xbm. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,352 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Xpm from the datatype registry for extension xpm. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,352 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Rgb from the datatype registry for extension rgb. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,353 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Pbm from the datatype registry for extension pbm. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,353 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Pgm from the datatype registry for extension pgm. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,353 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Nrrd from the datatype registry for extension nrrd. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,353 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Nrrd from the datatype registry for extension nhdr. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,353 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:RNADotPlotMatrix from the datatype registry for extension rna_eps. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,354 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.qiime2:QIIME2Artifact from the datatype registry for extension qza. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,354 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.qiime2:QIIME2Visualization from the datatype registry for extension qzv. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,354 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.qiime2:QIIME2Metadata from the datatype registry for extension qiime2.tabular. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,354 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CompressedZipArchive from the datatype registry for extension zip. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,354 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CompressedZipArchive from the datatype registry for extension ncbi_genome_dataset.zip. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,354 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension tar. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,354 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Directory from the datatype registry for extension directory. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,354 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Yaml from the datatype registry for extension yaml. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,354 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension mrm. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,357 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Dta from the datatype registry for extension dta. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,357 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Dta2d from the datatype registry for extension dta2d. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,357 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Edta from the datatype registry for extension edta. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,357 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry for extension pepxml. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,357 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry for extension raw_pepxml. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,357 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry for extension peptideprophet_pepxml. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,357 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry for extension interprophet_pepxml. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,357 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:ProtXML from the datatype registry for extension protxml. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,357 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:ParamXml from the datatype registry for extension paramxml. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,357 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Kroenik from the datatype registry for extension kroenik. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,357 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PepList from the datatype registry for extension peplist. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,357 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PSMS from the datatype registry for extension psms. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,358 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PepXmlReport from the datatype registry for extension pepxml.tsv. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,358 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:ProtXmlReport from the datatype registry for extension protxml.tsv. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,358 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MascotDat from the datatype registry for extension mascotdat. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,358 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MzIdentML from the datatype registry for extension mzid. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,358 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:IdXML from the datatype registry for extension idxml. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,358 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:TandemXML from the datatype registry for extension tandem. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,358 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension sirius.ms. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,358 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:ThermoRAW from the datatype registry for extension thermo.raw. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,358 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:BafTar from the datatype registry for extension brukerbaf.d.tar. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,358 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:YepTar from the datatype registry for extension agilentbrukeryep.d.tar. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,358 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:TdfTar from the datatype registry for extension brukertdf.d.tar. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,358 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:MassHunterTar from the datatype registry for extension agilentmasshunter.d.tar. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,358 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:MassLynxTar from the datatype registry for extension watersmasslynx.raw.tar. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,359 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:WiffTar from the datatype registry for extension wiff.tar. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,359 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Wiff2Tar from the datatype registry for extension wiff2.tar. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,359 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MascotXML from the datatype registry for extension mascotxml. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,359 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MzTab from the datatype registry for extension mztab. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,359 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MzTab2 from the datatype registry for extension mztab2. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,359 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MzML from the datatype registry for extension mzml. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,359 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:NmrML from the datatype registry for extension nmrml. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,359 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Meryldb from the datatype registry for extension meryldb. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,359 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Bref3 from the datatype registry for extension bref3. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,359 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Mgf from the datatype registry for extension mgf. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,359 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Wiff from the datatype registry for extension wiff. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,359 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Wiff2 from the datatype registry for extension wiff2. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,360 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MzXML from the datatype registry for extension mzxml. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,360 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MzData from the datatype registry for extension mzdata. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,360 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Ms2 from the datatype registry for extension ms2. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,360 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MzQuantML from the datatype registry for extension mzq. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,360 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:SQlite from the datatype registry for extension sqlite. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,360 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:MzSQlite from the datatype registry for extension mz.sqlite. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,360 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:OSW from the datatype registry for extension osw. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,360 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:PQP from the datatype registry for extension pqp. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,360 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:TraML from the datatype registry for extension traml. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,360 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:TrafoXML from the datatype registry for extension trafoxml. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,360 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:FeatureXML from the datatype registry for extension featurexml. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,360 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:ConsensusXML from the datatype registry for extension consensusxml. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,360 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:UniProtXML from the datatype registry for extension uniprotxml. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,361 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:XquestXML from the datatype registry for extension xquest.xml. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,361 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:XquestSpecXML from the datatype registry for extension spec.xml. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,361 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:QCML from the datatype registry for extension qcml. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,361 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension mzqc. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,361 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Msp from the datatype registry for extension msp. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,361 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:SPLibNoIndex from the datatype registry for extension splib_noindex. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,361 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:SPLib from the datatype registry for extension splib. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,361 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:BlibSQlite from the datatype registry for extension blib. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,361 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:DlibSQlite from the datatype registry for extension dlib. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,361 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:ElibSQlite from the datatype registry for extension elib. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,362 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:XHunterAslFormat from the datatype registry for extension hlf. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,362 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:IdpDB from the datatype registry for extension idpdb. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,362 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Sf3 from the datatype registry for extension sf3. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,362 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension cps. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,362 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:ConnectivityTable from the datatype registry for extension ct. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,362 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:PostgresqlArchive from the datatype registry for extension postgresql. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,362 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:MongoDBArchive from the datatype registry for extension mongodb. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,362 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:GeneNoteBook from the datatype registry for extension genenotebook. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,362 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:SearchGuiArchive from the datatype registry for extension searchgui_archive. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,362 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Fast5Archive from the datatype registry for extension fast5.tar. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,362 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Fast5ArchiveGz from the datatype registry for extension fast5.tar.gz. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,363 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Fast5ArchiveBz2 from the datatype registry for extension fast5.tar.bz2. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,363 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension peptideshaker_archive. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,363 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension percin. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,363 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry for extension percout. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,363 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension hardklor. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,363 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension kronik. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,363 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:ImzML from the datatype registry for extension imzml. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,364 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Analyze75 from the datatype registry for extension analyze75. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,364 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Nifti1 from the datatype registry for extension nii1. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,364 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Nifti2 from the datatype registry for extension nii2. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,364 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Gifti from the datatype registry for extension gii. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,364 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tck from the datatype registry for extension tck. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,365 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Trk from the datatype registry for extension trk. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,365 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Mrc2014 from the datatype registry for extension mrc. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,365 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Star from the datatype registry for extension star. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,365 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PEFF from the datatype registry for extension peff. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,365 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension toml. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,365 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.flow:FCS from the datatype registry for extension fcs. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,366 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowtext. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,366 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowclr. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,366 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowmfi. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,366 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowstat1. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,366 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowstat2. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,366 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowstat3. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,367 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowscore. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,367 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension flowframe. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,367 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension fsom. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,367 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension flowset. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,367 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension metacyto_clr.txt. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,367 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.metacyto:mSummary from the datatype registry for extension metacyto_summary.txt. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,368 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.metacyto:mStats from the datatype registry for extension metacyto_stats.txt. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,368 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension deeptools_compute_matrix_archive. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,368 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension deeptools_coverage_matrix. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,368 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:NetCDF from the datatype registry for extension netcdf. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,368 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Eps from the datatype registry for extension eps. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,368 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Rast from the datatype registry for extension rast. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,368 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Laj from the datatype registry for extension laj. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,368 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Lav from the datatype registry for extension lav. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,368 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Maf from the datatype registry for extension maf. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,369 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:MafCustomTrack from the datatype registry for extension mafcustomtrack. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,369 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:MatrixMarket from the datatype registry for extension mtx. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,369 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:CMAP from the datatype registry for extension cmap. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,369 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:ENCODEPeak from the datatype registry for extension encodepeak. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,369 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Pdf from the datatype registry for extension pdf. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,369 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Pileup from the datatype registry for extension pileup. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,369 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Psl from the datatype registry for extension psl. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,369 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Obo from the datatype registry for extension obo. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,369 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:Owl from the datatype registry for extension owl. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,369 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Png from the datatype registry for extension png. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,369 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore from the datatype registry for extension qual. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,369 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSolexa from the datatype registry for extension qualsolexa. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,370 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreIllumina from the datatype registry for extension qualillumina. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,370 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSOLiD from the datatype registry for extension qualsolid. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,370 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore454 from the datatype registry for extension qual454. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,370 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.assembly:Roadmaps from the datatype registry for extension roadmaps. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,370 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Sam from the datatype registry for extension sam. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,370 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Scf from the datatype registry for extension scf. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,370 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.assembly:Sequences from the datatype registry for extension sequences. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,370 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:SnpEffDb from the datatype registry for extension snpeffdb. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,370 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:SnpSiftDbNSFP from the datatype registry for extension snpsiftdbnsfp. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,370 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension dbnsfp.tabular. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,370 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Sff from the datatype registry for extension sff. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,371 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Sra from the datatype registry for extension sra. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,371 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:SraManifest from the datatype registry for extension sra_manifest.tabular. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,371 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry for extension svg. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,371 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Taxonomy from the datatype registry for extension taxonomy. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,371 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension tabular. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,371 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:TwoBit from the datatype registry for extension twobit. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,371 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:SQmass from the datatype registry for extension sqmass. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,371 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:GeminiSQLite from the datatype registry for extension gemini.sqlite. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,371 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:ChiraSQLite from the datatype registry for extension chira.sqlite. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,371 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CuffDiffSQlite from the datatype registry for extension cuffdiff.sqlite. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,371 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:GAFASQLite from the datatype registry for extension gafa.sqlite. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,371 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:NcbiTaxonomySQlite from the datatype registry for extension ncbitaxonomy.sqlite. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,372 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension txt. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,372 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:LineCount from the datatype registry for extension linecount. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,372 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:MemePsp from the datatype registry for extension memepsp. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,372 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:MEMEXml from the datatype registry for extension memexml. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,372 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:CisML from the datatype registry for extension cisml. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,372 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry for extension xml. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,372 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry for extension xsd. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,372 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:Dzi from the datatype registry for extension dzi. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,372 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Vcf from the datatype registry for extension vcf. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,372 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry for extension bcf. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,372 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry for extension bcf_bgzip. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,372 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:BcfUncompressed from the datatype registry for extension bcf_uncompressed. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,373 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.assembly:Velvet from the datatype registry for extension velvet. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,373 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:Wiggle from the datatype registry for extension wig. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,373 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension interval_index. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,373 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension odgi. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,373 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension vg. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,373 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension xg. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,373 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension protobuf2. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,373 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension protobuf3. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,373 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension onnx. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,374 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension tabix. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,374 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:IntervalTabix from the datatype registry for extension interval_tabix.gz. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,374 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:JuicerMediumTabix from the datatype registry for extension juicer_medium_tabix.gz. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,374 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:BedTabix from the datatype registry for extension bed_tabix.gz. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,374 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:GffTabix from the datatype registry for extension gff_tabix.gz. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,374 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension bgzip. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,374 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:VcfGz from the datatype registry for extension vcf_bgzip. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,374 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension bus. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,374 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension kallisto.idx. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,374 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:Phyloxml from the datatype registry for extension phyloxml. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,374 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Newick from the datatype registry for extension newick. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,374 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Newick from the datatype registry for extension nhx. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,375 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Nexus from the datatype registry for extension nex. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,375 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:IQTree from the datatype registry for extension iqtree. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,376 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:SquareDistanceMatrix from the datatype registry for extension mldist. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,379 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Affybatch from the datatype registry for extension affybatch. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,379 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Eigenstratgeno from the datatype registry for extension eigenstratgeno. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,380 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Eigenstratpca from the datatype registry for extension eigenstratpca. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,380 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Eset from the datatype registry for extension eset. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,380 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Fped from the datatype registry for extension fped. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,380 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Fphe from the datatype registry for extension fphe. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,380 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:GenomeGraphs from the datatype registry for extension gg. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,380 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:ldIndep from the datatype registry for extension ldindep. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,380 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:MAlist from the datatype registry for extension malist. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,380 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Lped from the datatype registry for extension lped. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,380 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Pbed from the datatype registry for extension pbed. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,381 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Pheno from the datatype registry for extension pheno. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,381 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Pphe from the datatype registry for extension pphe. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,381 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:RexpBase from the datatype registry for extension rexpbase. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,381 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Rgenetics from the datatype registry for extension rgenetics. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,381 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Snptest from the datatype registry for extension snptest. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,381 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:SNPMatrix from the datatype registry for extension snpmatrix. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,381 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:ExcelXls from the datatype registry for extension xls. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,381 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Ipynb from the datatype registry for extension ipynb. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,381 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension json. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,381 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:ExpressionJson from the datatype registry for extension expression.json. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,382 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.graph:Xgmml from the datatype registry for extension xgmml. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,382 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.graph:Sif from the datatype registry for extension sif. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,383 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.triples:Triples from the datatype registry for extension triples. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,383 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.triples:HDT from the datatype registry for extension hdt. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,383 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.triples:NTriples from the datatype registry for extension nt. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,383 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.triples:N3 from the datatype registry for extension n3. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,383 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.triples:Turtle from the datatype registry for extension ttl. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,384 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.triples:Rdf from the datatype registry for extension rdf. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,384 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.triples:Jsonld from the datatype registry for extension jsonld. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,384 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:ExcelXls from the datatype registry for extension excel.xls. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,384 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Xlsx from the datatype registry for extension xlsx. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,384 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension btwisted. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,384 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cai. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,384 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cat_db. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,384 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension charge. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,384 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension checktrans. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,384 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension chips. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,385 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension codcmp. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,385 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension coderet. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,385 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension compseq. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,385 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cpgplot. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,385 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cpgreport. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,385 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cusp. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,385 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cut. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,385 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension dan. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,385 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension digest. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,386 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension dreg. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,386 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension einverted. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,386 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension epestfind. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,386 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension equicktandem. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,386 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension est2genome. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,386 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension etandem. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,386 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension freak. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,386 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension fuzznuc. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,386 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension fuzzpro. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,387 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension fuzztran. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,387 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension garnier. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,387 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension geecee. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,387 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension helixturnhelix. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,387 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension hmoment. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,387 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension isochore. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,387 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension match. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,387 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension nametable. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,387 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension needle. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,387 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension newcpgreport. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,388 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension newcpgseek. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,388 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension noreturn. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,388 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension palindrome. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,388 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension pepcoil. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,388 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension pepinfo. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,388 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension pepstats. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,388 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension polydot. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,388 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension preg. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,388 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension prettyseq. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,388 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension primersearch. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,388 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension showfeat. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,388 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension showorf. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,389 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension sixpack. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,389 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension strider. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,389 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension supermatcher. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,389 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension syco. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,389 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension textsearch. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,389 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension vectorstrip. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,389 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension wobble. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,389 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension wordcount. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,389 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension dbmotif. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,389 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension diffseq. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,390 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension excel. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,390 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension feattable. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,390 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension motif. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,390 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension regions. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,390 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension seqtable. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,390 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension simple. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,390 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension table. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,390 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension tagseq. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,390 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension acedb. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,390 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension clustal. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,390 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension codata. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,391 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension embl. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,391 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension fitch. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,391 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension gcg. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,391 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Genbank from the datatype registry for extension genbank. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,391 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension hennig86. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,391 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension ig. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,391 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension jackknifer. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,391 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension jackknifernon. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,391 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension mega. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,392 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension meganon. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,392 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension ncbi. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,392 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension nexus. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,392 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension nexusnon. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,393 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.phylip:Phylip from the datatype registry for extension phylip. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,393 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension phylipnon. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,393 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension pir. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,393 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension staden. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,393 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension swiss. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,394 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.msa:Msf from the datatype registry for extension msf. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,394 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension markx0. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,394 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension markx1. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,395 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension markx10. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,395 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension markx2. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,395 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension markx3. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,395 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension pair. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,395 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension score. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,395 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension srs. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,395 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension srspair. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,396 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.annotation:SnapHmm from the datatype registry for extension snaphmm. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,396 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.annotation:Augustus from the datatype registry for extension augustus. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,396 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:ICM from the datatype registry for extension icm. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,396 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.msa:InfernalCM from the datatype registry for extension cm. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,396 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.msa:Hmmer2 from the datatype registry for extension hmm2. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,396 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.msa:Hmmer3 from the datatype registry for extension hmm3. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,396 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.msa:Stockholm_1_0 from the datatype registry for extension stockholm. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,396 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.msa:MauveXmfa from the datatype registry for extension xmfa. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,397 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.microarrays:Cel from the datatype registry for extension cel. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,397 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.microarrays:Gpr from the datatype registry for extension gpr. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,397 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.microarrays:Gal from the datatype registry for extension gal. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,397 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension rds. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,397 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension phyloseq. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,397 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,397 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.sce. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,397 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.xcms.raw. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,397 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.msnbase.raw. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,398 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.xcms.findchrompeaks. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,398 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.xcms.group. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,398 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.xcms.retcor. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,398 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.xcms.fillpeaks. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,398 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.camera.positive. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,398 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.camera.negative. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,398 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.camera.quick. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,399 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.hdf5:HDF5SummarizedExperiment from the datatype registry for extension rdata.se. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,399 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension rdock_as. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,399 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:OxliCountGraph from the datatype registry for extension oxlicg. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,399 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:OxliNodeGraph from the datatype registry for extension oxling. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,399 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:OxliTagSet from the datatype registry for extension oxlits. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,399 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:OxliStopTags from the datatype registry for extension oxlist. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,399 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:OxliSubset from the datatype registry for extension oxliss. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,399 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:OxliGraphLabels from the datatype registry for extension oxligl. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,401 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:STL from the datatype registry for extension stl. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,401 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyAscii from the datatype registry for extension plyascii. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,401 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyBinary from the datatype registry for extension plybinary. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,401 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkAscii from the datatype registry for extension vtkascii. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,401 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkBinary from the datatype registry for extension vtkbinary. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,401 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Biom1 from the datatype registry for extension biom1. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,401 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Biom2 from the datatype registry for extension biom2. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,401 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:MashSketch from the datatype registry for extension msh. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,401 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:ScIdx from the datatype registry for extension scidx. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,403 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:SMILES from the datatype registry for extension smi. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,403 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:SDF from the datatype registry for extension sdf. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,403 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:InChI from the datatype registry for extension inchi. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,404 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:MOL from the datatype registry for extension mol. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,404 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:MOL2 from the datatype registry for extension mol2. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,404 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:CML from the datatype registry for extension cml. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,404 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:FPS from the datatype registry for extension fps. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,404 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:OBFS from the datatype registry for extension obfs. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,404 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:DRF from the datatype registry for extension drf. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,404 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:PHAR from the datatype registry for extension phar. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,404 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:PDB from the datatype registry for extension pdb. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,404 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:PDBQT from the datatype registry for extension pdbqt. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,404 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:PQR from the datatype registry for extension pqr. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,404 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:Cell from the datatype registry for extension cell. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,404 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:CIF from the datatype registry for extension cif. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,405 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:XYZ from the datatype registry for extension xyz. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,405 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:ExtendedXYZ from the datatype registry for extension extxyz. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,405 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Trr from the datatype registry for extension trr. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,405 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Dcd from the datatype registry for extension dcd. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,405 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension top. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,405 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension prmtop. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,405 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension itp. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,405 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension mdp. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,405 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension ndx. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,405 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension xvg. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,405 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Xtc from the datatype registry for extension xtc. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,406 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Cpt from the datatype registry for extension cpt. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,406 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Edr from the datatype registry for extension edr. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,406 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension tpr. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,406 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:GRO from the datatype registry for extension gro. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,406 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension inpcrd. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,406 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Vel from the datatype registry for extension vel. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,406 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:grd from the datatype registry for extension grd. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,406 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:grdtgz from the datatype registry for extension grd.tgz. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,406 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Otu from the datatype registry for extension mothur.otu. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,406 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Otu from the datatype registry for extension mothur.list. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,406 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Sabund from the datatype registry for extension mothur.sabund. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,406 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Sabund from the datatype registry for extension mothur.rabund. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,407 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:GroupAbund from the datatype registry for extension mothur.shared. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,407 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:GroupAbund from the datatype registry for extension mothur.relabund. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,407 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Names from the datatype registry for extension mothur.names. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,407 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Group from the datatype registry for extension mothur.design. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,407 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Summary from the datatype registry for extension mothur.summary. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,407 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Group from the datatype registry for extension mothur.groups. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,407 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Oligos from the datatype registry for extension mothur.oligos. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,407 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry for extension mothur.align. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,407 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:AccNos from the datatype registry for extension mothur.accnos. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,408 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:AccNos from the datatype registry for extension mothur.otulabels. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,408 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension mothur.otu.corr. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,408 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:SecondaryStructureMap from the datatype registry for extension mothur.map. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,408 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:AlignCheck from the datatype registry for extension mothur.align.check. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,408 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:AlignReport from the datatype registry for extension mothur.align.report. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,408 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:LaneMask from the datatype registry for extension mothur.filter. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,408 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:DistanceMatrix from the datatype registry for extension mothur.dist. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,408 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension mothur.tre. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,408 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:PairwiseDistanceMatrix from the datatype registry for extension mothur.pair.dist. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,408 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:SquareDistanceMatrix from the datatype registry for extension mothur.square.dist. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,408 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:LowerTriangleDistanceMatrix from the datatype registry for extension mothur.lower.dist. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,409 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry for extension mothur.ref.taxonomy. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,409 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry for extension mothur.seq.taxonomy. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,409 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry for extension mothur.rdp.taxonomy. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,409 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:ConsensusTaxonomy from the datatype registry for extension mothur.cons.taxonomy. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,409 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:TaxonomySummary from the datatype registry for extension mothur.tax.summary. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,409 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Frequency from the datatype registry for extension mothur.freq. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,409 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry for extension mothur.quan. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,409 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry for extension mothur.filtered.quan. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,409 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry for extension mothur.masked.quan. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,409 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry for extension mothur.filtered.masked.quan. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,410 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Axes from the datatype registry for extension mothur.axes. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,410 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:SffFlow from the datatype registry for extension mothur.sff.flow. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,410 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:CountTable from the datatype registry for extension mothur.count_table. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,410 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.neo4j:Neo4jDB from the datatype registry for extension neostore. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,410 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.neo4j:Neo4jDBzip from the datatype registry for extension neostore.zip. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,411 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tracks:UCSCTrackHub from the datatype registry for extension trackhub. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,411 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.blast:BlastXml from the datatype registry for extension blastxml. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,411 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.blast:BlastNucDb from the datatype registry for extension blastdbn. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,412 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.blast:BlastProtDb from the datatype registry for extension blastdbp. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,412 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.blast:BlastDomainDb from the datatype registry for extension blastdbd. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,412 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.blast:LastDb from the datatype registry for extension lastdb. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,412 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.blast:BlastNucDb5 from the datatype registry for extension blastdbn5. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,412 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.blast:BlastProtDb5 from the datatype registry for extension blastdbp5. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,412 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.blast:BlastDomainDb5 from the datatype registry for extension blastdbd5. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,412 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry for extension maskinfo-asn1. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,412 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry for extension maskinfo-asn1-binary. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,413 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry for extension pssm-asn1. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,413 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesKsComponents from the datatype registry for extension ptkscmp. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,413 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.plant_tribes:Smat from the datatype registry for extension smat. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,413 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:GenotypeMatrix from the datatype registry for extension alohomora_gts. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,413 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension alohomora_map. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,414 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension alohomora_maf. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,414 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension alohomora_ped. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,414 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension linkage_pedin. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,414 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:DataIn from the datatype registry for extension linkage_datain. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,414 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:MarkerMap from the datatype registry for extension linkage_map. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,414 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension allegro_ihaplo. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,414 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension allegro_descent. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,414 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:AllegroLOD from the datatype registry for extension allegro_fparam. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,414 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:IdeasPre from the datatype registry for extension ideaspre. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,414 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:Sbml from the datatype registry for extension sbml. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,415 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.spaln:SpalnNuclDb from the datatype registry for extension spalndbnp. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,415 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.spaln:SpalnProtDb from the datatype registry for extension spalndba. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,415 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension dada2_dada. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,415 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension dada2_errorrates. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,416 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension dada2_mergepairs. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,416 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension dada2_sequencetable. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,416 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension dada2_uniques. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,416 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension ampvis2. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,416 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension ckpt. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,416 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension tgz. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,422 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.media:Wav from the datatype registry for extension wav. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,422 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.media:Mp3 from the datatype registry for extension mp3. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,422 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.media:Mkv from the datatype registry for extension mkv. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,422 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.media:Mp4 from the datatype registry for extension mp4. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,422 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.media:Flv from the datatype registry for extension flv. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,422 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.media:Mpg from the datatype registry for extension mpg. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,422 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.speech:TextGrid from the datatype registry for extension textgrid. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,423 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.speech:BPF from the datatype registry for extension par. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,423 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension ffindex. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,423 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry for extension ffdata. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,423 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Pretext from the datatype registry for extension pretext. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,423 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Html from the datatype registry for extension immuneml_receptors.html. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,423 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:HexrdMaterials from the datatype registry for extension hexrd.materials.h5. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,423 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Npz from the datatype registry for extension npz. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,423 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:HexrdImagesNpz from the datatype registry for extension hexrd.images.npz. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,423 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:HexrdEtaOmeNpz from the datatype registry for extension hexrd.eta_ome.npz. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,423 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Npz from the datatype registry for extension hexrd.scored_orientations.npz. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,424 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension hexrd.accepted_orientations. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,424 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Yaml from the datatype registry for extension hexrd.yml. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,424 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:NeperTess from the datatype registry for extension neper.tess. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,424 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:NeperTesr from the datatype registry for extension neper.tesr. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,424 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:NeperPoints from the datatype registry for extension neper.points. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,424 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:NeperPointsTabular from the datatype registry for extension neper.points.tsv. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,424 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:NeperMultiScaleCell from the datatype registry for extension neper.mscell. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,424 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:GmshMsh from the datatype registry for extension gmsh.msh. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,424 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:GmshGeo from the datatype registry for extension gmsh.geo. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,424 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:ZsetGeof from the datatype registry for extension zset.geof. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,424 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Text from the datatype registry for extension pov. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,424 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:PithyaResult from the datatype registry for extension pithya.result. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,424 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:PithyaProperty from the datatype registry for extension pithya.property. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,425 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:PithyaModel from the datatype registry for extension pithya.model. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,425 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:BCSLts from the datatype registry for extension bcsl.ts. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,425 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:BCSLmodel from the datatype registry for extension bcsl.model. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,425 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:StormSample from the datatype registry for extension storm.sample. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,425 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:StormCheck from the datatype registry for extension storm.check. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,425 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:CTLresult from the datatype registry for extension ctl.result. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,425 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Castep from the datatype registry for extension castep. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,425 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Param from the datatype registry for extension param. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,425 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:FormattedDensity from the datatype registry for extension den_fmt. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,425 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension bil. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,425 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension hdr. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,426 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.gis:Shapefile from the datatype registry for extension shp. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,426 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:FITS from the datatype registry for extension fits. +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,426 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.plant_tribes:PlantTribesKsComponents' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,426 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.plant_tribes:Smat' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,426 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Sabund' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,426 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Otu' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,426 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:GroupAbund' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,426 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:SecondaryStructureMap' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,426 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:LowerTriangleDistanceMatrix' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,426 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:SquareDistanceMatrix' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,426 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:PairwiseDistanceMatrix' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,427 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Oligos' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,427 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Quantile' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,427 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Frequency' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,427 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:LaneMask' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,427 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:RefTaxonomy' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,427 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Axes' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,427 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyAscii' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,428 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyBinary' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,428 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkAscii' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,428 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkBinary' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,428 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:NeperTess' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,428 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:NeperTesr' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,428 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:GmshMsh' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,428 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.goldenpath:GoldenPath' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,428 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:ScIdx' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,428 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:Vcf' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,428 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:JP2' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,428 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:TwoBit' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,428 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:GeminiSQLite' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,428 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:SQmass' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,428 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:MzSQlite' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,428 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OSW' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,428 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:PQP' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,428 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:IdpDB' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,428 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:ElibSQlite' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,428 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:DlibSQlite' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,428 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:BlibSQlite' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,428 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:ChiraSQLite' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,428 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:CuffDiffSQlite' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,428 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:GAFASQLite' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,428 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:NcbiTaxonomySQlite' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,429 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:SQlite' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,429 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:H5MLM' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,429 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Cool' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,429 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:MCool' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,429 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Loom' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,429 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Anndata' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,429 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Biom2' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,429 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:HexrdMaterials' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,429 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:H5' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,429 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Grib' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,429 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:HexrdImagesNpz' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,429 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:HexrdEtaOmeNpz' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,429 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Npz' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,429 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Bam' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,429 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:BamQuerynameSorted' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,429 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:BamNative' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,429 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:CRAM' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,429 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Sff' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,429 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Sra' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,429 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:NetCDF' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,429 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:DAA' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,429 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:RMA6' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,429 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:DMND' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,430 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Parquet' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,430 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:BafTar' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,430 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:TdfTar' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,430 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:MassHunterTar' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,430 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:MassLynxTar' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,430 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:YepTar' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,430 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:WiffTar' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,430 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5ArchiveGz' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,430 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5ArchiveBz2' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,430 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5Archive' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,430 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Meryldb' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,430 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Bref3' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,430 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:PostgresqlArchive' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,430 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:ICM' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,430 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Idat' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,430 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Trr' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,430 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Dcd' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,430 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Xtc' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,430 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Cpt' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,430 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Edr' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,430 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Vel' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,430 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Xlsx' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,431 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.qiime2:QIIME2Metadata' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,431 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.qiime2:QIIME2Artifact' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,431 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.qiime2:QIIME2Visualization' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,431 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:CompressedZipArchive' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,431 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Pretext' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,431 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.annotation:Augustus' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,431 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.xml:Owl' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,431 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.triples:Rdf' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,431 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.blast:BlastXml' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,431 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Gifti' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,431 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.xml:Phyloxml' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,431 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.xml:Dzi' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,431 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.xml:Sbml' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,431 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Dta2d' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,431 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Edta' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,431 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ConsensusXML' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,431 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:IdXML' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,431 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:FeatureXML' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,431 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MascotXML' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,432 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Mgf' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,432 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Ms2' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,432 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Msp' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,432 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzData' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,432 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzIdentML' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,432 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzML' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,432 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzQuantML' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,432 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzTab' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,432 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzTab2' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,432 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ParamXml' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,432 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzXML' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,432 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:NmrML' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,432 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Kroenik' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,432 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PepList' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,432 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PSMS' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,432 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PepXml' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,432 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ProtXML' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,432 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:SPLib' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,433 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TandemXML' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,433 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ThermoRAW' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,433 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TraML' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,433 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TrafoXML' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,433 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:UniProtXML' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,433 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:XquestXML' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,433 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:XquestSpecXML' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,433 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:QCML' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,433 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Wiff' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,433 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PEFF' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,433 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:CML' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,433 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.xml:GenericXml' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,433 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.triples:HDT' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,433 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.triples:Turtle' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,433 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.triples:NTriples' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,433 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.triples:Jsonld' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,433 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Maf' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,434 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Lav' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,434 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:MemePsp' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,434 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastg' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,434 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:csFasta' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,434 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,434 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,434 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:SDF' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,706 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:PDB' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,706 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:Cell' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,706 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:CIF' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,706 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:ExtendedXYZ' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,707 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:XYZ' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,707 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:MOL2' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,707 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:InChI' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,707 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:FPS' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,707 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:PQR' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,707 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:GRO' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,707 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.phylip:Phylip' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,707 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fasta' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,707 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqCSSanger' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,707 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqSanger' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,707 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastq' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,707 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:Wiggle' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,707 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Html' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,707 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Pdf' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,707 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Axt' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,707 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Genbank' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,707 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:Bed' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,708 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:CustomTrack' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,708 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:Gtf' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,708 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,708 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff3' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,708 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:Pileup' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,708 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:Psl' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,708 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Paf' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,708 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:Interval' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,708 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:Sam' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,708 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.data:Newick' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,708 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.data:Nexus' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,708 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:IQTree' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,708 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Obo' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,708 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Arff' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,708 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Ipynb' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,708 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Biom1' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,708 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:ImgtJson' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,709 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:GeoJson' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,709 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:PithyaResult' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,709 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:BCSLts' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,709 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Json' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,709 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.genetics:GenotypeMatrix' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,709 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.genetics:DataIn' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,709 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.genetics:MarkerMap' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,709 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.genetics:AllegroLOD' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,709 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:RNADotPlotMatrix' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,709 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:DotBracket' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,709 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:CMAP' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,709 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:ConnectivityTable' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,709 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:CSV' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,709 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.metacyto:mSummary' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,709 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.metacyto:mStats' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,710 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:TSV' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,710 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:MatrixMarket' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,710 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer2' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,710 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer3' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,710 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.msa:Stockholm_1_0' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,710 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.msa:MauveXmfa' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,710 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.msa:InfernalCM' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,710 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.annotation:SnapHmm' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,710 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.microarrays:Cel' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,710 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.microarrays:Gpr' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,710 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.microarrays:Gal' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,710 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:RData' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,710 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:RDS' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,710 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Mrc2014' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,710 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Jpg' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,710 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Png' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,711 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:OMETiff' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,711 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Tiff' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,711 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Bmp' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,711 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Gif' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,711 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Im' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,711 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Pcd' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,711 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Pcx' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,711 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Ppm' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,711 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Psd' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,711 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Xbm' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,711 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Rgb' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,711 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,711 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,712 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,712 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Eps' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,712 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Rast' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,712 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Tck' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,712 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Trk' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,712 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Nifti1' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,712 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Nifti2' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,712 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Star' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,712 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Wav' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,712 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Mkv' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,712 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Mp3' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,712 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Mp4' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,712 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Flv' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,712 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Mpg' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,712 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.speech:TextGrid' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,713 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.speech:BPF' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,713 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Castep' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,713 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:CTLresult' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,713 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:FormattedDensity' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,713 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Param' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,713 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Yaml' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,713 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliCountGraph' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,713 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliNodeGraph' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,713 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliTagSet' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,713 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliStopTags' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,713 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliSubset' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,713 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliGraphLabels' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,713 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:FITS' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,714 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.neo4j:Neo4jDBzip' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,714 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:PithyaProperty' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,714 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:PithyaModel' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,714 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:BCSLmodel' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,714 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:StormSample' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,714 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:StormCheck' +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,718 [pN:job_handler_0,p:8,tN:MainThread] Loaded build site 'ucsc': /cvmfs/data.galaxyproject.org/managed/location/ucsc_build_sites.txt with display sites: ['main', 'archaea', 'ucla'] +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,718 [pN:job_handler_0,p:8,tN:MainThread] Loaded build site 'gbrowse': /galaxy/server/tool-data/shared/gbrowse/gbrowse_build_sites.txt with display sites: ['wormbase', 'tair', 'modencode_worm', 'modencode_fly'] +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,718 [pN:job_handler_0,p:8,tN:MainThread] Loaded build site 'ensembl': /galaxy/server/tool-data/shared/ensembl/ensembl_sites.txt +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,718 [pN:job_handler_0,p:8,tN:MainThread] Loaded build site 'ensembl_data_url': /galaxy/server/tool-data/shared/ensembl/ensembl_sites_data_URL.txt +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,718 [pN:job_handler_0,p:8,tN:MainThread] Loaded build site 'igv': /galaxy/server/tool-data/shared/igv/igv_build_sites.txt.sample +galaxy.datatypes.registry DEBUG 2024-12-30 00:50:50,719 [pN:job_handler_0,p:8,tN:MainThread] Loaded build site 'rviewer': /galaxy/server/tool-data/shared/rviewer/rviewer_build_sites.txt.sample +galaxy.util.tool_shed.tool_shed_registry DEBUG 2024-12-30 00:50:50,720 [pN:job_handler_0,p:8,tN:MainThread] Loading references to tool sheds from internal default config +galaxy.util.tool_shed.tool_shed_registry DEBUG 2024-12-30 00:50:50,720 [pN:job_handler_0,p:8,tN:MainThread] Loaded reference to tool shed: Galaxy Main Tool Shed +galaxy.web_stack DEBUG 2024-12-30 00:50:50,721 [pN:job_handler_0,p:8,tN:MainThread] server_name set to: job_handler_0 +galaxy.queue_worker INFO 2024-12-30 00:50:50,725 [pN:job_handler_0,p:8,tN:MainThread] Initializing job_handler_0 Galaxy Queue Worker on amqp://default_user_dtBQJ6o7BPQZXA7fPnx:********@prod-24-12-30-00-37-1-galaxy-rabbitmq-server:5672 +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,748 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/db536ad45f28/primer_scheme_bedfiles.loc' for tool data table 'primer_scheme_bedfiles' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,748 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'primer_scheme_bedfiles' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,748 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ee2beb764a7b/primer_scheme_bedfiles.loc' for tool data table 'primer_scheme_bedfiles' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,748 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'primer_scheme_bedfiles' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,748 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/78bbd17d0703/primer_scheme_bedfiles.loc' for tool data table 'primer_scheme_bedfiles' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,748 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'primer_scheme_bedfiles' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,749 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/7fe36019c073/primer_scheme_bedfiles.loc' for tool data table 'primer_scheme_bedfiles' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,749 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'primer_scheme_bedfiles' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,749 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/ivar_getmasked/2cf4a1cafc16/primer_scheme_bedfiles.loc' for tool data table 'primer_scheme_bedfiles' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,749 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'primer_scheme_bedfiles' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,749 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/f95f403841ad/primer_scheme_bedfiles.loc' for tool data table 'primer_scheme_bedfiles' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,749 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'primer_scheme_bedfiles' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,749 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/d6dc477167f8/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,749 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,749 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/672b6c02fbc7/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,749 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,750 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/365325116147/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,750 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,750 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/fec517907949/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,750 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,751 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/c077f71d351f/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,751 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,751 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/ed4ea9de1791/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,751 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,751 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/dfef7a353ed0/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,751 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,751 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/01d6b7d6365e/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,751 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,752 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/8abfcd1a6949/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,752 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,752 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/4813f99d81b7/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,752 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,752 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/0dbff46d5a1b/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,752 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,752 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bf235558f2cf/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,752 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,752 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/d40d4bf05718/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,752 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,753 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/b8e9da766b0f/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,753 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,753 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/776ad0b21536/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,753 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,753 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/9ef52d95114b/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,753 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,753 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/b17394940c7a/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,753 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,753 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/582f8b13873d/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,753 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,753 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bf7d6acd9884/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,753 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,754 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/02f349bdbf96/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,754 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,754 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/e03f2f3ac3a9/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,754 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,754 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/b76adb2f1c51/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,754 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,754 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/072f606e2e69/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,754 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,754 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/23680a42e149/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,754 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,755 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/6ca7c55a27e8/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,755 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,755 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/fdd127bd4a32/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,755 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,755 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/403553ae19f6/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,755 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,755 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/5c232a738c74/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,756 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,756 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/c9c5718edc19/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,756 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,756 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bdfdf5f6e950/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,756 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,756 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/vcfcheck/2968c6916579/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,756 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,756 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/vcfgeno2haplo/a3dea556218d/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,756 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,757 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/vcfleftalign/29f9b782727e/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,757 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,757 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/vcfprimers/17096387c0e6/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,757 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,757 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/166c4f50525f/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,757 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,757 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bedtools/ce3c7f062223/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,757 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,757 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bedtools/ce3c7f062223/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,757 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,757 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bedtools/ce3c7f062223/all_gff.loc' for tool data table 'all_gff' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,757 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'all_gff' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,758 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bedtools/ce3c7f062223/dbkeys.loc' for tool data table '__dbkeys__' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,758 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table '__dbkeys__' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,758 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/093678460093/adapters.loc' for tool data table 'adapters' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,758 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'adapters' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,758 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/7d37cfda8e00/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,758 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,758 [pN:job_handler_0,p:8,tN:MainThread] While attempting to merge tool data table "all_fasta", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,758 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/circos/df7356989ac1/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,758 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,758 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/4542035c1075/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,758 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,759 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/minimap2/f54f5baedfdd/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,759 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,759 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/09b2cdb7ace5/bowtie2_indices.loc' for tool data table 'bowtie2_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,759 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'bowtie2_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,759 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/bwa/3fe632431b68/bwa_mem_index.loc' for tool data table 'bwa_mem_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,759 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'bwa_mem_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,759 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bwameth/29bdbc353f20/bwameth_indexes.loc' for tool data table 'bwameth_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,759 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'bwameth_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,759 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/lastz/e7f19d6a9af8/lastz_seqs.loc' for tool data table 'lastz_seqs' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,759 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'lastz_seqs' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,759 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/43815fa60f3a/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,760 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,760 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/a7228a7ea146/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,760 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,760 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/336b3def9b2b/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,760 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,760 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/db25ec99c3ea/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,760 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,760 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/salmon/cc05793bb896/salmon_indexes_versioned.loc' for tool data table 'salmon_indexes_versioned' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,760 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'salmon_indexes_versioned' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,760 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/a8f343909c17/sailfish_indexes.loc' for tool data table 'sailfish_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,760 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'sailfish_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,761 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/hisat2/26371a1df031/hisat2_indexes.loc' for tool data table 'hisat2_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,761 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'hisat2_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,761 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/stringtie/1ebd14235b92/gene_sets.loc' for tool data table 'gene_sets' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,761 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'gene_sets' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,761 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/b72793637686/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,761 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,761 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/a3b4ad6858ff/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,761 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,761 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/bamtools/4d343c1f606b/sam_fa_indices.loc' for tool data table 'sam_fa_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,761 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'sam_fa_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,762 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/145f6d74ff5e/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,762 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,762 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/06dc50b7b711/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,762 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,762 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/fa7ad9b89f4a/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,762 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,762 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/cf1ffd88f895/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,762 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,762 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/e1461b5c52a0/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,762 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,762 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/aa35ee7f3ab2/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,763 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,763 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/426d707dfc47/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,763 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,763 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/7dfca164d2e3/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,763 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,763 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/09d6e4693887/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,763 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,763 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/freebayes/ef2c525bd8cd/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,763 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,763 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/snpsift_genesets/d12a810c837e/snpeff_msigdb_database.loc' for tool data table 'snpeff_msigdb_database' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,763 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'snpeff_msigdb_database' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,764 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/snpsift_dbnsfp/4e21e4f2bc48/snpsift_dbnsfps.loc' for tool data table 'snpsift_dbnsfps' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,764 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'snpsift_dbnsfps' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,764 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/snpeff/74aebe30fb52/snpeffv_genomedb.loc' for tool data table 'snpeffv_genomedb' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,764 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'snpeffv_genomedb' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,764 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/snpeff/74aebe30fb52/snpeffv_regulationdb.loc' for tool data table 'snpeffv_regulationdb' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,764 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'snpeffv_regulationdb' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,764 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/jasminesv/2b62154e39c8/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,764 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,764 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,764 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,764 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/alevin/e4c01dcece8b/salmon_indexes_versioned.loc' for tool data table 'salmon_indexes_versioned' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,765 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'salmon_indexes_versioned' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,765 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/salmonquantmerge/88c07fc4024c/salmon_indexes_versioned.loc' for tool data table 'salmon_indexes_versioned' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,765 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'salmon_indexes_versioned' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,765 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/093678460093/adapters.loc' for tool data table 'adapters' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,765 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'adapters' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,765 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/7d37cfda8e00/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,765 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,765 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/c772497b2c32/rnastar_index2x_versioned.loc' for tool data table 'rnastar_index2x_versioned' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,765 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'rnastar_index2x_versioned' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,765 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/eec9494fdafa/rnastar_index2x_versioned.loc' for tool data table 'rnastar_index2x_versioned' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,765 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'rnastar_index2x_versioned' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,766 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/38b6d12edc68/gene_sets.loc' for tool data table 'gene_sets' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,766 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'gene_sets' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,766 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/38b6d12edc68/featurecounts_anno.loc' for tool data table 'featurecounts_anno' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,766 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'featurecounts_anno' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,766 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/alevin/ecb9ea6269ee/salmon_indexes_versioned.loc' for tool data table 'salmon_indexes_versioned' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,766 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'salmon_indexes_versioned' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,766 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/2055c2667eb3/rnastar_index2.loc' for tool data table 'rnastar_index2' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,766 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'rnastar_index2' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,766 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/f3a5f075498f/gene_sets.loc' for tool data table 'gene_sets' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,766 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'gene_sets' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,767 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/f3a5f075498f/featurecounts_anno.loc' for tool data table 'featurecounts_anno' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,767 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'featurecounts_anno' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,767 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/24c5d43cb545/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,767 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,767 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bedtools/07e8b80f278c/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,767 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,767 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bedtools/07e8b80f278c/all_gff.loc' for tool data table 'all_gff' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,767 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_gff' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,767 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bedtools/07e8b80f278c/dbkeys.loc' for tool data table '__dbkeys__' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,767 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table '__dbkeys__' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,767 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/135b80fb1ac2/adapters.loc' for tool data table 'adapters' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,767 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'adapters' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,768 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/980d2a2e1180/rnastar_index2x_versioned.loc' for tool data table 'rnastar_index2x_versioned' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,768 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'rnastar_index2x_versioned' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,768 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/picard/b502c227b5e6/picard_index.loc' for tool data table 'picard_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,768 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'picard_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,768 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/hisat2/f4af63aaf57a/hisat2_indexes.loc' for tool data table 'hisat2_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,768 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'hisat2_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,768 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/c5e2e5902201/adapters.loc' for tool data table 'adapters' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,768 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'adapters' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,768 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/660cffd8d92a/adapters.loc' for tool data table 'adapters' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,769 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'adapters' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,769 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/e3ba567abdf5/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,769 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,769 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/e3ba567abdf5/gene_sets.loc' for tool data table 'gene_sets' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,769 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'gene_sets' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,769 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/f088370d2a3c/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,769 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,769 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/f088370d2a3c/gene_sets.loc' for tool data table 'gene_sets' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,769 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'gene_sets' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,769 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/bwa/e188dc7a68e6/bwa_mem_index.loc' for tool data table 'bwa_mem_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,769 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'bwa_mem_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,770 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/picard/a1f0b3f4b781/picard_index.loc' for tool data table 'picard_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,770 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'picard_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,770 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/picard/b9fbec5ac6b2/picard_index.loc' for tool data table 'picard_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,770 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'picard_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,770 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/hisat2/61ee47027bd3/hisat2_indexes.loc' for tool data table 'hisat2_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,770 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'hisat2_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,770 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/1759d845181e/gene_sets.loc' for tool data table 'gene_sets' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,770 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'gene_sets' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,770 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/1759d845181e/featurecounts_anno.loc' for tool data table 'featurecounts_anno' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,770 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'featurecounts_anno' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,770 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/d080005cffe1/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,771 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,771 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/5826298f6a73/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,771 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,771 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/0dbf49c414ae/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,771 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,771 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/4805fe3d8fda/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,771 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,771 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/65432c3abf6c/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,771 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,771 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/2270a8b83c12/gemini_versioned_databases.loc' for tool data table 'gemini_versioned_databases' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,771 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'gemini_versioned_databases' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,772 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/cf61daf064fe/gemini_databases.loc' for tool data table 'gemini_databases' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,772 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'gemini_databases' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,772 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/gemini_db_info/c2a413e47fe9/gemini_versioned_databases.loc' for tool data table 'gemini_versioned_databases' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,772 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'gemini_versioned_databases' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,772 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/gemini_db_info/4c5f4e9b1931/gemini_databases.loc' for tool data table 'gemini_databases' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,772 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'gemini_databases' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,772 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/gemini_query/77a1e60fd1de/gemini_versioned_databases.loc' for tool data table 'gemini_versioned_databases' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,772 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'gemini_versioned_databases' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,772 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/gemini_query/666f60a9331a/gemini_databases.loc' for tool data table 'gemini_databases' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,772 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'gemini_databases' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,772 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/freebayes/a5937157062f/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,773 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,773 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/freebayes/156b60c1530f/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,773 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,773 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/snpeff/5b80f544c67f/snpeffv_genomedb.loc' for tool data table 'snpeffv_genomedb' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,773 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'snpeffv_genomedb' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,773 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/snpeff/5b80f544c67f/snpeffv_regulationdb.loc' for tool data table 'snpeffv_regulationdb' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,773 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'snpeffv_regulationdb' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,773 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/snpeff/68693743661e/snpeffv_genomedb.loc' for tool data table 'snpeffv_genomedb' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,773 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'snpeffv_genomedb' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,773 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/snpeff/68693743661e/snpeffv_regulationdb.loc' for tool data table 'snpeffv_regulationdb' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,773 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'snpeffv_regulationdb' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,773 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bedtools/64e2edfe7a2c/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,774 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,774 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bedtools/64e2edfe7a2c/all_gff.loc' for tool data table 'all_gff' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,774 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_gff' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,774 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bedtools/64e2edfe7a2c/dbkeys.loc' for tool data table '__dbkeys__' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,774 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table '__dbkeys__' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,774 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/a60c359ec43c/lastz_seqs.loc' for tool data table 'lastz_seqs' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,774 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'lastz_seqs' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,774 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/e4c7985d4585/lastz_seqs.loc' for tool data table 'lastz_seqs' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,774 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'lastz_seqs' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,774 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/c929a006727f/lastz_seqs.loc' for tool data table 'lastz_seqs' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,774 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'lastz_seqs' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,774 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/c06951d10364/lastz_seqs.loc' for tool data table 'lastz_seqs' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,774 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'lastz_seqs' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,775 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/07418a30ed01/lastz_seqs.loc' for tool data table 'lastz_seqs' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,775 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'lastz_seqs' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,775 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/26983857c91a/lastz_seqs.loc' for tool data table 'lastz_seqs' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,775 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'lastz_seqs' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,775 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/e479c7ca5570/lastz_seqs.loc' for tool data table 'lastz_seqs' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,775 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'lastz_seqs' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,775 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/01fb6a7654e6/lastz_seqs.loc' for tool data table 'lastz_seqs' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,775 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'lastz_seqs' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,775 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/137c4beed34b/lastz_seqs.loc' for tool data table 'lastz_seqs' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,775 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'lastz_seqs' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,775 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/bad3ca889618/lastz_seqs.loc' for tool data table 'lastz_seqs' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,775 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'lastz_seqs' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,775 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/231994413f89/lastz_seqs.loc' for tool data table 'lastz_seqs' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,775 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'lastz_seqs' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,775 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_enrichment/4431f39ede55/lastz_seqs.loc' for tool data table 'lastz_seqs' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,775 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'lastz_seqs' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,776 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/4ed32329e0ed/lastz_seqs.loc' for tool data table 'lastz_seqs' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,776 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'lastz_seqs' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,776 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/443d9a9d6d11/lastz_seqs.loc' for tool data table 'lastz_seqs' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,776 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'lastz_seqs' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,776 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/0e49b109abc2/lastz_seqs.loc' for tool data table 'lastz_seqs' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,776 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'lastz_seqs' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,776 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/6662b1a8d326/lastz_seqs.loc' for tool data table 'lastz_seqs' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,776 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'lastz_seqs' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,776 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/5eb7e84243f2/adapters.loc' for tool data table 'adapters' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,776 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'adapters' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,776 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/aa784cb3810d/adapters.loc' for tool data table 'adapters' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,776 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'adapters' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,776 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/36b848d5f3ec/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,776 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,776 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/circos/c4bde687c846/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,777 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,777 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/minimap2/5cc34c3f440d/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,777 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,777 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/d5ceb9f3c25b/bowtie2_indices.loc' for tool data table 'bowtie2_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,777 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'bowtie2_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,777 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/bwa/2477830927ec/bwa_mem_index.loc' for tool data table 'bwa_mem_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,777 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'bwa_mem_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,777 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bwameth/cf1322aeb137/bwameth_indexes.loc' for tool data table 'bwameth_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,777 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'bwameth_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,777 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/lastz/37b497aa133f/lastz_seqs.loc' for tool data table 'lastz_seqs' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,777 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'lastz_seqs' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,777 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/4014de1b6daf/rnastar_index2x_versioned.loc' for tool data table 'rnastar_index2x_versioned' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,777 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'rnastar_index2x_versioned' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,777 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/b0f2be869d6d/rnastar_index2x_versioned.loc' for tool data table 'rnastar_index2x_versioned' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,777 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'rnastar_index2x_versioned' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,778 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/42ce70172b72/rnastar_index2x_versioned.loc' for tool data table 'rnastar_index2x_versioned' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,778 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'rnastar_index2x_versioned' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,778 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/45795f582ae9/rnastar_index2x_versioned.loc' for tool data table 'rnastar_index2x_versioned' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,778 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'rnastar_index2x_versioned' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,778 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/eb746fa6f514/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,778 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,778 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/fc8804320156/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,778 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,778 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/1d62240feff3/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,779 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,779 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/18505fe2bdb1/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,779 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,779 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/picard/3f254c5ced1d/picard_index.loc' for tool data table 'picard_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,779 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'picard_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,779 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/salmon/f4d5237a84f6/salmon_indexes_versioned.loc' for tool data table 'salmon_indexes_versioned' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,779 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'salmon_indexes_versioned' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,779 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/ce5d418183c5/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,779 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,779 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/ce5d418183c5/kallisto_indexes.loc' for tool data table 'kallisto_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,779 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'kallisto_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,779 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/4f9c4e6566e5/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,779 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,779 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/4f9c4e6566e5/kallisto_indexes.loc' for tool data table 'kallisto_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,779 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'kallisto_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,779 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/stringtie/cbf488da3b2c/gene_sets.loc' for tool data table 'gene_sets' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,780 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'gene_sets' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,780 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/f9d49f5cb597/gene_sets.loc' for tool data table 'gene_sets' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,780 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'gene_sets' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,780 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/f9d49f5cb597/featurecounts_anno.loc' for tool data table 'featurecounts_anno' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,780 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'featurecounts_anno' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,780 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/32dc5f781059/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,780 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,780 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/c370440f901e/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,781 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,781 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/bamtools/970e6333f07e/sam_fa_indices.loc' for tool data table 'sam_fa_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,781 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'sam_fa_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,781 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/541082d03bef/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,781 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,781 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/26b4f9f98aca/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,781 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,781 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/b61f5d6a7f25/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,781 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,781 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/0e60e2dd20af/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,781 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,781 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/alevin/c9944a2600f1/salmon_indexes_versioned.loc' for tool data table 'salmon_indexes_versioned' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,781 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'salmon_indexes_versioned' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,781 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/salmonquantmerge/a896b8b7d264/salmon_indexes_versioned.loc' for tool data table 'salmon_indexes_versioned' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,782 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'salmon_indexes_versioned' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,782 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/971e07ca4456/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,782 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,782 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/791f73caa0c8/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,782 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,782 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/snpeff/9473cd297a76/snpeffv_genomedb.loc' for tool data table 'snpeffv_genomedb' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,782 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'snpeffv_genomedb' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,782 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/snpeff/9473cd297a76/snpeffv_regulationdb.loc' for tool data table 'snpeffv_regulationdb' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,782 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'snpeffv_regulationdb' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,782 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/8aa352093d73/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,782 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,782 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/7b4454382d39/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,782 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,782 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/dd72ff87cfd0/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,782 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,783 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/cfd81f17580b/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,783 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,783 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/271965b55437/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,783 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,783 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/2c80b0d6bde0/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,783 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,783 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/8b260d252ff4/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,783 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,783 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/ccb83bf54de0/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,783 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,783 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/a730269af659/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,783 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,783 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/dadbd61dc4cf/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,783 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,783 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/0a5dcc9a8ec2/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,783 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,784 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/8f5962c43868/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,784 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,784 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/05f317e50e61/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,784 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,784 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/012656fd329f/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,784 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,784 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/bc5332d47b1c/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,784 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,784 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/2331ddcbd5aa/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,784 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,784 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/591cc8518033/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,784 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,784 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/a12844ca467a/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,784 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,784 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/b10d1510fa84/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,784 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,785 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/39bca000353d/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,785 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,785 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/5b006286a458/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,785 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,785 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/fa65af07ce7d/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,785 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,785 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/07396b423218/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,785 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,785 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/1a2ef636f48e/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,785 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,785 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/46fcafba49ec/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,785 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,785 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/d237eaef451f/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,785 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,785 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/2c372041ed8c/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,785 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,785 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/283911fe7e1a/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,786 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,786 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/31a1b89eab9b/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,786 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,786 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/3897eaadfbff/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,786 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,786 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/a250929be21b/primer_scheme_bedfiles.loc' for tool data table 'primer_scheme_bedfiles' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,786 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'primer_scheme_bedfiles' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,786 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/5dc33613c288/primer_scheme_bedfiles.loc' for tool data table 'primer_scheme_bedfiles' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,786 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'primer_scheme_bedfiles' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,786 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/3a72fede57ce/primer_scheme_bedfiles.loc' for tool data table 'primer_scheme_bedfiles' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,786 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'primer_scheme_bedfiles' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,786 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/fcbeda41d0ac/primer_scheme_bedfiles.loc' for tool data table 'primer_scheme_bedfiles' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,786 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'primer_scheme_bedfiles' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,786 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/abbc8041e8ec/primer_scheme_bedfiles.loc' for tool data table 'primer_scheme_bedfiles' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,786 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'primer_scheme_bedfiles' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,786 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/5cbde03c1103/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,787 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,787 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/1b851f87fbe0/gene_sets.loc' for tool data table 'gene_sets' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,787 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'gene_sets' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,787 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/1b851f87fbe0/featurecounts_anno.loc' for tool data table 'featurecounts_anno' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,787 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'featurecounts_anno' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,787 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/6926716bbfb5/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,787 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,787 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/b11e8e9c23bf/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,787 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,787 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/freebayes/3e954e7125bf/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,787 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,787 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/snpeff/ca2b512e8d7c/snpeffv_genomedb.loc' for tool data table 'snpeffv_genomedb' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,787 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'snpeffv_genomedb' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,787 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/snpeff/ca2b512e8d7c/snpeffv_regulationdb.loc' for tool data table 'snpeffv_regulationdb' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,787 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'snpeffv_regulationdb' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,787 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/sniffles/43fffeed243f/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,787 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,789 [pN:job_handler_0,p:8,tN:MainThread] Loaded 4 lines from '/cvmfs/data.galaxyproject.org/managed/location/all_fasta_dbkeys.loc' for 'all_fasta' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,789 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,790 [pN:job_handler_0,p:8,tN:MainThread] Loaded 2 lines from '/cvmfs/data.galaxyproject.org/managed/location/dbkeys.loc' for '__dbkeys__' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,791 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table '__dbkeys__' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,792 [pN:job_handler_0,p:8,tN:MainThread] Loaded 18 lines from '/cvmfs/data.galaxyproject.org/managed/location/all_fasta.loc' for 'all_fasta' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,792 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,793 [pN:job_handler_0,p:8,tN:MainThread] Loaded 21 lines from '/cvmfs/data.galaxyproject.org/managed/location/alignseq.loc' for 'alignseq_seq' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,793 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'alignseq_seq' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,794 [pN:job_handler_0,p:8,tN:MainThread] Loaded 21 lines from '/cvmfs/data.galaxyproject.org/managed/location/twobit.loc' for 'twobit' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,794 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'twobit' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,795 [pN:job_handler_0,p:8,tN:MainThread] Loaded 21 lines from '/cvmfs/data.galaxyproject.org/managed/location/lastz_seqs.loc' for 'lastz_seqs' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,795 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'lastz_seqs' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,796 [pN:job_handler_0,p:8,tN:MainThread] Loaded 35 lines from '/cvmfs/data.galaxyproject.org/managed/location/bowtie2_indices.loc' for 'bowtie2_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,796 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'bowtie2_indexes' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,797 [pN:job_handler_0,p:8,tN:MainThread] Loaded 35 lines from '/cvmfs/data.galaxyproject.org/managed/location/tophat2_indices.loc' for 'tophat2_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,798 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'tophat2_indexes' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,799 [pN:job_handler_0,p:8,tN:MainThread] Loaded 59 lines from '/cvmfs/data.galaxyproject.org/managed/location/hisat2_indexes.loc' for 'hisat2_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,799 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'hisat2_indexes' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,799 [pN:job_handler_0,p:8,tN:MainThread] Attempted to add fields (['ce9', 'ce9', 'C. elegans (WS210): ce9', '/cvmfs/data.galaxyproject.org/managed/hisat2_index/ce9/ce9']) to data table 'hisat2_indexes', but this entry already exists and allow_duplicates is False. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,800 [pN:job_handler_0,p:8,tN:MainThread] Loaded 47 lines from '/cvmfs/data.galaxyproject.org/managed/location/bwa_mem_index.loc' for 'bwa_mem_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,801 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'bwa_mem_indexes' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,801 [pN:job_handler_0,p:8,tN:MainThread] Attempted to add fields (['papHam1', 'papHam1', 'Baboon (Papio anubis): papHam1', '/cvmfs/data.galaxyproject.org/managed/bwa_mem_index/papHam1/papHam1.fa']) to data table 'bwa_mem_indexes', but this entry already exists and allow_duplicates is False. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,802 [pN:job_handler_0,p:8,tN:MainThread] Loaded 20 lines from '/cvmfs/data.galaxyproject.org/managed/location/fasta_indexes.loc' for 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,802 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,803 [pN:job_handler_0,p:8,tN:MainThread] Loaded 19 lines from '/cvmfs/data.galaxyproject.org/managed/location/picard_index.loc' for 'picard_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,803 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'picard_indexes' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,804 [pN:job_handler_0,p:8,tN:MainThread] Loaded 3 lines from '/cvmfs/data.galaxyproject.org/managed/location/kraken_databases.loc' for 'kraken_databases' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,804 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'kraken_databases' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,805 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/cvmfs/data.galaxyproject.org/managed/location/ncbi_taxonomy.loc' for 'ncbi_taxonomy' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,805 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'ncbi_taxonomy' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,809 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1208 lines from '/cvmfs/data.galaxyproject.org/managed/location/dbkeys_ucsc.loc' for '__dbkeys__' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,809 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table '__dbkeys__' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,834 [pN:job_handler_0,p:8,tN:MainThread] Loaded 14 lines from '/cvmfs/data.galaxyproject.org/managed/location/rnastar_index2.loc' for 'rnastar_index2' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,834 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'rnastar_index2' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,835 [pN:job_handler_0,p:8,tN:MainThread] Loaded 3 lines from '/cvmfs/data.galaxyproject.org/managed/location/plant_tribes_scaffolds.loc' for 'plant_tribes_scaffolds' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,835 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'plant_tribes_scaffolds' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,836 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/cvmfs/data.galaxyproject.org/managed/location/maf_indexes.loc' for 'maf_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,836 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'maf_indexes' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,837 [pN:job_handler_0,p:8,tN:MainThread] Loaded 15 lines from '/cvmfs/data.galaxyproject.org/managed/location/rnastar_index2x_versioned.loc' for 'rnastar_index2x_versioned' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,837 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'rnastar_index2x_versioned' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,838 [pN:job_handler_0,p:8,tN:MainThread] Loaded 19 lines from '/cvmfs/data.galaxyproject.org/managed/location/kraken2_databases.loc' for 'kraken2_databases' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,838 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'kraken2_databases' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,839 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/cvmfs/data.galaxyproject.org/managed/location/gtdbtk_database_versioned.loc' for 'gtdbtk_database_versioned' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,839 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'gtdbtk_database_versioned' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,841 [pN:job_handler_0,p:8,tN:MainThread] Loaded 238 lines from '/cvmfs/data.galaxyproject.org/byhand/location/all_fasta.loc' for 'all_fasta' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,841 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,842 [pN:job_handler_0,p:8,tN:MainThread] Attempted to add fields (['ornAna1', 'ornAna1', 'Platypus (Ornithorhynchus anatinus): ornAna1', '/cvmfs/data.galaxyproject.org/byhand/ornAna1/seq/ornAna1.fa']) to data table 'all_fasta', but this entry already exists and allow_duplicates is False. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,844 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/cvmfs/data.galaxyproject.org/byhand/location/dbkeys.loc' for '__dbkeys__' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,844 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table '__dbkeys__' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,845 [pN:job_handler_0,p:8,tN:MainThread] Loaded 5 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bfast_indexes.loc' for 'bfast_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,845 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'bfast_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,846 [pN:job_handler_0,p:8,tN:MainThread] Loaded 6 lines from '/cvmfs/data.galaxyproject.org/byhand/location/blastdb.loc' for 'blastdb' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,846 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'blastdb' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,847 [pN:job_handler_0,p:8,tN:MainThread] Loaded 2 lines from '/cvmfs/data.galaxyproject.org/byhand/location/blastdb_p.loc' for 'blastdb_p' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,847 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'blastdb_p' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,848 [pN:job_handler_0,p:8,tN:MainThread] Loaded 123 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bowtie2_indices.loc' for 'bowtie2_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,848 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'bowtie2_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,850 [pN:job_handler_0,p:8,tN:MainThread] Loaded 17 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bwa_mem_index.loc' for 'bwa_mem_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,850 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'bwa_mem_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,851 [pN:job_handler_0,p:8,tN:MainThread] Loaded 201 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bwa_index.loc' for 'bwa_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,851 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'bwa_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,852 [pN:job_handler_0,p:8,tN:MainThread] Loaded 9 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bwa_index_color.loc' for 'bwa_indexes_color' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,852 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'bwa_indexes_color' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,853 [pN:job_handler_0,p:8,tN:MainThread] Loaded 24 lines from '/cvmfs/data.galaxyproject.org/byhand/location/maf_index.loc' for 'indexed_maf_files' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,853 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'indexed_maf_files' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,854 [pN:job_handler_0,p:8,tN:MainThread] Loaded 3 lines from '/cvmfs/data.galaxyproject.org/byhand/location/ngs_sim_fasta.loc' for 'ngs_sim_fasta' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,854 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'ngs_sim_fasta' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,855 [pN:job_handler_0,p:8,tN:MainThread] Loaded 10 lines from '/cvmfs/data.galaxyproject.org/byhand/location/perm_base_index.loc' for 'perm_base_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,855 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'perm_base_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,855 [pN:job_handler_0,p:8,tN:MainThread] Loaded 10 lines from '/cvmfs/data.galaxyproject.org/byhand/location/perm_color_index.loc' for 'perm_color_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,855 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'perm_color_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,857 [pN:job_handler_0,p:8,tN:MainThread] Loaded 182 lines from '/cvmfs/data.galaxyproject.org/byhand/location/picard_index.loc' for 'picard_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,857 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'picard_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,859 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/cvmfs/data.galaxyproject.org/byhand/location/gatk_sorted_picard_index.loc' for 'gatk_picard_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,859 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'gatk_picard_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,859 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/cvmfs/data.galaxyproject.org/byhand/location/gatk_annotations.txt' for tool data table 'gatk_annotations' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,859 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'gatk_annotations' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,861 [pN:job_handler_0,p:8,tN:MainThread] Loaded 182 lines from '/cvmfs/data.galaxyproject.org/byhand/location/picard_index.loc' for 'srma_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,861 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'srma_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,864 [pN:job_handler_0,p:8,tN:MainThread] Loaded 203 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bowtie_indices.loc' for 'tophat_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,864 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'tophat_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,866 [pN:job_handler_0,p:8,tN:MainThread] Loaded 194 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bowtie_indices_color.loc' for 'tophat_indexes_color' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,866 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'tophat_indexes_color' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,867 [pN:job_handler_0,p:8,tN:MainThread] Loaded 123 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bowtie2_indices.loc' for 'tophat2_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,867 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'tophat2_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,869 [pN:job_handler_0,p:8,tN:MainThread] Loaded 3 lines from '/cvmfs/data.galaxyproject.org/byhand/location/ccat_configurations.loc' for 'ccat_configurations' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,869 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'ccat_configurations' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,871 [pN:job_handler_0,p:8,tN:MainThread] Loaded 182 lines from '/cvmfs/data.galaxyproject.org/byhand/location/mosaik_index.loc' for 'mosaik_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,871 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'mosaik_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,872 [pN:job_handler_0,p:8,tN:MainThread] Loaded 203 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bowtie_indices.loc' for 'bowtie_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,872 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'bowtie_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,874 [pN:job_handler_0,p:8,tN:MainThread] Loaded 194 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bowtie_indices_color.loc' for 'bowtie_indexes_color' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,874 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'bowtie_indexes_color' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,875 [pN:job_handler_0,p:8,tN:MainThread] Loaded 193 lines from '/cvmfs/data.galaxyproject.org/byhand/location/lastz_seqs.loc' for 'lastz_seqs' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,875 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'lastz_seqs' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,877 [pN:job_handler_0,p:8,tN:MainThread] Loaded 180 lines from '/cvmfs/data.galaxyproject.org/byhand/location/sam_fa_indices.loc' for 'sam_fa_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,878 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'sam_fa_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,880 [pN:job_handler_0,p:8,tN:MainThread] Loaded 178 lines from '/cvmfs/data.galaxyproject.org/byhand/location/fasta_indexes.loc' for 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,880 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,885 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1181 lines from '/cvmfs/data.galaxyproject.org/byhand/location/liftOver.loc' for 'liftOver' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,885 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'liftOver' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,886 [pN:job_handler_0,p:8,tN:MainThread] Loaded 26 lines from '/cvmfs/data.galaxyproject.org/byhand/location/twobit.loc' for 'twobit' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,886 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'twobit' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,887 [pN:job_handler_0,p:8,tN:MainThread] Loaded 106 lines from '/cvmfs/data.galaxyproject.org/byhand/location/customProDB.loc' for 'customProDB' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,887 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'customProDB' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,888 [pN:job_handler_0,p:8,tN:MainThread] Loaded 2 lines from '/cvmfs/data.galaxyproject.org/byhand/location/hisat2_indexes.loc' for 'hisat2_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,888 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'hisat2_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,889 [pN:job_handler_0,p:8,tN:MainThread] Loaded 2 lines from '/cvmfs/data.galaxyproject.org/byhand/location/rnastar_index2x_versioned.loc' for 'rnastar_index2x_versioned' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,890 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'rnastar_index2x_versioned' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,890 [pN:job_handler_0,p:8,tN:MainThread] Loaded 4 lines from '/cvmfs/data.galaxyproject.org/byhand/location/snpeffv_genomedb.loc' for 'snpeffv_genomedb' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,891 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'snpeffv_genomedb' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,891 [pN:job_handler_0,p:8,tN:MainThread] Loaded 5 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bwameth_indexes.loc' for 'bwameth_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,891 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'bwameth_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,893 [pN:job_handler_0,p:8,tN:MainThread] Loaded 2 lines from '/cvmfs/data.galaxyproject.org/byhand/location/metaphlan_database_versioned.loc' for 'metaphlan_database_versioned' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,893 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'metaphlan_database_versioned' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,894 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/cvmfs/data.galaxyproject.org/byhand/location/busco_database.loc' for 'busco_database' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,894 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'busco_database' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,895 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/cvmfs/data.galaxyproject.org/byhand/location/ncbi_fcs_gx_databases.loc' for 'ncbi_fcs_gx_databases' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,895 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'ncbi_fcs_gx_databases' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,896 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/cvmfs/data.galaxyproject.org/byhand/location/ncbi_fcs_gx_databases_ext.loc' for 'ncbi_fcs_gx_databases_ext' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,896 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'ncbi_fcs_gx_databases_ext' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,897 [pN:job_handler_0,p:8,tN:MainThread] Loaded 63 lines from '/cvmfs/data.galaxyproject.org/byhand/location/ncbi_fcs_gx_divisions.tsv' for 'ncbi_fcs_gx_divisions' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,897 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'ncbi_fcs_gx_divisions' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,898 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/cvmfs/data.galaxyproject.org/byhand/location/ncbi_fcs_gx_config.tsv' for 'ncbi_fcs_gx_config' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,898 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'ncbi_fcs_gx_config' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,899 [pN:job_handler_0,p:8,tN:MainThread] Loaded 8 lines from '/cvmfs/data.galaxyproject.org/byhand/location/rRNA_databases.loc' for 'rRNA_databases' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,899 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'rRNA_databases' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,900 [pN:job_handler_0,p:8,tN:MainThread] Loaded 6 lines from '/cvmfs/data.galaxyproject.org/byhand/location/mitos.loc' for 'mitos' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,900 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'mitos' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,901 [pN:job_handler_0,p:8,tN:MainThread] Loaded 3 lines from '/cvmfs/data.galaxyproject.org/byhand/location/dada2_species.loc' for 'dada2_species' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,901 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'dada2_species' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,902 [pN:job_handler_0,p:8,tN:MainThread] Loaded 9 lines from '/cvmfs/data.galaxyproject.org/byhand/location/dada2_taxonomy.loc' for 'dada2_taxonomy' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,903 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'dada2_taxonomy' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,903 [pN:job_handler_0,p:8,tN:MainThread] Loaded 4 lines from '/cvmfs/data.galaxyproject.org/byhand/location/mapseq_db.loc' for 'mapseq_db' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,903 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'mapseq_db' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,904 [pN:job_handler_0,p:8,tN:MainThread] Loaded 3 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bracken_databases.loc' for 'bracken_databases' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,904 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'bracken_databases' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,905 [pN:job_handler_0,p:8,tN:MainThread] Loaded 2 lines from '/cvmfs/data.galaxyproject.org/byhand/location/plasmidfinder_database.loc' for 'plasmidfinder_database' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,905 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'plasmidfinder_database' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,906 [pN:job_handler_0,p:8,tN:MainThread] Loaded 2 lines from '/cvmfs/data.galaxyproject.org/byhand/location/amrfinderplus.loc' for 'amrfinderplus_database' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,906 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'amrfinderplus_database' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,907 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/cvmfs/data.galaxyproject.org/byhand/location/amrfinderplus_versioned.loc' for 'amrfinderplus_versioned_database' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,908 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'amrfinderplus_versioned_database' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,909 [pN:job_handler_0,p:8,tN:MainThread] Loaded 2 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bakta_database.loc' for 'bakta_database' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,909 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'bakta_database' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,910 [pN:job_handler_0,p:8,tN:MainThread] Loaded 3 lines from '/cvmfs/data.galaxyproject.org/byhand/location/ncbi_taxonomy.loc' for 'ncbi_taxonomy' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,910 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'ncbi_taxonomy' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,911 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/cvmfs/data.galaxyproject.org/byhand/location/humann_protein_database.loc' for 'humann_protein_database' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,911 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'humann_protein_database' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,912 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/cvmfs/data.galaxyproject.org/byhand/location/humann_nucleotide_database.loc' for 'humann_nucleotide_database' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,912 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'humann_nucleotide_database' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,913 [pN:job_handler_0,p:8,tN:MainThread] Loaded 5 lines from '/cvmfs/data.galaxyproject.org/byhand/location/omamer.loc' for 'omamer' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,913 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'omamer' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,914 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bwa_mem2_index.loc' for 'bwa_mem2_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,914 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'bwa_mem2_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,915 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/cvmfs/data.galaxyproject.org/byhand/location/eggnog_mapper_db_versioned.loc' for 'eggnog_mapper_db_versioned' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,916 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'eggnog_mapper_db_versioned' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,916 [pN:job_handler_0,p:8,tN:MainThread] Loaded 4 lines from '/cvmfs/data.galaxyproject.org/byhand/location/infernal.loc' for 'infernal' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,917 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'infernal' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,918 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/cvmfs/data.galaxyproject.org/byhand/location/funannotate.loc' for 'funannotate' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,918 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'funannotate' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,919 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/cvmfs/data.galaxyproject.org/byhand/location/interproscan.loc' for 'interproscan' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,919 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'interproscan' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data INFO 2024-12-30 00:50:50,920 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/all_fasta.loc, reading sample +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,921 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/all_fasta.loc.sample' for 'all_fasta' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,921 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data INFO 2024-12-30 00:50:50,922 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/bfast_indexes.loc, reading sample +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,923 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/bfast_indexes.loc.sample' for 'bfast_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,923 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'bfast_indexes' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,923 [pN:job_handler_0,p:8,tN:MainThread] While attempting to merge tool data table "bfast_indexes", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries. +galaxy.tool_util.data INFO 2024-12-30 00:50:50,923 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/blastdb.loc, reading sample +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,924 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/blastdb.loc.sample' for 'blastdb' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,924 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'blastdb' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,924 [pN:job_handler_0,p:8,tN:MainThread] While attempting to merge tool data table "blastdb", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries. +galaxy.tool_util.data INFO 2024-12-30 00:50:50,925 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/blastdb_p.loc, reading sample +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,926 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/blastdb_p.loc.sample' for 'blastdb_p' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,926 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'blastdb_p' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,926 [pN:job_handler_0,p:8,tN:MainThread] While attempting to merge tool data table "blastdb_p", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries. +galaxy.tool_util.data INFO 2024-12-30 00:50:50,927 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/blastdb_d.loc, reading sample +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,927 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/blastdb_d.loc.sample' for 'blastdb_d' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,927 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'blastdb_d' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,928 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file 'bwa_index.loc' for tool data table 'bwa_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,928 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'bwa_indexes' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,928 [pN:job_handler_0,p:8,tN:MainThread] While attempting to merge tool data table "bwa_indexes", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries. +galaxy.tool_util.data WARNING 2024-12-30 00:50:50,928 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file 'bwa_index_color.loc' for tool data table 'bwa_indexes_color' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,928 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'bwa_indexes_color' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,928 [pN:job_handler_0,p:8,tN:MainThread] While attempting to merge tool data table "bwa_indexes_color", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries. +galaxy.tool_util.data INFO 2024-12-30 00:50:50,928 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/maf_index.loc, reading sample +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,929 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/maf_index.loc.sample' for 'indexed_maf_files' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,929 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'indexed_maf_files' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data INFO 2024-12-30 00:50:50,930 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/ngs_sim_fasta.loc, reading sample +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,931 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/ngs_sim_fasta.loc.sample' for 'ngs_sim_fasta' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,931 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'ngs_sim_fasta' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,931 [pN:job_handler_0,p:8,tN:MainThread] While attempting to merge tool data table "ngs_sim_fasta", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries. +galaxy.tool_util.data INFO 2024-12-30 00:50:50,931 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/perm_base_index.loc, reading sample +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,932 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/perm_base_index.loc.sample' for 'perm_base_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,932 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'perm_base_indexes' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,932 [pN:job_handler_0,p:8,tN:MainThread] While attempting to merge tool data table "perm_base_indexes", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries. +galaxy.tool_util.data INFO 2024-12-30 00:50:50,932 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/perm_color_index.loc, reading sample +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,933 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/perm_color_index.loc.sample' for 'perm_color_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,933 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'perm_color_indexes' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,933 [pN:job_handler_0,p:8,tN:MainThread] While attempting to merge tool data table "perm_color_indexes", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries. +galaxy.tool_util.data INFO 2024-12-30 00:50:50,933 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/picard_index.loc, reading sample +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,934 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/picard_index.loc.sample' for 'picard_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,934 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'picard_indexes' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,934 [pN:job_handler_0,p:8,tN:MainThread] While attempting to merge tool data table "picard_indexes", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries. +galaxy.tool_util.data INFO 2024-12-30 00:50:50,934 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/picard_index.loc, reading sample +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,935 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/picard_index.loc.sample' for 'srma_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,935 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'srma_indexes' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,935 [pN:job_handler_0,p:8,tN:MainThread] While attempting to merge tool data table "srma_indexes", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries. +galaxy.tool_util.data INFO 2024-12-30 00:50:50,936 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/mosaik_index.loc, reading sample +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,936 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/mosaik_index.loc.sample' for 'mosaik_indexes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,937 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'mosaik_indexes' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,937 [pN:job_handler_0,p:8,tN:MainThread] While attempting to merge tool data table "mosaik_indexes", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries. +galaxy.tool_util.data INFO 2024-12-30 00:50:50,937 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/twobit.loc, reading sample +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,938 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/twobit.loc.sample' for 'twobit' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,938 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'twobit' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:50,938 [pN:job_handler_0,p:8,tN:MainThread] While attempting to merge tool data table "twobit", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries. +charset_normalizer DEBUG 2024-12-30 00:50:51,066 [pN:job_handler_0,p:8,tN:MainThread] Encoding detection: utf_8 is most likely the one. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:51,067 [pN:job_handler_0,p:8,tN:MainThread] Loading Data Table URL "http://igv.broadinstitute.org/genomes/genomes.txt" as filename "/galaxy/server/database/tmp/TTDT_URL_igv_broad_genomes-2cy3j_wp". +galaxy.tool_util.data WARNING 2024-12-30 00:50:51,071 [pN:job_handler_0,p:8,tN:MainThread] Line 1 in tool data table 'igv_broad_genomes' is invalid (HINT: '' characters must be used to separate fields): + +galaxy.tool_util.data WARNING 2024-12-30 00:50:51,072 [pN:job_handler_0,p:8,tN:MainThread] Line 2 in tool data table 'igv_broad_genomes' is invalid (HINT: '' characters must be used to separate fields): +AccessDeniedAccess DeniedCRZ1BQ6YG8XM2585apBtm6pEBX2BnHhk4hp9RvUux+ncd4RSlBAgbUyru77gUrduIWN2UrIWFQ/nY/nwoyMf7VTVpTo= +galaxy.tool_util.data DEBUG 2024-12-30 00:50:51,072 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tmp/TTDT_URL_igv_broad_genomes-2cy3j_wp' for 'igv_broad_genomes' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:51,072 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'igv_broad_genomes' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml' +galaxy.tool_util.data INFO 2024-12-30 00:50:51,073 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/liftOver.loc, reading sample +galaxy.tool_util.data DEBUG 2024-12-30 00:50:51,074 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/liftOver.loc.sample' for 'liftOver' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:51,074 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'liftOver' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:51,074 [pN:job_handler_0,p:8,tN:MainThread] While attempting to merge tool data table "liftOver", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries. +galaxy.tool_util.data INFO 2024-12-30 00:50:51,075 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/bam_iobio.loc, reading sample +galaxy.tool_util.data DEBUG 2024-12-30 00:50:51,076 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/galaxy/server/database/tool-data/bam_iobio.loc.sample' for 'bam_iobio' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:51,076 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'bam_iobio' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml' +galaxy.tool_util.data INFO 2024-12-30 00:50:51,077 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/vcf_iobio.loc, reading sample +galaxy.tool_util.data DEBUG 2024-12-30 00:50:51,078 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/galaxy/server/database/tool-data/vcf_iobio.loc.sample' for 'vcf_iobio' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:51,078 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'vcf_iobio' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml' +galaxy.tool_util.data INFO 2024-12-30 00:50:51,078 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/biom_simple_display.loc, reading sample +galaxy.tool_util.data DEBUG 2024-12-30 00:50:51,079 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/galaxy/server/database/tool-data/biom_simple_display.loc.sample' for 'biom_simple_display' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:51,079 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'biom_simple_display' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml' +galaxy.tool_util.data INFO 2024-12-30 00:50:51,079 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/intermine_simple_display.loc, reading sample +galaxy.tool_util.data DEBUG 2024-12-30 00:50:51,080 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/galaxy/server/database/tool-data/intermine_simple_display.loc.sample' for 'intermine_simple_display' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:51,080 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'intermine_simple_display' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml' +galaxy.tool_util.data INFO 2024-12-30 00:50:51,080 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/icn3d_simple_display.loc, reading sample +galaxy.tool_util.data DEBUG 2024-12-30 00:50:51,081 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/galaxy/server/database/tool-data/icn3d_simple_display.loc.sample' for 'icn3d_simple_display' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:51,082 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'icn3d_simple_display' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:51,082 [pN:job_handler_0,p:8,tN:MainThread] Encountered a file element () that does not contain a path value when loading tool data table '__dbkeys__'. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:51,082 [pN:job_handler_0,p:8,tN:MainThread] Encountered a file element () that does not contain a path value when loading tool data table '__dbkeys__'. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:51,082 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table '__dbkeys__' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:51,082 [pN:job_handler_0,p:8,tN:MainThread] Encountered a file element () that does not contain a path value when loading tool data table 'all_fasta'. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:51,082 [pN:job_handler_0,p:8,tN:MainThread] Encountered a file element () that does not contain a path value when loading tool data table 'all_fasta'. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:51,082 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:51,082 [pN:job_handler_0,p:8,tN:MainThread] Encountered a file element () that does not contain a path value when loading tool data table 'fasta_indexes'. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:51,082 [pN:job_handler_0,p:8,tN:MainThread] Encountered a file element () that does not contain a path value when loading tool data table 'fasta_indexes'. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:51,083 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:51,083 [pN:job_handler_0,p:8,tN:MainThread] Encountered a file element () that does not contain a path value when loading tool data table 'bowtie2_indexes'. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:51,083 [pN:job_handler_0,p:8,tN:MainThread] Encountered a file element () that does not contain a path value when loading tool data table 'bowtie2_indexes'. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:51,083 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'bowtie2_indexes' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:51,083 [pN:job_handler_0,p:8,tN:MainThread] Encountered a file element () that does not contain a path value when loading tool data table 'bwa_mem_indexes'. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:51,083 [pN:job_handler_0,p:8,tN:MainThread] Encountered a file element () that does not contain a path value when loading tool data table 'bwa_mem_indexes'. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:51,083 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'bwa_mem_indexes' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:51,083 [pN:job_handler_0,p:8,tN:MainThread] Encountered a file element () that does not contain a path value when loading tool data table 'hisat2_indexes'. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:51,083 [pN:job_handler_0,p:8,tN:MainThread] Encountered a file element () that does not contain a path value when loading tool data table 'hisat2_indexes'. +galaxy.tool_util.data DEBUG 2024-12-30 00:50:51,083 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'hisat2_indexes' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data INFO 2024-12-30 00:50:51,084 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/q2view_display.loc, reading sample +galaxy.tool_util.data DEBUG 2024-12-30 00:50:51,085 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/galaxy/server/database/tool-data/q2view_display.loc.sample' for 'q2view_display' +galaxy.tool_util.data DEBUG 2024-12-30 00:50:51,085 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'q2view_display' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml' +galaxy.util.dbkeys ERROR 2024-12-30 00:50:51,085 [pN:job_handler_0,p:8,tN:MainThread] ERROR: Unable to read builds file: [Errno 2] No such file or directory: '/galaxy/server/database/tool-data/\n/cvmfs/data.galaxyproject.org/managed/location/builds.txt' +galaxy.util WARNING 2024-12-30 00:50:51,172 [pN:job_handler_0,p:8,tN:MainThread] directory not found: /galaxy/server/lib/galaxy/util/../../../config/plugins/activities +galaxy.tools WARNING 2024-12-30 00:50:51,180 [pN:job_handler_0,p:8,tN:MainThread] The default shed tool config file (/galaxy/server/config/mutable/editable_shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2024-12-30 00:50:51,180 [pN:job_handler_0,p:8,tN:MainThread] Parsing the tool configuration /galaxy/server/config/tool_conf.xml +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:50:51,180 [pN:job_handler_0,p:8,tN:MainThread] Tool path for tool configuration /galaxy/server/config/tool_conf.xml is None +galaxy.tool_util.toolbox.base ERROR 2024-12-30 00:50:51,230 [pN:job_handler_0,p:8,tN:MainThread] Error reading tool configuration file from path 'genomespace/genomespace_importer.xml': [Errno 2] No such file or directory +galaxy.tool_util.toolbox.base ERROR 2024-12-30 00:50:51,230 [pN:job_handler_0,p:8,tN:MainThread] Error reading tool configuration file from path 'genomespace/genomespace_push.xml': [Errno 2] No such file or directory +galaxy.tool_util.toolbox.base ERROR 2024-12-30 00:50:51,411 [pN:job_handler_0,p:8,tN:MainThread] Error reading tool configuration file from path 'evolution/codingSnps.xml': [Errno 2] No such file or directory +galaxy.tool_util.toolbox.base ERROR 2024-12-30 00:50:51,411 [pN:job_handler_0,p:8,tN:MainThread] Error reading tool configuration file from path 'evolution/add_scores.xml': [Errno 2] No such file or directory +galaxy.tool_util.toolbox.base ERROR 2024-12-30 00:50:51,413 [pN:job_handler_0,p:8,tN:MainThread] Error reading tool from path: phenotype_association/sift.xml +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/tool_util/toolbox/base.py", line 865, in _load_tool_tag_set + tool = self.load_tool(concrete_path, use_cached=False, tool_cache_data_dir=tool_cache_data_dir) + File "/galaxy/server/lib/galaxy/tool_util/toolbox/base.py", line 1092, in load_tool + tool = self.create_tool( + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 530, in create_tool + return self._create_tool_from_source(tool_source, config_file=config_file, **kwds) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 546, in _create_tool_from_source + return create_tool_from_source(self.app, tool_source, **kwds) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 340, in create_tool_from_source + tool = ToolClass(config_file, tool_source, app, **kwds) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 802, in __init__ + raise e + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 799, in __init__ + self.parse(tool_source, guid=guid, dynamic=dynamic) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1123, in parse + self.parse_inputs(self.tool_source) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1414, in parse_inputs + inputs = self.parse_input_elem(page_source, enctypes) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1609, in parse_input_elem + param = self.parse_param_elem(input_source, enctypes, context) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1622, in parse_param_elem + param = ToolParameter.build(self, input_source) + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 319, in build + return parameter_types[param_type](tool, input_source) + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 2044, in __init__ + super().__init__(tool, input_source, trans) + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 1832, in __init__ + super().__init__(tool, input_source) + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 178, in __init__ + self.validators.append(validation.Validator.from_element(self, elem)) + File "/galaxy/server/lib/galaxy/tools/parameters/validation.py", line 50, in from_element + return validator_types[_type].from_element(param, elem) + File "/galaxy/server/lib/galaxy/tools/parameters/validation.py", line 727, in from_element + assert os.path.exists(filename), f"File {filename} specified by the 'filename' attribute not found" +AssertionError: File /galaxy/server/database/tool-data/sift_db.loc specified by the 'filename' attribute not found +galaxy.tools WARNING 2024-12-30 00:50:51,450 [pN:job_handler_0,p:8,tN:MainThread] The default shed tool config file (/galaxy/server/config/mutable/editable_shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2024-12-30 00:50:51,450 [pN:job_handler_0,p:8,tN:MainThread] Parsing the tool configuration /cvmfs/cloud.galaxyproject.org/config/shed_tool_conf.xml +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:50:51,471 [pN:job_handler_0,p:8,tN:MainThread] Tool path for shed tool configuration /cvmfs/cloud.galaxyproject.org/config/shed_tool_conf.xml is /cvmfs/cloud.galaxyproject.org/tools +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,474 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'ivar_trim' from owner 'iuc' was not found in database. Tool will be loaded without install database. +sqlitedict DEBUG 2024-12-30 00:50:51,475 [pN:job_handler_0,p:8,tN:MainThread] opening Sqlite table 'unnamed' in '/cvmfs/cloud.galaxyproject.org/var/tool_cache/cache.sqlite' +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,490 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'ivar_removereads' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,497 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'snpeff_sars_cov_2' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,507 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'ivar_consensus' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,512 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'ivar_filtervariants' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,517 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'ivar_getmasked' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,522 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'ivar_variants' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,527 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'ivar_trim' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,533 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'ivar_removereads' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,538 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'ivar_consensus' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,543 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'ivar_filtervariants' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,548 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'ivar_variants' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,554 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_consensus' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,561 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_gtcheck' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,567 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_fixploidy' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,575 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_convert_to_vcf' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,583 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_norm' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,592 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_query_list_samples' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,597 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_missing2ref' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,605 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_cnv' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,612 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_setgt' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,621 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_counts' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,628 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_mpileup' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,638 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_mendelian' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,645 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_concat' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,652 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_convert_from_vcf' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,662 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_impute_info' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,669 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_reheader' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,677 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_stats' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,687 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_fill_an_ac' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,694 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_fill_tags' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,703 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_isec' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,711 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_merge' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,716 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_roh' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,724 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_call' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,733 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_view' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,742 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_filter' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,751 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_csq' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,760 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_annotate' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,770 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_dosage' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,777 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_query' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,786 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_tag2tag' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,796 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcf2tsv' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,802 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfaddinfo' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,808 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfallelicprimitives' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,815 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfannotate' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,821 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfannotategenotypes' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,828 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfbedintersect' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,835 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfbreakcreatemulti' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,841 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfcheck' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,847 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfcombine' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,853 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfcommonsamples' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,858 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcffixup' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,864 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfflatten' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,870 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfgeno2haplo' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,876 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfgenotypes' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,883 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfhethom' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,889 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfleftalign' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,895 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfprimers' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,901 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfrandomsample' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,907 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfsort' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,912 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfvcfintersect' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,919 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfselectsamples' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,927 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfdistance' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,934 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcffilter' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,941 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfdistance' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,947 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcftools_annotate' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,953 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcftools_slice' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,958 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfallelicprimitives' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,964 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_consensus' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,973 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_gtcheck' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,979 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_fixploidy' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,987 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_convert_to_vcf' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:51,994 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_norm' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,002 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_query_list_samples' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,007 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_missing2ref' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,013 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_cnv' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,021 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_setgt' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,028 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_counts' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,035 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_mpileup' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,046 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_mendelian' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,053 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_concat' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,059 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_convert_from_vcf' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,068 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_impute_info' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,075 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_reheader' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,081 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_stats' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,089 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_fill_an_ac' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,098 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_fill_tags' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,105 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_isec' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,113 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_merge' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,120 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_roh' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,128 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_call' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,139 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_view' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,147 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_filter' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,156 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_csq' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,165 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_annotate' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,174 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_dosage' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,182 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_query' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,189 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_tag2tag' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,197 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bedtools' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,382 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bedtools' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,551 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bedtools' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,729 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'collapse_collections' from owner 'nml' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,734 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'split_file_to_collection' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,746 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'pick_value' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,753 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'split_file_to_collection' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,766 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'collection_element_identifiers' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,771 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'collection_column_join' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,777 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_compute_matrix' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,786 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_plot_heatmap' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,796 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_bam_compare' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,804 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_bam_pe_fragmentsize' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,811 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_bigwig_compare' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,817 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_compute_gc_bias' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,824 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_correct_gc_bias' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,830 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_multi_bam_summary' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,837 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_multi_bigwig_summary' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,844 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_plot_correlation' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,851 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_plot_coverage' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,857 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_plot_enrichment' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,863 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_plot_fingerprint' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,869 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_plot_pca' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,875 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_bam_coverage' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,882 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_plot_profile' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,891 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_compute_matrix' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,898 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_plot_heatmap' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,909 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_bam_compare' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,917 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_bam_pe_fragmentsize' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,924 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_bigwig_compare' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,931 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_compute_gc_bias' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,940 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_correct_gc_bias' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,946 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_multi_bam_summary' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,954 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_multi_bigwig_summary' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,962 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_plot_correlation' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,970 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_plot_coverage' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,979 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_plot_enrichment' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,986 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_plot_fingerprint' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:52,995 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_plot_pca' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:53,002 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_bam_coverage' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:53,011 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_plot_profile' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:53,020 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'multiqc' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:53,034 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fastp' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:53,046 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fastqc' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:53,052 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'trimmomatic' from owner 'pjbriggs' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:53,062 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'multiqc' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:53,074 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fastqc' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:53,079 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'multiqc' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:53,090 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'multiqc' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:53,103 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'multiqc' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:53,114 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'multiqc' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:53,126 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fastp' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:53,135 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fastqc' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:53,140 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'multiqc' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:53,159 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fastp' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:53,168 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fastqc' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:53,174 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fastp' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:53,183 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'trimmomatic' from owner 'pjbriggs' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:53,191 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sra_tools' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:53,210 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'ncbi_acc_download' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:53,215 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sra_tools' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:53,234 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sra_tools' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:53,255 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'ncbi_acc_download' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:53,261 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'pygenometracks' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:53,287 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'circos' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:53,357 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'jbrowse' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tools.parameters.sanitize DEBUG 2024-12-30 00:50:53,371 [pN:job_handler_0,p:8,tN:MainThread] Invalid preset name specified: galaxy.util.mapped_chars +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:53,379 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'volcanoplot' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:53,386 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'jbrowse' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tools.parameters.sanitize DEBUG 2024-12-30 00:50:53,400 [pN:job_handler_0,p:8,tN:MainThread] Invalid preset name specified: galaxy.util.mapped_chars +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:53,410 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'pathview' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:53,418 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'pathview' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:53,424 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'ggplot2_heatmap2' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:53,431 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'ggplot2_heatmap2' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:53,437 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'ggplot2_heatmap2' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:53,441 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'volcanoplot' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:53,446 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'minimap2' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:53,457 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bowtie2' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:53,473 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bwa' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:53,492 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bwameth' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:53,499 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'lastz' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:53,515 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'rgrnastar' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:53,530 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'rna_starsolo' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:53,545 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'rgrnastar' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:53,556 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'rgrnastar' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:53,573 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bwa' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:53,593 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'minimap2' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:53,603 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bowtie2' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:53,619 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bwa' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:53,913 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bwameth' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:53,920 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'lastz' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:53,938 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'rgrnastar' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:53,956 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'rgrnastar' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:53,973 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'rna_starsolo' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:53,992 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'rna_starsolo' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,010 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'mummer_nucmer' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,017 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'mummer_mummerplot' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,023 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'mummer_show_coords' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,029 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'mummer_dnadiff' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,036 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'mummer_mummer' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,043 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'mummer_delta_filter' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,049 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'mummer_nucmer' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,057 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'mummer_mummerplot' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,063 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'mummer_show_coords' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,070 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'mummer_dnadiff' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,077 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'mummer_mummer' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,085 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'mummer_delta_filter' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,091 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'medaka_variant' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,099 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'flye' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,106 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'medaka_consensus_pipeline' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,113 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'medaka_variant_pipeline' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,121 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'medaka_consensus' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,128 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'nanoplot' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,137 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'poretools_events' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,141 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'poretools_hist' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,148 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'poretools_occupancy' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,155 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'poretools_qualpos' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,161 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'poretools_squiggle' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,168 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'poretools_yield_plot' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,174 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'porechop' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,182 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'poretools_winner' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,188 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'poretools_times' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,194 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'poretools_tabular' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,199 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'poretools_stats' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,205 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'poretools_qualdist' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,212 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'poretools_nucdist' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,217 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'poretools_extract' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,222 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'medaka_variant' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,228 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'flye' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,236 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'medaka_consensus_pipeline' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,243 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'medaka_variant_pipeline' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,250 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'medaka_consensus' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,257 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'nanoplot' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,265 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'porechop' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,272 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'flye' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,280 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'salmon' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tools.parameters.basic WARNING 2024-12-30 00:50:54,287 [pN:job_handler_0,p:8,tN:MainThread] Datatype class not found for extension 'fa', which is used in the 'format' attribute of parameter 'transcript' +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,292 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'kallisto_pseudo' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,298 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'kallisto_quant' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,305 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deseq2' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,314 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'limma_voom' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,325 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'edger' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,334 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sailfish' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,343 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'hisat2' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,359 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'stringtie' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,374 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'featurecounts' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,382 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'featurecounts' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,391 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'limma_voom' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,400 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'hisat2' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,416 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deseq2' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,427 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'hisat2' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,441 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'featurecounts' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,449 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'cufflinks' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,457 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deg_annotate' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,464 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'goseq' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,472 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'goseq' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,482 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deseq2' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,492 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'limma_voom' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,504 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'egsea' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,512 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fgsea' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,518 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'salmon' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tools.parameters.basic WARNING 2024-12-30 00:50:54,526 [pN:job_handler_0,p:8,tN:MainThread] Datatype class not found for extension 'fa', which is used in the 'format' attribute of parameter 'transcript' +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,529 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'kallisto_pseudo' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,535 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'kallisto_quant' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,541 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deseq2' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,551 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'limma_voom' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,562 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'edger' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,572 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'stringtie' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,587 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'featurecounts' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,596 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'brew3r_r' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,602 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'featurecounts' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,612 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'cufflinks' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,620 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'brew3r_r' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,625 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'seurat' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,636 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'dexseq' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,657 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'rseqc' from owner 'nilesh' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,766 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'rseqc' from owner 'nilesh' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:54,884 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'rseqc' from owner 'nilesh' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,001 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'pileup_interval' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,006 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qualimap_bamqc' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,013 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_view' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,024 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_reheader' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,031 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sam_pileup' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,037 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bamtools' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,045 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bamtools_split' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,051 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sam2interval' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,057 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qualimap_multi_bamqc' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,063 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_phase' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,070 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_merge' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,075 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_markdup' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,082 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_fixmate' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,087 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_fastx' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,095 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_depth' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,101 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_stats' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,110 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_split' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,116 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_bedcov' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,121 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_calmd' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,127 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_idxstats' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,133 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtool_filter2' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,140 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_flagstat' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,145 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_sort' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,151 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_mpileup' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,160 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bam_to_sam' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,165 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bamtools_filter' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,173 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sam_to_bam' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,179 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_slice_bam' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,185 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_rmdup' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,190 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'filter_on_md' from owner 'boris' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,195 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sam_merge' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,199 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_stats' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,206 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_phase' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,211 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_merge' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,217 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_markdup' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,223 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_idxstats' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,229 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bamtools_filter' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,236 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_view' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,246 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_view' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,256 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_idxstats' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,261 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'revertr2orientationinbam' from owner 'lldelisle' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,266 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qualimap_bamqc' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,272 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_view' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,285 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_view' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,295 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_reheader' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,300 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bamtools' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,306 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bamtools_split' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,312 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qualimap_multi_bamqc' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,318 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_merge' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,324 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_markdup' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,331 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_fixmate' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,336 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_fastx' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,345 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_depth' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,352 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_stats' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,360 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_split' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,365 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_bedcov' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,370 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_calmd' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,376 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_idxstats' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,381 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_flagstat' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,387 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_sort' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,392 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_mpileup' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,401 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bam_to_sam' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,406 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bamtools_filter' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,413 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sam_to_bam' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,418 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_slice_bam' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,425 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'filter_tabular' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,433 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'query_tabular' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,448 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'column_maker' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,453 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sqlite_to_tabular' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,461 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'annotatemyids' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,468 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'concatenate_multiple_datasets' from owner 'mvdbeek' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,473 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'regex_find_replace' from owner 'galaxyp' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,485 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'table_compute' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,498 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'split_file_on_column' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,506 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'add_input_name_as_column' from owner 'mvdbeek' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,512 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'text_processing' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,611 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'reshape2_melt' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,615 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'reshape2_cast' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,620 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'jq' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,625 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'gff3_rebase' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,630 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'column_remove_by_header' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,634 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'column_order_header_sort' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,638 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'replace_column_by_key_value_file' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,641 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'text_processing' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,734 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'query_tabular' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,746 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'annotatemyids' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,753 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'column_maker' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,759 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'table_compute' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,772 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'text_processing' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,863 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'annotatemyids' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,871 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'annotatemyids' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,878 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'text_processing' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,969 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'merge_cols' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,975 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'merge_cols' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,980 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'filter_tabular' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:55,988 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'query_tabular' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,002 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'column_maker' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,011 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sqlite_to_tabular' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,017 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'annotatemyids' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,023 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'regex_find_replace' from owner 'galaxyp' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,036 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'split_file_on_column' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,041 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'text_processing' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,150 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'text_processing' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,256 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'column_remove_by_header' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,262 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'lofreq_call' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,270 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'lofreq_viterbi' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,277 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'lofreq_indelqual' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,282 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'lofreq_filter' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,291 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'lofreq_alnqual' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,300 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'freebayes' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,316 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'snpsift_genesets' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,321 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'snpsift_dbnsfp' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,326 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'snpeff' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,355 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'snpsift' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,394 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'snpfreqplot' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,400 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sniffles' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,406 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'jasminesv' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,413 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'snpfreqplot' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,419 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'lofreq_call' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,429 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'lofreq_call' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,439 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'freebayes' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,457 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'freebayes' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,474 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'snpeff' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,508 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'snpeff' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,523 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'lofreq_indelqual' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,530 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'lofreq_alnqual' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,536 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'snpeff' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,567 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'lofreq_call' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,576 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'freebayes' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,594 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'snpeff' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,626 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sniffles' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,635 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'diff' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,643 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'unicycler' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,652 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'spades' from owner 'nml' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,662 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'miniasm' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,669 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'racon' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,675 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'unicycler' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,685 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'miniasm' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,692 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'racon' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,698 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'gfastats' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tools DEBUG 2024-12-30 00:50:56,704 [pN:job_handler_0,p:8,tN:MainThread] Tool with id 'toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0': a when tag has been defined for 'target_condition (target_option) --> false', but does not appear to be selectable. +galaxy.tools.parameters.basic WARNING 2024-12-30 00:50:56,704 [pN:job_handler_0,p:8,tN:MainThread] Datatype class not found for extension 'text', which is used in the 'format' attribute of parameter 'swiss_army_knife' +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,707 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'spades' from owner 'nml' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,718 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'gfastats' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base ERROR 2024-12-30 00:50:56,721 [pN:job_handler_0,p:8,tN:MainThread] Error reading tool from path: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/f4a3eff8ab85/gfastats/gfastats.xml +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/tool_util/toolbox/base.py", line 857, in _load_tool_tag_set + tool = self.load_tool( + File "/galaxy/server/lib/galaxy/tool_util/toolbox/base.py", line 1092, in load_tool + tool = self.create_tool( + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 530, in create_tool + return self._create_tool_from_source(tool_source, config_file=config_file, **kwds) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 546, in _create_tool_from_source + return create_tool_from_source(self.app, tool_source, **kwds) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 340, in create_tool_from_source + tool = ToolClass(config_file, tool_source, app, **kwds) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 802, in __init__ + raise e + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 799, in __init__ + self.parse(tool_source, guid=guid, dynamic=dynamic) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1000, in parse + raise Exception(message) +Exception: The tool [toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0] targets version 23.2 of Galaxy, you should upgrade Galaxy to ensure proper functioning of this tool. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,722 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'quast' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,737 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sra_tools' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,755 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'pharmcat' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,760 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'pharmcat' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,766 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name '10x_bamtofastq' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,772 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'anndata_import' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,779 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'anndata_export' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,787 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'anndata_manipulate' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,794 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'chromeister' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,800 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'anndata_inspect' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,810 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'modify_loom' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,816 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'dropletutils' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,823 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'dropletutils_read_10x' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tools WARNING 2024-12-30 00:50:56,828 [pN:job_handler_0,p:8,tN:MainThread] Tool with id 'toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_read_10x/dropletutils_read_10x/1.0.4+galaxy0': a when tag has not been defined for 'add_metadata (add_metadata_file) --> false', assuming empty inputs. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,830 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'dropletutils_empty_drops' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,836 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'raceid_inspectclusters' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,846 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'raceid_filtnormconf' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,853 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'raceid_clustering' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,861 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'raceid_trajectory' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,869 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'raceid_inspecttrajectory' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,878 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'alevin' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,888 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'salmonquantmerge' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,894 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'slice_image' from owner 'imgteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,900 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scater_create_qcmetric_ready_sce' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,906 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scater_plot_tsne' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,913 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scater_filter' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,920 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scater_normalize' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,926 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scater_plot_dist_scatter' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,933 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scater_plot_exprs_freq' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,939 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scater_plot_pca' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,946 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_cluster_reduce_dimension' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,958 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_filter' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,967 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_inspect' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,982 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_normalize' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:56,990 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_plot' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tools DEBUG 2024-12-30 00:50:57,039 [pN:job_handler_0,p:8,tN:MainThread] Tool with id 'toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1': a when tag has been defined for 'method (method) --> pl.rank_genes_groups_violin', but does not appear to be selectable. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,056 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_remove_confounders' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,063 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_parameter_iterator' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,070 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'droplet_barcode_plot' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,075 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_read_10x' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,080 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'gtf2gene_list' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,086 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'salmon_kallisto_mtx_to_10x' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,092 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sceasy_convert' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,098 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'anndata_ops' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tools WARNING 2024-12-30 00:50:57,103 [pN:job_handler_0,p:8,tN:MainThread] Tool with id 'toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/0.0.3+galaxy0': a when tag has not been defined for 'copy_u (default) --> false', assuming empty inputs. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,105 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'retrieve_scxa' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,111 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'music_inspect_eset' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tools.parameters.basic WARNING 2024-12-30 00:50:57,115 [pN:job_handler_0,p:8,tN:MainThread] Datatype class not found for extension 'rdata.eset', which is used in the 'format' attribute of parameter 'rds_eset' +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,117 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'music_construct_eset' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,125 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'raceid_inspectclusters' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,134 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'raceid_clustering' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,142 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'raceid_trajectory' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,148 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'raceid_inspecttrajectory' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,157 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'alevin' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,167 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scater_create_qcmetric_ready_sce' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,174 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scater_filter' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,180 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scater_plot_dist_scatter' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,186 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scater_plot_pca' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,192 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_plot' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tools DEBUG 2024-12-30 00:50:57,236 [pN:job_handler_0,p:8,tN:MainThread] Tool with id 'toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0': a when tag has been defined for 'method (method) --> pl.rank_genes_groups_violin', but does not appear to be selectable. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,257 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_read_10x' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,263 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'salmon_kallisto_mtx_to_10x' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,268 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'anndata_ops' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tools WARNING 2024-12-30 00:50:57,274 [pN:job_handler_0,p:8,tN:MainThread] Tool with id 'toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.6.0+galaxy1': a when tag has not been defined for 'copy_u (default) --> false', assuming empty inputs. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,276 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_filter_cells' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,283 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_filter_cells' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,289 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_filter_genes' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,295 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_filter_genes' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,303 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_normalise_data' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tools WARNING 2024-12-30 00:50:57,309 [pN:job_handler_0,p:8,tN:MainThread] Tool with id 'toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_normalise_data/scanpy_normalise_data/1.8.1+3+galaxy0': a when tag has not been defined for 'exclude (exclude_highly_expressed) --> false', assuming empty inputs. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,311 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_normalise_data' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tools WARNING 2024-12-30 00:50:57,316 [pN:job_handler_0,p:8,tN:MainThread] Tool with id 'toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_normalise_data/scanpy_normalise_data/1.6.0+galaxy0': a when tag has not been defined for 'exclude (exclude_highly_expressed) --> false', assuming empty inputs. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,317 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_find_variable_genes' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,324 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_find_variable_genes' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,330 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_scale_data' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,337 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_scale_data' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,343 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_run_pca' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,348 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_run_pca' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,353 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_compute_graph' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,359 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_compute_graph' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,364 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_run_tsne' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,371 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_run_tsne' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,376 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_run_umap' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,383 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_run_umap' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,390 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_find_cluster' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,396 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_find_cluster' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,402 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_find_markers' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,410 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_find_markers' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,416 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_plot_embed' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,421 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_plot_embed' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,428 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'anndata_inspect' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,436 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'dropletutils' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,442 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'raceid_filtnormconf' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,449 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_plot' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,830 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'anndata_import' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,838 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'anndata_export' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,846 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'anndata_manipulate' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,855 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'anndata_inspect' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,863 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'cutadapt' from owner 'lparsons' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,887 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fastq_filter' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,894 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fastq_groomer' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,903 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fastq_manipulation' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,913 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fasta_compute_length' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,919 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fastq_paired_end_deinterlacer' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,926 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fastq_paired_end_interlacer' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,934 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'flash' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,941 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'trim_galore' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,951 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'umi_tools_count' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,957 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'umi_tools_extract' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,966 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'umi_tools_count' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,973 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'umi_tools_extract' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:57,981 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'cutadapt' from owner 'lparsons' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:58,006 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'umi_tools_count' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:58,015 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'umi_tools_extract' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:58,025 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'seq_filter_by_id' from owner 'peterjc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:58,031 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'cutadapt' from owner 'lparsons' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:58,057 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'cutadapt' from owner 'lparsons' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:58,072 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'length_and_gc_content' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:58,079 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'length_and_gc_content' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:58,086 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'cutadapt' from owner 'lparsons' was not found in database. Tool will be loaded without install database. +galaxy.tools.parameters.basic WARNING 2024-12-30 00:50:58,095 [pN:job_handler_0,p:8,tN:MainThread] Datatype class not found for extension 'fasta.bz2', which is used in the 'format' attribute of parameter 'input_1' +galaxy.tools.parameters.basic WARNING 2024-12-30 00:50:58,097 [pN:job_handler_0,p:8,tN:MainThread] Datatype class not found for extension 'fasta.bz2', which is used in the 'format' attribute of parameter 'input_1' +galaxy.tools.parameters.basic WARNING 2024-12-30 00:50:58,097 [pN:job_handler_0,p:8,tN:MainThread] Datatype class not found for extension 'fasta.bz2', which is used in the 'format' attribute of parameter 'input_2' +galaxy.tools.parameters.basic WARNING 2024-12-30 00:50:58,098 [pN:job_handler_0,p:8,tN:MainThread] Datatype class not found for extension 'fasta.bz2', which is used in the 'format' attribute of parameter 'input_1' +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:58,107 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'cutadapt' from owner 'lparsons' was not found in database. Tool will be loaded without install database. +galaxy.tools.parameters.basic WARNING 2024-12-30 00:50:58,116 [pN:job_handler_0,p:8,tN:MainThread] Datatype class not found for extension 'fasta.bz2', which is used in the 'format' attribute of parameter 'input_1' +galaxy.tools.parameters.basic WARNING 2024-12-30 00:50:58,118 [pN:job_handler_0,p:8,tN:MainThread] Datatype class not found for extension 'fasta.bz2', which is used in the 'format' attribute of parameter 'input_1' +galaxy.tools.parameters.basic WARNING 2024-12-30 00:50:58,118 [pN:job_handler_0,p:8,tN:MainThread] Datatype class not found for extension 'fasta.bz2', which is used in the 'format' attribute of parameter 'input_2' +galaxy.tools.parameters.basic WARNING 2024-12-30 00:50:58,121 [pN:job_handler_0,p:8,tN:MainThread] Datatype class not found for extension 'fasta.bz2', which is used in the 'format' attribute of parameter 'input_1' +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:58,132 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'trim_galore' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:58,143 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fastq_filter' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:58,152 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fastq_groomer' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:58,161 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fastq_manipulation' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:58,169 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fasta_compute_length' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:58,176 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fastq_paired_end_deinterlacer' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:58,182 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fastq_paired_end_interlacer' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:58,188 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'umi_tools_count' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:58,198 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'umi_tools_extract' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:58,208 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'seq_filter_by_id' from owner 'peterjc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:58,215 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'datamash_reverse' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:58,221 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'datamash_transpose' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:58,227 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'datamash_ops' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:58,236 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'datamash_transpose' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:58,241 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'datamash_transpose' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:58,248 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'datamash_reverse' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:58,254 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'datamash_transpose' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:58,260 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'datamash_ops' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:58,267 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'picard' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:58,436 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'picard' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:58,613 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'picard' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:58,788 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'picard' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:58,980 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'map_param_value' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:58,987 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'compose_text_param' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:58,993 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'map_param_value' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,001 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'gtftobed12' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,007 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'gemini_load' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,014 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'gemini_load' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,020 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'gemini_db_info' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,026 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'gemini_db_info' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,031 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'gemini_query' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,045 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'gemini_query' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,052 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2_core__tools__export' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,070 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2_core__tools__import' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,107 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__alignment__mafft_add' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,112 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__alignment__mafft' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,119 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__alignment__mask' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,124 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__composition__add_pseudocount' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,129 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__composition__ancombc' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,135 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__composition__tabulate' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,141 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__composition__ancom' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,146 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__cutadapt__trim_single' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,154 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__cutadapt__trim_paired' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,161 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__cutadapt__demux_single' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,167 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__cutadapt__demux_paired' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,173 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__dada2__denoise_pyro' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,178 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__dada2__denoise_ccs' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,183 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__dada2__denoise_single' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,188 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__dada2__denoise_paired' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,194 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__deblur__denoise_16s' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,201 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__deblur__denoise_other' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,206 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__deblur__visualize_stats' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,210 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__demux__emp_paired' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,214 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__demux__subsample_paired' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,218 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__demux__subsample_single' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,222 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__demux__summarize' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,225 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__demux__filter_samples' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,229 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__demux__emp_single' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,235 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__beta_correlation' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,239 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__adonis' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,244 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__umap' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,249 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__pcoa' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,253 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__bioenv' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,259 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__pcoa_biplot' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,264 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__tsne' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,270 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__beta_group_significance' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,276 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__procrustes_analysis' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,281 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__mantel' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,288 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__beta' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,294 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__alpha_group_significance' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,298 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__core_metrics_phylogenetic' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,306 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__core_metrics' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,313 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__alpha_correlation' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,318 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__filter_distance_matrix' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,326 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__alpha' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,331 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__beta_phylogenetic' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,336 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__alpha_phylogenetic' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,342 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__alpha_rarefaction' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,348 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__beta_rarefaction' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,355 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__observed_features' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,360 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__bray_curtis' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,366 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__beta_passthrough' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,372 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__alpha_passthrough' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,378 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__shannon_entropy' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,384 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__jaccard' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,389 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__pielou_evenness' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,395 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__beta_phylogenetic_meta_passthrough' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,401 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__weighted_unifrac' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,407 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__unweighted_unifrac' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,413 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__beta_phylogenetic_passthrough' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,419 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__faith_pd' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,425 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__emperor__procrustes_plot' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,433 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__emperor__plot' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,439 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__emperor__biplot' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,445 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_classifier__classify_sklearn' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,451 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_classifier__fit_classifier_sklearn' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,456 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_classifier__fit_classifier_naive_bayes' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,463 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_classifier__classify_consensus_blast' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,470 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_classifier__extract_reads' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,476 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_classifier__classify_hybrid_vsearch_sklearn' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,484 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_classifier__classify_consensus_vsearch' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,490 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_classifier__blast' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,495 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_classifier__find_consensus_annotation' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,501 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_classifier__vsearch_global' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,507 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__tabulate_seqs' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,513 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__presence_absence' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,518 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__filter_samples' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,526 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__summarize' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,531 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__filter_features_conditionally' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,535 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__rename_ids' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,542 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__merge_seqs' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,547 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__relative_frequency' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,552 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__merge' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,557 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__filter_features' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,563 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__rarefy' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,567 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__transpose' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,572 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__subsample' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,577 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__heatmap' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,585 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__merge_taxa' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,590 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__core_features' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,595 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__group' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,602 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__filter_seqs' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,608 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__fragment_insertion__sepp' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,613 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__fragment_insertion__classify_otus_experimental' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,619 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__fragment_insertion__filter_features' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,624 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__gneiss__ilr_phylogenetic' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,630 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__gneiss__correlation_clustering' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,635 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__gneiss__dendrogram_heatmap' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,644 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__gneiss__gradient_clustering' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,650 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__gneiss__ilr_phylogenetic_ordination' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,657 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__gneiss__assign_ids' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,662 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__gneiss__ilr_phylogenetic_differential' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,668 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__gneiss__ilr_hierarchical' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,673 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__longitudinal__pairwise_distances' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,681 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__longitudinal__feature_volatility' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,689 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__longitudinal__nmit' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,694 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__longitudinal__first_differences' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,701 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__longitudinal__plot_feature_volatility' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,707 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__longitudinal__first_distances' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,713 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__longitudinal__linear_mixed_effects' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,721 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__longitudinal__volatility' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,726 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__longitudinal__pairwise_differences' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,734 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__longitudinal__anova' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,740 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__longitudinal__maturity_index' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,746 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__metadata__shuffle_groups' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,751 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__metadata__distance_matrix' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,757 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__metadata__tabulate' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,764 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__raxml_rapid_bootstrap' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,770 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__fasttree' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,776 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__align_to_tree_mafft_iqtree' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,784 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__iqtree' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,795 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__robinson_foulds' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,802 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__align_to_tree_mafft_raxml' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,809 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__filter_table' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,818 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__midpoint_root' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,823 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__align_to_tree_mafft_fasttree' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,828 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__raxml' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,833 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__filter_tree' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,839 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__iqtree_ultrafast_bootstrap' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,847 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__quality_control__evaluate_composition' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,853 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__quality_control__evaluate_seqs' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,857 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__quality_control__filter_reads' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,861 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__quality_control__bowtie2_build' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,867 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__quality_control__evaluate_taxonomy' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,873 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__quality_control__exclude_seqs' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,878 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__quality_filter__q_score' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,883 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__metatable' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,889 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__fit_classifier' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,895 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__regress_samples' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,902 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__classify_samples' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,910 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__scatterplot' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,916 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__classify_samples_from_dist' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,922 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__confusion_matrix' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,928 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__split_table' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,933 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__summarize' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,938 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__heatmap' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,946 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__classify_samples_ncv' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,951 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__fit_regressor' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,957 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__predict_classification' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,962 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__regress_samples_ncv' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,969 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__predict_regression' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,975 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__taxa__collapse' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,980 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__taxa__filter_table' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,989 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__taxa__barplot' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:50:59,994 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__taxa__filter_seqs' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,000 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__vsearch__cluster_features_closed_reference' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,006 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__vsearch__cluster_features_open_reference' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,012 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__vsearch__merge_pairs' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,017 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__vsearch__uchime_denovo' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,023 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__vsearch__dereplicate_sequences' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,028 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__vsearch__fastq_stats' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,033 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__vsearch__uchime_ref' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,039 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__vsearch__cluster_features_de_novo' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,043 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2_core__tools__import_fastq' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,047 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2_core__tools__import' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,107 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2_core__tools__export' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,127 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__alignment__mask' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,133 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__alignment__mafft_add' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,139 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__alignment__mafft' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,144 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__composition__ancom' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,151 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__composition__add_pseudocount' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,156 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__composition__tabulate' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,162 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__composition__da_barplot' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,169 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__composition__ancombc' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,176 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__cutadapt__trim_single' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,184 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__cutadapt__demux_paired' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,192 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__cutadapt__demux_single' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,199 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__cutadapt__trim_paired' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,207 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__dada2__denoise_paired' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,213 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__dada2__denoise_ccs' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,219 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__dada2__denoise_single' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,225 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__dada2__denoise_pyro' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,231 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__deblur__denoise_16s' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,236 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__deblur__visualize_stats' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,241 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__deblur__denoise_other' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,247 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__demux__emp_single' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,252 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__demux__summarize' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,257 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__demux__tabulate_read_counts' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,262 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__demux__subsample_paired' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,267 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__demux__subsample_single' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,272 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__demux__partition_samples_single' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,277 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__demux__partition_samples_paired' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,282 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__demux__emp_paired' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,287 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__demux__filter_samples' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,292 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__tsne' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,298 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__alpha_phylogenetic' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,303 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__pcoa' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,309 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__beta_phylogenetic' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,314 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__beta_group_significance' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,320 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__core_metrics_phylogenetic' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,326 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__alpha_correlation' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,332 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__pcoa_biplot' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,337 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__core_metrics' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,344 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__beta' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,348 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__partial_procrustes' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,355 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__alpha' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,360 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__procrustes_analysis' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,365 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__filter_distance_matrix' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,371 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__alpha_group_significance' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,376 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__bioenv' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,382 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__mantel' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,388 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__beta_correlation' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,393 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__adonis' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,399 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__umap' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,405 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__alpha_rarefaction' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,411 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__filter_alpha_diversity' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,417 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__beta_rarefaction' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,423 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__beta_phylogenetic_passthrough' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,429 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__beta_passthrough' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,434 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__beta_phylogenetic_meta_passthrough' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,441 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__alpha_passthrough' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,447 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__shannon_entropy' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,453 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__weighted_unifrac' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,458 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__jaccard' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,463 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__faith_pd' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,469 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__pielou_evenness' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,474 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__unweighted_unifrac' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,479 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__bray_curtis' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,484 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__observed_features' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,489 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__emperor__plot' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,494 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__emperor__procrustes_plot' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,500 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__emperor__biplot' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,506 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_classifier__classify_consensus_vsearch' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,513 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_classifier__makeblastdb' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,518 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_classifier__vsearch_global' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,525 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_classifier__classify_sklearn' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,530 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_classifier__classify_hybrid_vsearch_sklearn' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,537 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_classifier__classify_consensus_blast' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,543 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_classifier__fit_classifier_naive_bayes' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,549 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_classifier__find_consensus_annotation' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,555 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_classifier__fit_classifier_sklearn' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,560 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_classifier__extract_reads' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,566 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_classifier__blast' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,572 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__relative_frequency' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,576 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__split' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,582 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__tabulate_seqs' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,587 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__filter_features' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,592 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__tabulate_feature_frequencies' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,596 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__rarefy' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,600 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__merge_taxa' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,603 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__core_features' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,608 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__tabulate_sample_frequencies' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,613 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__subsample_ids' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,619 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__summarize_plus' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,625 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__rename_ids' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,631 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__transpose' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,636 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__heatmap' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,644 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__summarize' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,650 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__filter_seqs' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,656 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__merge_seqs' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,660 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__group' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,665 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__filter_features_conditionally' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,670 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__merge' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,675 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__presence_absence' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,680 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__filter_samples' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,687 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__fragment_insertion__filter_features' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,691 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__fragment_insertion__classify_otus_experimental' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,696 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__fragment_insertion__sepp' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,701 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__rescript__get_silva_data' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,708 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__rescript__evaluate_classifications' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,714 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__rescript__parse_silva_taxonomy' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,718 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__rescript__orient_seqs' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,726 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__rescript__merge_taxa' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,733 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__rescript__degap_seqs' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,740 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__rescript__cull_seqs' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,745 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__rescript__get_ncbi_data_protein' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,754 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__rescript__get_bv_brc_metadata' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,762 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__rescript__get_gtdb_data' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,769 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__rescript__filter_seqs_length' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,774 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__rescript__subsample_fasta' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,781 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__rescript__get_ncbi_data' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,789 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__rescript__filter_seqs_length_by_taxon' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,796 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__rescript__extract_seq_segments' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,802 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__rescript__evaluate_seqs' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,809 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__rescript__get_bv_brc_genomes' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,816 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__rescript__evaluate_taxonomy' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,821 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__rescript__get_bv_brc_genome_features' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,829 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__rescript__get_ncbi_genomes' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,835 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__rescript__trim_alignment' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,842 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__rescript__filter_taxa' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,847 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__rescript__get_unite_data' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,853 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__rescript__reverse_transcribe' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,858 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__rescript__dereplicate' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,864 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__rescript__evaluate_cross_validate' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,871 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__rescript__evaluate_fit_classifier' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,879 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__rescript__edit_taxonomy' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,885 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__longitudinal__first_distances' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,891 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__longitudinal__nmit' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,896 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__longitudinal__pairwise_differences' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,904 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__longitudinal__plot_feature_volatility' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,910 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__longitudinal__linear_mixed_effects' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,917 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__longitudinal__first_differences' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,923 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__longitudinal__volatility' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,930 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__longitudinal__pairwise_distances' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,936 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__longitudinal__maturity_index' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,943 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__longitudinal__feature_volatility' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,950 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__longitudinal__anova' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,956 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__metadata__shuffle_groups' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,961 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__metadata__merge' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,966 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__metadata__distance_matrix' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,972 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__metadata__tabulate' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,977 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__align_to_tree_mafft_iqtree' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,985 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__align_to_tree_mafft_fasttree' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,989 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__align_to_tree_mafft_raxml' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:00,995 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__fasttree' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,001 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__iqtree' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,009 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__midpoint_root' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,015 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__filter_table' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,020 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__raxml_rapid_bootstrap' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,025 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__filter_tree' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,031 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__robinson_foulds' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,036 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__iqtree_ultrafast_bootstrap' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,043 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__raxml' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,048 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__quality_control__bowtie2_build' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,053 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__quality_control__decontam_remove' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,058 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__quality_control__decontam_score_viz' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,064 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__quality_control__filter_reads' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,069 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__quality_control__evaluate_taxonomy' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,075 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__quality_control__decontam_identify_batches' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,081 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__quality_control__exclude_seqs' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,087 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__quality_control__decontam_identify' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,094 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__quality_control__evaluate_seqs' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,100 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__quality_control__evaluate_composition' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,107 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__quality_filter__q_score' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,112 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__regress_samples_ncv' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,119 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__scatterplot' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,124 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__fit_regressor' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,131 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__classify_samples' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,138 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__regress_samples' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,144 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__fit_classifier' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,149 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__metatable' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,155 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__classify_samples_ncv' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,160 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__split_table' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,166 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__summarize' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,170 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__predict_regression' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,176 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__confusion_matrix' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,183 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__predict_classification' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,187 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__classify_samples_from_dist' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,194 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__heatmap' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,202 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__stats__prep_alpha_distribution' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tools DEBUG 2024-12-30 00:51:01,207 [pN:job_handler_0,p:8,tN:MainThread] Tool with id 'toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__stats__prep_alpha_distribution/qiime2__stats__prep_alpha_distribution/0+unknown-q2galaxy.2024.10.0': a when tag has been defined for '__q2galaxy__GUI__conditional__subject__ (__q2galaxy__GUI__select__) --> __q2galaxy__::control::Str', but does not appear to be selectable. +galaxy.tools DEBUG 2024-12-30 00:51:01,207 [pN:job_handler_0,p:8,tN:MainThread] Tool with id 'toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__stats__prep_alpha_distribution/qiime2__stats__prep_alpha_distribution/0+unknown-q2galaxy.2024.10.0': a when tag has been defined for '__q2galaxy__GUI__conditional__timepoint__ (__q2galaxy__GUI__select__) --> __q2galaxy__::control::Str', but does not appear to be selectable. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,209 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__stats__facet_within' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,214 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__stats__facet_across' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,220 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__stats__mann_whitney_u' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,227 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__stats__plot_rainclouds' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,232 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__stats__wilcoxon_srt' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,239 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__stats__collate_stats' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,243 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__taxa__filter_table' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,249 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__taxa__filter_seqs' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,257 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__taxa__barplot' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,263 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__taxa__collapse' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,270 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__vizard__boxplot' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,275 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__vsearch__cluster_features_de_novo' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,280 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__vsearch__merge_pairs' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,286 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__vsearch__uchime_ref' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,291 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__vsearch__dereplicate_sequences' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,298 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__vsearch__cluster_features_open_reference' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,304 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__vsearch__fastq_stats' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,310 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__vsearch__cluster_features_closed_reference' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,317 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__vsearch__uchime_denovo' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,323 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sklearn_build_pipeline' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,348 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sklearn_build_pipeline' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,370 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sklearn_searchcv' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,394 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sklearn_searchcv' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,412 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'plotly_parallel_coordinates_plot' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,417 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'plotly_parallel_coordinates_plot' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,421 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sklearn_ensemble' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,436 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sklearn_ensemble' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,454 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'plotly_regression_performance_plots' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,460 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'pygenometracks' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,493 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'circos' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,566 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'volcanoplot' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,574 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'ggplot2_heatmap2' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,581 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'ggplot2_heatmap2' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,587 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'anndata_import' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,594 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'anndata_export' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,601 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'anndata_manipulate' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,608 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'chromeister' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,614 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'anndata_inspect' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,627 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'modify_loom' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,633 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'raceid_inspectclusters' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,644 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'raceid_filtnormconf' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,652 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'raceid_clustering' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,661 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'raceid_trajectory' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,668 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'raceid_inspecttrajectory' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,677 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'alevin' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,687 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'salmonquantmerge' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,693 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_cluster_reduce_dimension' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,704 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_filter' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,716 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_inspect' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,727 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_normalize' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:01,737 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_plot' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:02,189 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_remove_confounders' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:02,196 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_read_10x' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:02,202 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'gtf2gene_list' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:02,209 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'anndata_ops' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tools WARNING 2024-12-30 00:51:02,215 [pN:job_handler_0,p:8,tN:MainThread] Tool with id 'toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.9.3+galaxy0': a when tag has not been defined for 'copy_u (default) --> false', assuming empty inputs. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:02,217 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_parameter_iterator' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:02,223 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_filter_cells' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:02,229 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_filter_genes' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:02,236 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_normalise_data' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tools WARNING 2024-12-30 00:51:02,242 [pN:job_handler_0,p:8,tN:MainThread] Tool with id 'toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_normalise_data/scanpy_normalise_data/1.9.3+galaxy0': a when tag has not been defined for 'exclude (exclude_highly_expressed) --> false', assuming empty inputs. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:02,244 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_find_variable_genes' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:02,252 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_scale_data' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:02,259 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_run_pca' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:02,266 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_compute_graph' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:02,273 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_run_tsne' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:02,279 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_run_umap' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:02,285 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_find_cluster' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:02,291 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_find_markers' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:02,298 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_plot_embed' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:02,306 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'cite_seq_count' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:02,314 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'anndata_import' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:02,320 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'anndata_export' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:02,325 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'anndata_manipulate' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:02,333 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'anndata_inspect' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:02,342 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'modify_loom' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:02,348 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'slice_image' from owner 'imgteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:02,355 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_cluster_reduce_dimension' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:02,366 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_filter' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:02,378 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_inspect' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:02,391 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_normalize' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:02,398 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_plot' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:51:02,478 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_remove_confounders' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tools WARNING 2024-12-30 00:51:02,488 [pN:job_handler_0,p:8,tN:MainThread] The default shed tool config file (/galaxy/server/config/mutable/editable_shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2024-12-30 00:51:02,488 [pN:job_handler_0,p:8,tN:MainThread] Parsing the tool configuration /galaxy/server/config/mutable/editable_shed_tool_conf.xml +galaxy.tool_util.toolbox.base INFO 2024-12-30 00:51:02,488 [pN:job_handler_0,p:8,tN:MainThread] Shed-enabled tool configuration file does not exist, but will be created on demand: /galaxy/server/config/mutable/editable_shed_tool_conf.xml +galaxy.tools WARNING 2024-12-30 00:51:02,488 [pN:job_handler_0,p:8,tN:MainThread] The default shed tool config file (/galaxy/server/config/mutable/editable_shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2024-12-30 00:51:02,488 [pN:job_handler_0,p:8,tN:MainThread] Parsing the tool configuration /galaxy/server/config/migrated_tools_conf.xml +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,488 [pN:job_handler_0,p:8,tN:MainThread] Tool path for shed tool configuration /galaxy/server/config/migrated_tools_conf.xml is /galaxy/server/database/shed_tools +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,488 [pN:job_handler_0,p:8,tN:MainThread] Reading tools from config files finished (11309.124 ms) +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,489 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Get Data +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,489 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,489 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,489 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,490 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.5+galaxy0, version: 0.2.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,490 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy1, version: 2.11.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,490 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,490 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,490 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,490 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,490 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,490 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0, version: 0.2.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,490 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: upload1, version: 1.1.7 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,490 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,490 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,490 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,490 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,490 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: intermine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,491 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: flymine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,491 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: modmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,491 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: mousemine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,491 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ratmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,491 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: yeastmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,491 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,491 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: wormbase, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,491 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,491 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: eupathdb, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,491 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hbvar, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,491 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Send Data +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,491 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: export_remote, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,491 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Send Data +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,491 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Expression Tools +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,491 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,491 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,491 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0, version: 0.2.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,491 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: param_value_from_file, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,491 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Collection Operations +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,492 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,492 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,492 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0, version: 0.5.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,492 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0, version: 5.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,492 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2, version: 0.5.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,492 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0, version: 0.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,492 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,492 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,492 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,492 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __FILTER_EMPTY_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,492 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,492 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,492 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,492 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,492 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,492 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __TAG_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,492 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __APPLY_RULES__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,493 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __BUILD_LIST__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,493 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __EXTRACT_DATASET__, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,493 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Text Manipulation +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,493 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/diff/diff/3.7+galaxy0, version: 3.7+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,493 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,493 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,493 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6, version: 1.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,493 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,493 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.12.0, version: 3.12.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,493 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,493 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,493 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,493 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/0.9.2, version: 0.9.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,493 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.4, version: 0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,493 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0, version: 0.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,494 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,494 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,494 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,494 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,494 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,494 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,494 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,495 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0, version: 0.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,495 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,495 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,495 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,495 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,495 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,495 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,495 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,495 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,495 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,495 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,495 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,495 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_melt/melt/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,496 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_cast/cast/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,496 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jq/jq/1.0, version: 1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,496 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gff3_rebase/gff3.rebase/1.2, version: 1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,496 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,496 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_order_header_sort/column_order_header_sort/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,496 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,496 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: addValue, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,496 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: cat1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,496 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Condense characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,496 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,496 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,496 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: createInterval, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,496 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Cut1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,496 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,496 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Paste1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,496 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,496 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: random_lines1, version: 2.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,497 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Show beginning1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,497 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Show tail1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,497 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: trimmer, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,497 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,497 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: secure_hash_message_digest, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,497 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0, version: 3.3.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,497 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1, version: 3.14.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,497 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0, version: 2.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,497 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0, version: 1.2.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,498 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4, version: 1.1.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,498 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1, version: 0.1.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,498 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0+galaxy0, version: 1.1.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,498 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.16.0+galaxy1, version: 3.16.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,498 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,498 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.3.1, version: 3.3.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,498 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2, version: 3.3.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,498 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1, version: 2.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,498 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/3.2.1, version: 3.2.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,499 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.18.0+galaxy0, version: 3.18.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,499 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3, version: 1.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,499 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3, version: 1.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,499 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.6, version: 0.6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,499 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,499 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,499 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,499 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,499 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,499 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,499 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,499 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/nl/9.3+galaxy1, version: 9.3+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,499 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,500 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,500 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,500 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,500 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,500 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,500 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,500 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,501 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,501 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,501 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy2, version: 9.3+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,501 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,501 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/1.0, version: 1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,501 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Filter and Sort +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,501 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Filter1, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,501 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: sort1, version: 1.2.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,501 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Grep1, version: 1.0.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,501 [pN:job_handler_0,p:8,tN:MainThread] Loaded label: GFF +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,501 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,501 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,501 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,502 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,502 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Join, Subtract and Group +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,502 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: join1, version: 2.1.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,502 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: comp1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,502 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Grouping1, version: 2.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,502 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Datamash +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,502 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,502 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,502 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,502 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,502 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,502 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy1, version: 1.8+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,502 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,502 [pN:job_handler_0,p:8,tN:MainThread] Loading section: FASTA/FASTQ +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,503 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.8, version: 1.16.8 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,503 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,503 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,503 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,503 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,503 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,503 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0, version: 1.2.0.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,503 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/flash/flash/1.2.11.4, version: 1.2.11.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,503 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.3, version: 0.6.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,503 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,503 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,503 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1, version: 4.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,504 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,504 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,504 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.7, version: 0.2.7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,504 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/length_and_gc_content/0.1.2, version: 0.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,504 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1, version: 4.9+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,504 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.7+galaxy0, version: 0.6.7+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,504 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5+galaxy2, version: 1.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,504 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5+galaxy2, version: 1.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,505 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.5+galaxy2, version: 1.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,505 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.4, version: 1.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,505 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.5+galaxy2, version: 1.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,505 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.5+galaxy1, version: 1.1.5+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,505 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.5+galaxy1, version: 1.1.5+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,505 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.9, version: 0.2.9 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,505 [pN:job_handler_0,p:8,tN:MainThread] Loading section: FASTQ Quality Control +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,505 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,505 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0, version: 0.20.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,505 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1, version: 0.72+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,505 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1, version: 0.38.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,506 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0, version: 1.11+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,506 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0, version: 0.73+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,506 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1, version: 1.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,506 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0, version: 0.23.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,506 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0, version: 1.24.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,506 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1, version: 0.23.4+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,506 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1, version: 0.74+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,506 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy2, version: 0.23.4+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,506 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.39+galaxy2, version: 0.39+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,506 [pN:job_handler_0,p:8,tN:MainThread] Loading section: SAM/BAM +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,506 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/pileup_interval/pileup_interval/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,506 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3, version: 2.2.2d+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,507 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3, version: 1.9+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,507 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0.1+galaxy1, version: 2.0.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,507 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,507 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.4.0.0, version: 2.4.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,507 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamtools_split/2.4.0, version: 2.4.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,507 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam2interval/sam2interval/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,507 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_multi_bamqc/qualimap_multi_bamqc/2.2.2d, version: 2.2.2d into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,507 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,507 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,507 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2, version: 1.9+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,507 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,507 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,507 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,508 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2, version: 2.0.2+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,508 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,508 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,508 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,508 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,508 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8+galaxy1, version: 1.8+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,508 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,508 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,508 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.4, version: 2.1.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,508 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,508 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1, version: 2.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,508 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,508 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,508 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,508 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/boris/filter_on_md/MDtag_filter/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,509 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.2.0, version: 1.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,509 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.2, version: 2.0.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,509 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,509 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,509 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,509 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy1, version: 2.5.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,509 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,509 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lldelisle/revertr2orientationinbam/revertR2orientationInBam/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,509 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.3+galaxy0, version: 2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,509 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3, version: 1.20+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,509 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0.3, version: 2.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,509 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.2+galaxy2, version: 2.5.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,510 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamtools_split/2.5.2+galaxy0, version: 2.5.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,510 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_multi_bamqc/qualimap_multi_bamqc/2.3+galaxy0, version: 2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,510 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,510 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,510 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,510 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,511 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.15.1+galaxy2, version: 1.15.1+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,511 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,511 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,511 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,511 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,512 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,512 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,512 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,512 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.7, version: 2.1.7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,512 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,512 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy2, version: 2.5.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,512 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.2, version: 2.1.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,512 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.3, version: 2.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,512 [pN:job_handler_0,p:8,tN:MainThread] Loading section: BED +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,512 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,512 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,512 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,512 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,513 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,513 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,513 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,513 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,513 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,513 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,513 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,513 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,513 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_links/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,513 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,513 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_expandbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,513 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,513 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,513 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,514 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_jaccard/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,514 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,514 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,514 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,514 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_reldistbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,514 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,514 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bed12tobed6/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,514 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,514 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,514 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,514 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.2, version: 2.30.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,514 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,514 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,514 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,514 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,515 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,515 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,515 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,515 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,515 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,515 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,515 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0+galaxy2, version: 2.30.0+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,515 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.3, version: 2.30.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,515 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,515 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,515 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,515 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,515 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,515 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,516 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,516 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,516 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,516 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_links/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,516 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,516 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,516 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,516 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,516 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,516 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,516 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_expandbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,516 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,516 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,516 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_jaccard/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,517 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.31.1.3, version: 2.31.1.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,517 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,517 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bed12tobed6/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,517 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,517 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,517 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,517 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,517 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,517 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,517 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,517 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,517 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,517 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,517 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,518 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,518 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,518 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,518 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,518 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,518 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_reldistbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,518 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,518 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,518 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,518 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,518 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,518 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,518 [pN:job_handler_0,p:8,tN:MainThread] Loading section: VCF/BCF +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,518 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,519 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,519 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/bcftools_plugin_fixploidy/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,519 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/bcftools_convert_to_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,519 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,519 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,519 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/bcftools_plugin_missing2ref/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,519 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,519 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,520 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/bcftools_plugin_counts/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,520 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,520 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,520 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,520 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/bcftools_convert_from_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,520 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/bcftools_plugin_impute_info/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,520 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,520 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,520 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/bcftools_plugin_fill_an_ac/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,520 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bcftools_plugin_fill_tags/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,520 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,520 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,521 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,521 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,521 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,521 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/bcftools_filter/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,521 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/bcftools_csq/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,521 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,521 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/bcftools_plugin_dosage/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,521 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/bcftools_query/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,521 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,521 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcf2tsv/vcf2tsv/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,521 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfaddinfo/vcfaddinfo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,522 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,522 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotate/vcfannotate/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,522 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotategenotypes/vcfannotategenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,522 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbedintersect/vcfbedintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,522 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbreakcreatemulti/vcfbreakcreatemulti/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,522 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcheck/vcfcheck/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,522 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcombine/vcfcombine/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,522 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcommonsamples/vcfcommonsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,522 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffixup/vcffixup/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,522 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfflatten/vcfflatten2/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,522 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgeno2haplo/vcfgeno2haplo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,522 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgenotypes/vcfgenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,522 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfhethom/vcfhethom/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,522 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfleftalign/vcfleftalign/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,522 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfprimers/vcfprimers/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,522 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfrandomsample/vcfrandomsample/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,522 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfsort/vcfsort/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,523 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,523 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfselectsamples/vcfselectsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,523 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfdistance/vcfdistance/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,523 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffilter/vcffilter2/1.0.0_rc3+galaxy3, version: 1.0.0_rc3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,523 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/vcfdistance/vcfdistance/1.0.0_rc1+galaxy0, version: 1.0.0_rc1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,523 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_annotate/vcftools_annotate/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,523 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_slice/vcftools_slice/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,523 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,523 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,523 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/bcftools_plugin_fixploidy/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,523 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/bcftools_convert_to_vcf/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,523 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,523 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,524 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/bcftools_plugin_missing2ref/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,524 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,524 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,524 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/bcftools_plugin_counts/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,524 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,524 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,524 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,524 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/bcftools_convert_from_vcf/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,524 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/bcftools_plugin_impute_info/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,524 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,524 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,524 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/bcftools_plugin_fill_an_ac/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,524 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bcftools_plugin_fill_tags/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,525 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,525 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,525 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,525 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5, version: 1.15.1+galaxy5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,525 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,525 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/bcftools_filter/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,525 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/bcftools_csq/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,525 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,525 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/bcftools_plugin_dosage/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,525 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/bcftools_query/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,525 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,525 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Nanopore +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,526 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.0.3+galaxy7, version: 1.0.3+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,526 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6, version: 2.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,526 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,526 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,526 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,526 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1, version: 1.28.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,526 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_events/poretools_events/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,526 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_hist/poretools_hist/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,526 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_occupancy/poretools_occupancy/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,526 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualpos/poretools_qualpos/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,526 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_squiggle/poretools_squiggle/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,526 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_yield_plot/poretools_yield_plot/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,526 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3, version: 0.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,526 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_winner/poretools_winner/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,526 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_times/poretools_times/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,526 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_tabular/poretools_tabular/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,527 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_stats/poretools_stats/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,527 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualdist/poretools_qualdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,527 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_nucdist/poretools_nucdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,527 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_extract/poretools_extract/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,527 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.7.2+galaxy1, version: 1.7.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,527 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.4+galaxy0, version: 2.9.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,527 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy1, version: 1.7.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,527 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.4.4+galaxy1, version: 1.4.4+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,527 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.7.2+galaxy0, version: 1.7.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,527 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.43.0+galaxy0, version: 1.43.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,527 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0, version: 0.2.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,527 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.5+galaxy0, version: 2.9.5+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,527 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Convert Formats +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,527 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,527 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,528 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,528 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,528 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,528 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,528 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: wig_to_bigWig, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,528 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: bed_to_bigBed, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,528 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Lift-Over +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,528 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: liftOver1, version: 1.0.6 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,528 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Virology +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,528 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,528 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,528 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19, version: 4.5covid19 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,528 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,528 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/ivar_filtervariants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,528 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_getmasked/ivar_getmasked/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,528 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,528 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,529 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,529 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,529 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/ivar_filtervariants/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,529 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.4.3+galaxy1, version: 1.4.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,529 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Operate on Genomic Intervals +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,529 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: wiggle2simple1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,529 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,529 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,529 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Fetch Sequences/Alignments +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,529 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Extract genomic DNA 1, version: 2.2.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,529 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,529 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,529 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,529 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,529 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,529 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,530 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,530 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,530 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,530 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,530 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,530 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Assembly +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,530 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, version: 0.4.8.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,530 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.12.0+galaxy1, version: 3.12.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,530 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3+galaxy0, version: 0.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,530 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.4.13, version: 1.4.13 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,530 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.1+galaxy0, version: 0.5.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,530 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3_r179+galaxy1, version: 0.3_r179+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,530 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1, version: 1.5.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,530 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0, version: 1.3.6+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,530 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.15.5+galaxy2, version: 3.15.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,531 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1, version: 5.2.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,531 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Annotation +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,531 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Mapping +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,531 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy4, version: 2.17+galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,531 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0, version: 2.4.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,531 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4, version: 0.7.17.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,531 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1, version: 0.7.17.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,531 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.2, version: 0.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,531 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,531 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,532 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,532 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,532 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1, version: 2.7.8a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,532 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.5, version: 0.7.17.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,532 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2, version: 0.7.17.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,532 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0, version: 2.28+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,532 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1, version: 2.5.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,532 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.18, version: 0.7.18 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,532 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.18, version: 0.7.18 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,532 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.7+galaxy0, version: 0.2.7+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,532 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.04.22+galaxy0, version: 1.04.22+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,532 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.04.22+galaxy0, version: 1.04.22+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,533 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy1, version: 2.7.11a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,533 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy0, version: 2.7.11a+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,533 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy1, version: 2.7.11a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,533 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Variant Calling +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,533 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,533 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,533 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,533 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,533 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,533 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,533 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,533 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_genesets/snpSift_geneSets/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,533 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_dbnsfp/snpSift_dbnsfp/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,533 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,534 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_get_chr_names/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,534 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy4, version: 4.3+T.galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,534 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,534 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1, version: 4.3+T.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,534 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_caseControl/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,534 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_annotate/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,534 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_vcfCheck/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,534 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,534 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,534 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_int/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,534 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpsift_vartype/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,534 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_rmInfo/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,534 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy1, version: 1.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,534 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/1.0.12+galaxy0, version: 1.0.12+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,534 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jasminesv/jasminesv/1.0.11+galaxy1, version: 1.0.11+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,535 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3, version: 1.0+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,535 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2, version: 2.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,535 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0, version: 1.3.6+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,535 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.6, version: 1.3.6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,535 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy5, version: 4.3+T.galaxy5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,535 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,535 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,535 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,535 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,535 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,535 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,536 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy6, version: 4.3+T.galaxy6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,536 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy3, version: 2.1.5+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,536 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.8+galaxy0, version: 1.3.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,536 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.8, version: 1.3.8 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,536 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/5.2+galaxy0, version: 5.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,536 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_get_chr_names/5.2+galaxy0, version: 5.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,536 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/5.2+galaxy0, version: 5.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,536 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/5.2+galaxy0, version: 5.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,536 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/5.2+galaxy0, version: 5.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,536 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/2.4+galaxy1, version: 2.4+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,536 [pN:job_handler_0,p:8,tN:MainThread] Loading section: ChIP-seq +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,537 [pN:job_handler_0,p:8,tN:MainThread] Loading section: RNA-seq +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,537 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1, version: 1.3.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,537 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1, version: 0.46.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,537 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.46.0.4, version: 0.46.0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,537 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1, version: 2.11.40.6+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,537 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.38.3+galaxy3, version: 3.38.3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,537 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.24.1+galaxy1, version: 3.24.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,537 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.10.1.1, version: 0.10.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,537 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy7, version: 2.1.0+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,537 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,537 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,537 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.1+galaxy2, version: 2.0.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,538 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.50.1+galaxy0, version: 3.50.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,538 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1, version: 2.2.1+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,538 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.7+galaxy2, version: 2.11.40.7+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,538 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3, version: 2.2.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,538 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deg_annotate/deg_annotate/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,538 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.50.0+galaxy0, version: 1.50.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,538 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea/1.20.0, version: 1.20.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,538 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fgsea/fgsea/1.8.0+galaxy1, version: 1.8.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,538 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.10.1+galaxy2, version: 1.10.1+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,538 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.48.0+galaxy1, version: 0.48.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,539 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.48.0+galaxy1, version: 0.48.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,539 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.8+galaxy0, version: 2.11.40.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,539 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.58.1+galaxy0, version: 3.58.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,539 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.36.0+galaxy5, version: 3.36.0+galaxy5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,539 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.2.3+galaxy0, version: 2.2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,539 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0, version: 2.2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,539 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2, version: 2.0.3+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,539 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/brew3r_r/brew3r_r/1.0.2+galaxy0, version: 1.0.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,539 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.6+galaxy0, version: 2.0.6+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,539 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.4, version: 2.2.1.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,539 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/brew3r_r/brew3r_r/1.0.2+galaxy1, version: 1.0.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,540 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/seurat/seurat/4.3.0.1+galaxy1, version: 4.3.0.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,540 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq/1.48.0+galaxy0, version: 1.48.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,540 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq_count/1.48.0+galaxy0, version: 1.48.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,540 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dexseq/plotdexseq/1.48.0+galaxy0, version: 1.48.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,540 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Multiple Alignments +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,540 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,540 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,540 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,540 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,540 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,540 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,540 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,540 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,540 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,540 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,541 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,541 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,541 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Phenotype Association +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,541 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,541 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_david, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,541 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,541 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_pass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,541 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_gpass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,541 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_beam, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,541 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_lps, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,541 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,541 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Regional Variation +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,541 [pN:job_handler_0,p:8,tN:MainThread] Loading section: STR-FM: Microsatellite Analysis +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,541 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Motif +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,541 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Chromosome Conformation +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,541 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Metagenomic Analysis +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,541 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Mothur +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,542 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Picard +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,542 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,542 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,542 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,542 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,542 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,542 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,542 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,542 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,542 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,543 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,543 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,543 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,543 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,543 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.3, version: 2.18.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,543 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,543 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_artifact_metrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,543 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,543 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,543 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,543 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,544 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,544 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,544 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ValidateSamFile/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,544 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,544 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeBamAlignment/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,544 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,544 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,544 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectHsMetrics/2.18.2, version: 2.18.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,544 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_EstimateLibraryComplexity/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,544 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,544 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,545 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,545 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,545 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,545 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,545 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,545 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,545 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,545 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,545 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,545 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,545 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,545 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,545 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,546 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,546 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,546 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_artifact_metrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,546 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,546 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,546 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,546 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,546 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,546 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,546 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ValidateSamFile/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,546 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,546 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeBamAlignment/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,547 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,547 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,547 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectHsMetrics/3.1.1, version: 3.1.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,547 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_EstimateLibraryComplexity/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,547 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,547 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,547 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Pharmacology +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,547 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/pharmcat/pharmcat/1.3.1+galaxy0, version: 1.3.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,547 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/pharmcat/pharmcat/1.7.0+galaxy0, version: 1.7.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,547 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Single-Cell +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,547 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/10x_bamtofastq/10x_bamtofastq/1.4.1, version: 1.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,547 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,548 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_export/anndata_export/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,548 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,548 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a, version: 1.5.a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,548 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,548 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/modify_loom/modify_loom/0.7.5+galaxy1, version: 0.7.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,548 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, version: 1.10.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,548 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_read_10x/dropletutils_read_10x/1.0.4+galaxy0, version: 1.0.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,548 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_empty_drops/dropletutils_empty_drops/1.0.4+galaxy0, version: 1.0.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,548 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspectclusters/raceid_inspectclusters/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,548 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_filtnormconf/raceid_filtnormconf/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,548 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_clustering/raceid_clustering/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,548 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_trajectory/raceid_trajectory/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,548 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspecttrajectory/raceid_inspecttrajectory/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,549 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.5.1+galaxy0, version: 1.5.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,549 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmonquantmerge/salmonquantmerge/1.5.1+galaxy0, version: 1.5.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,549 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/imgteam/slice_image/ip_slice_image/0.3, version: 0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,549 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_create_qcmetric_ready_sce/scater_create_qcmetric_ready_sce/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,549 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_tsne/scater_plot_tsne/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,549 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: 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2024-12-30 00:51:02,557 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,557 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,558 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/deeptools_bam_pe_fragmentsize/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,558 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,558 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,558 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/deeptools_correct_gc_bias/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,558 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,558 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: 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[pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,559 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,559 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,559 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,559 [pN:job_handler_0,p:8,tN:MainThread] Loading section: EMBOSS +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,559 [pN:job_handler_0,p:8,tN:MainThread] Loading section: GATK +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,559 [pN:job_handler_0,p:8,tN:MainThread] Loading section: NCBI BLAST+ +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,559 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Convert Formats +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,559 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gtftobed12/gtftobed12/357, version: 357 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,559 [pN:job_handler_0,p:8,tN:MainThread] Loading section: GEMINI +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,559 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.20.1+galaxy2, version: 0.20.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,560 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gemini_db_info/gemini_db_info/0.20.1, version: 0.20.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,560 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gemini_query/gemini_query/0.20.1+galaxy2, version: 0.20.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,560 [pN:job_handler_0,p:8,tN:MainThread] Loading section: QIIME2 +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,560 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__export/qiime2_core__tools__export/2022.11.1+dist.h2bda5906.2, version: 2022.11.1+dist.h2bda5906.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,560 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2022.11.1+dist.h2bda5906.2, version: 2022.11.1+dist.h2bda5906.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,560 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__alignment__mafft_add/qiime2__alignment__mafft_add/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,560 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__alignment__mafft/qiime2__alignment__mafft/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,560 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: 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toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__subsample_single/qiime2__demux__subsample_single/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,562 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__summarize/qiime2__demux__summarize/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,562 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__filter_samples/qiime2__demux__filter_samples/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,562 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: 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[pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__core_metrics_phylogenetic/qiime2__diversity__core_metrics_phylogenetic/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,564 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__core_metrics/qiime2__diversity__core_metrics/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,564 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_correlation/qiime2__diversity__alpha_correlation/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,564 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: 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[pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__classify_consensus_blast/qiime2__feature_classifier__classify_consensus_blast/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,567 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__extract_reads/qiime2__feature_classifier__extract_reads/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,567 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__classify_hybrid_vsearch_sklearn/qiime2__feature_classifier__classify_hybrid_vsearch_sklearn/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,567 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__classify_consensus_vsearch/qiime2__feature_classifier__classify_consensus_vsearch/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,568 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__blast/qiime2__feature_classifier__blast/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,568 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__find_consensus_annotation/qiime2__feature_classifier__find_consensus_annotation/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,568 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__vsearch_global/qiime2__feature_classifier__vsearch_global/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,568 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_table__tabulate_seqs/qiime2__feature_table__tabulate_seqs/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,568 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_table__presence_absence/qiime2__feature_table__presence_absence/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 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DEBUG 2024-12-30 00:51:02,578 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__vsearch__uchime_ref/qiime2__vsearch__uchime_ref/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,578 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__vsearch__cluster_features_de_novo/qiime2__vsearch__cluster_features_de_novo/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,578 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import_fastq/qiime2_core__tools__import_fastq/2024.10.0+dist.h3d8a7e27, version: 2024.10.0+dist.h3d8a7e27 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,578 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: 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into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,579 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__alignment__mafft/qiime2__alignment__mafft/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,579 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__composition__ancom/qiime2__composition__ancom/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,579 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__composition__add_pseudocount/qiime2__composition__add_pseudocount/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,579 [pN:job_handler_0,p:8,tN:MainThread] Loaded 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version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,580 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__dada2__denoise_pyro/qiime2__dada2__denoise_pyro/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,580 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__deblur__denoise_16s/qiime2__deblur__denoise_16S/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,581 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__deblur__visualize_stats/qiime2__deblur__visualize_stats/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,581 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__deblur__denoise_other/qiime2__deblur__denoise_other/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,581 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__emp_single/qiime2__demux__emp_single/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,581 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__summarize/qiime2__demux__summarize/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,581 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: 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version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,582 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__beta_phylogenetic/qiime2__diversity__beta_phylogenetic/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,582 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__beta_group_significance/qiime2__diversity__beta_group_significance/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,582 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__core_metrics_phylogenetic/qiime2__diversity__core_metrics_phylogenetic/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,582 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_correlation/qiime2__diversity__alpha_correlation/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,583 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__pcoa_biplot/qiime2__diversity__pcoa_biplot/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,583 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__core_metrics/qiime2__diversity__core_metrics/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,583 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__beta/qiime2__diversity__beta/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,583 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__partial_procrustes/qiime2__diversity__partial_procrustes/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,583 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha/qiime2__diversity__alpha/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,583 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__procrustes_analysis/qiime2__diversity__procrustes_analysis/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,583 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__filter_distance_matrix/qiime2__diversity__filter_distance_matrix/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,583 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_group_significance/qiime2__diversity__alpha_group_significance/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,583 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: 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2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,584 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__umap/qiime2__diversity__umap/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,584 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_rarefaction/qiime2__diversity__alpha_rarefaction/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,584 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__filter_alpha_diversity/qiime2__diversity__filter_alpha_diversity/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 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[pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity_lib__beta_phylogenetic_meta_passthrough/qiime2__diversity_lib__beta_phylogenetic_meta_passthrough/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,585 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity_lib__alpha_passthrough/qiime2__diversity_lib__alpha_passthrough/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,585 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity_lib__shannon_entropy/qiime2__diversity_lib__shannon_entropy/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,585 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity_lib__weighted_unifrac/qiime2__diversity_lib__weighted_unifrac/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,585 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity_lib__jaccard/qiime2__diversity_lib__jaccard/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,585 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity_lib__faith_pd/qiime2__diversity_lib__faith_pd/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,585 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: 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+galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,612 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,612 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_mismatch_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,612 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_inner_distance/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,612 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_quality/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,612 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_hexamer/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,612 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_insertion_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,612 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam2wig/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,613 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam_stat/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,613 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_GC/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,613 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_saturation/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,613 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage2/2.6.4.2, version: 2.6.4.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,613 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RPKM_saturation/2.6.4.2, version: 2.6.4.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,613 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,613 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_duplication/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,613 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_saturation/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,614 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_tin/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,614 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_clipping_profile/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,614 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_inner_distance/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,614 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage2/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,614 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_annotation/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,614 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_FPKM_count/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,614 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam_stat/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,615 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_GC/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,615 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_quality/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,615 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_insertion_profile/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,615 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,615 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RPKM_saturation/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,615 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,615 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RNA_fragment_size/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,615 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam2wig/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,615 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_hexamer/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,616 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_NVC/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,616 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_deletion_profile/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,616 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_mismatch_profile/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,616 [pN:job_handler_0,p:8,tN:MainThread] Loading section: MiModD +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,616 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Du Novo +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,616 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Seqtk +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,616 [pN:job_handler_0,p:8,tN:MainThread] Loading section: TRANSIT +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,616 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Statistics +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,616 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Summary_Statistics1, version: 1.1.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,616 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Count1, version: 1.0.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,616 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Graph/Display Data +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,616 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.6, version: 3.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,617 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,617 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,617 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,617 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,617 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,617 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,617 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,617 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,617 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,617 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,618 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,618 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,618 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,618 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,618 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,618 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,618 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0, version: 1.34.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,618 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.1.3+galaxy0, version: 3.1.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,619 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.5, version: 0.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,619 [pN:job_handler_0,p:8,tN:MainThread] Skipping tool panel addition of hidden tool: qual_stats_boxplot, version: 1.0.1 +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,619 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,619 [pN:job_handler_0,p:8,tN:MainThread] Loading section: RNA Analysis (deprecated) +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,619 [pN:job_handler_0,p:8,tN:MainThread] Loading section: CloudMap (deprecated) +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,619 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Metagenomic Analysis (deprecated) +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,619 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Text Manipulation +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,619 [pN:job_handler_0,p:8,tN:MainThread] Loading tool panel finished (130.014 ms) +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,625 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,625 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,625 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1, version: 2.7.8a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,625 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0, version: 2.28+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,626 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy1, version: 2.7.11a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,626 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy0, version: 2.7.11a+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,626 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy1, version: 2.7.11a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,626 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,626 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,626 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,626 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,626 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,627 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1, version: 4.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,627 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1, version: 4.9+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,627 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5+galaxy2, version: 1.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,627 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.5+galaxy2, version: 1.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,627 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.4+galaxy0, version: 2.9.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,627 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.5+galaxy0, version: 2.9.5+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,627 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, version: 0.4.8.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,627 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.1+galaxy0, version: 0.5.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,628 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.50.1+galaxy0, version: 3.50.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,628 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.50.0+galaxy0, version: 1.50.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,628 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.58.1+galaxy0, version: 3.58.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,628 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.36.0+galaxy5, version: 3.36.0+galaxy5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,628 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, version: 1.10.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,628 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/imgteam/slice_image/ip_slice_image/0.3-4, version: 0.3-4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,628 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,629 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,629 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,629 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,629 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,629 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,629 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: bed_to_bigBed, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,630 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,630 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,630 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,630 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,630 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,630 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,630 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,630 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,630 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,631 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,631 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,631 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: upload1, version: 1.1.7 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,631 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,631 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,631 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,631 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,631 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: intermine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,631 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: flymine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,631 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: modmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,631 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: mousemine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,632 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ratmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,632 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: yeastmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,632 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,632 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: wormbase, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,632 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,632 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: eupathdb, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,632 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hbvar, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,632 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,632 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,632 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,632 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __FILTER_EMPTY_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,632 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,633 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,633 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,633 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,633 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,633 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __TAG_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,633 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __APPLY_RULES__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,633 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __BUILD_LIST__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,633 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __EXTRACT_DATASET__, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,633 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: addValue, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,633 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: cat1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,633 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Cut1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,633 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Show beginning1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,633 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Filter1, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,633 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: sort1, version: 1.2.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,634 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Grep1, version: 1.0.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,634 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: comp1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,634 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,634 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,634 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0, version: 1.2.0.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,634 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5+galaxy2, version: 1.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,634 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.5+galaxy2, version: 1.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,634 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy1, version: 1.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,635 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3, version: 1.0+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,635 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, version: 1.10.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,635 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,635 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,635 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,635 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,635 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,635 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,635 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,635 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,635 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,635 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,636 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.7+galaxy2, version: 2.11.40.7+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,636 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.8+galaxy0, version: 2.11.40.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,636 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,636 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,636 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.6, version: 0.0.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,636 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,636 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,637 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,637 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,637 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,637 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.5+galaxy0, version: 0.2.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,637 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy1, version: 2.11.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,637 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,637 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,637 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0, version: 0.2.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,637 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: export_remote, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,637 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,637 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,637 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0, version: 0.2.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,637 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: param_value_from_file, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,638 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,638 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,638 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0, version: 0.5.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,638 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0, version: 5.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,638 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2, version: 0.5.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,638 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0, version: 0.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,638 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/diff/diff/3.7+galaxy0, version: 3.7+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,638 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,638 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,638 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6, version: 1.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,639 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,639 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.12.0, version: 3.12.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,639 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,639 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,639 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,639 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/0.9.2, version: 0.9.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,639 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.4, version: 0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,639 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0, version: 0.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,639 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,639 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,639 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,640 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,640 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,640 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,640 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,640 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0, version: 0.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,640 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,640 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,640 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,640 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,640 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,640 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,640 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,640 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,640 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,640 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,641 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,641 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_melt/melt/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,641 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_cast/cast/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,641 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jq/jq/1.0, version: 1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,641 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gff3_rebase/gff3.rebase/1.2, version: 1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,641 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,641 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_order_header_sort/column_order_header_sort/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,641 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,641 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Condense characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,641 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,641 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,641 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: createInterval, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,641 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,641 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Paste1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,641 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,641 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: random_lines1, version: 2.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,642 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Show tail1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,642 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: trimmer, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,642 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,642 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: secure_hash_message_digest, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,642 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0, version: 3.3.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,642 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1, version: 3.14.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,642 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0, version: 2.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,642 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0, version: 1.2.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,642 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4, version: 1.1.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,642 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1, version: 0.1.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,643 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0+galaxy0, version: 1.1.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,643 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.16.0+galaxy1, version: 3.16.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,643 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,643 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.3.1, version: 3.3.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,643 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2, version: 3.3.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,643 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1, version: 2.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,643 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/3.2.1, version: 3.2.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,643 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.18.0+galaxy0, version: 3.18.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,644 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3, version: 1.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,644 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3, version: 1.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,644 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.6, version: 0.6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,644 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,644 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,644 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,644 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,644 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,644 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,644 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,645 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/nl/9.3+galaxy1, version: 9.3+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,645 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,645 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,645 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,645 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,645 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,645 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,645 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,645 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,645 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,645 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,645 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy2, version: 9.3+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,646 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,646 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/1.0, version: 1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,646 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,646 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,646 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,646 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,646 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: join1, version: 2.1.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,646 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Grouping1, version: 2.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,646 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,646 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,646 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,647 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,647 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,647 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy1, version: 1.8+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,647 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,647 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.8, version: 1.16.8 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,647 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,647 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/flash/flash/1.2.11.4, version: 1.2.11.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,647 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.3, version: 0.6.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,648 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,648 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,648 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,648 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,648 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.7, version: 0.2.7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,648 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/length_and_gc_content/0.1.2, version: 0.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,648 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.7+galaxy0, version: 0.6.7+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,648 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.4, version: 1.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,649 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.5+galaxy1, version: 1.1.5+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,649 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.5+galaxy1, version: 1.1.5+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,649 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.9, version: 0.2.9 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,649 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,649 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0, version: 0.20.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,649 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1, version: 0.72+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,649 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1, version: 0.38.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,649 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0, version: 1.11+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,649 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0, version: 0.73+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,650 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1, version: 1.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,650 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0, version: 0.23.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,650 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0, version: 1.24.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,650 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1, version: 0.23.4+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,650 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1, version: 0.74+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,650 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy2, version: 0.23.4+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,651 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.39+galaxy2, version: 0.39+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,651 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/pileup_interval/pileup_interval/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,651 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3, version: 2.2.2d+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,651 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3, version: 1.9+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,651 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0.1+galaxy1, version: 2.0.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,651 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,651 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.4.0.0, version: 2.4.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,651 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamtools_split/2.4.0, version: 2.4.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,651 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam2interval/sam2interval/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,651 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_multi_bamqc/qualimap_multi_bamqc/2.2.2d, version: 2.2.2d into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,651 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,652 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,652 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2, version: 1.9+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,652 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,652 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,652 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,652 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2, version: 2.0.2+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,652 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,652 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,652 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,652 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,652 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8+galaxy1, version: 1.8+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,652 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,652 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,653 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.4, version: 2.1.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,653 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,653 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1, version: 2.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,653 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,653 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,653 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,653 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/boris/filter_on_md/MDtag_filter/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,653 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.2.0, version: 1.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,653 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.2, version: 2.0.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,654 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,654 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,654 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,654 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy1, version: 2.5.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,654 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,654 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lldelisle/revertr2orientationinbam/revertR2orientationInBam/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,654 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.3+galaxy0, version: 2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,654 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3, version: 1.20+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,655 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0.3, version: 2.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,655 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.2+galaxy2, version: 2.5.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,655 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamtools_split/2.5.2+galaxy0, version: 2.5.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,655 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_multi_bamqc/qualimap_multi_bamqc/2.3+galaxy0, version: 2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,655 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,656 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,656 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,656 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,656 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.15.1+galaxy2, version: 1.15.1+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,656 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,656 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,656 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,657 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,657 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,657 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,657 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,657 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.7, version: 2.1.7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,657 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,657 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy2, version: 2.5.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,657 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.2, version: 2.1.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,657 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.3, version: 2.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,657 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,658 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,658 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,658 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,658 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,658 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,658 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,658 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,658 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,658 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,659 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,659 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,659 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_links/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,659 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,659 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_expandbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,659 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,659 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,659 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,659 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_jaccard/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,659 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,660 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,660 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,660 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_reldistbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,660 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,660 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bed12tobed6/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,660 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,660 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,660 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,660 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.2, version: 2.30.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,660 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,661 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,661 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,661 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,661 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,661 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,662 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,662 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,662 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,662 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,662 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0+galaxy2, version: 2.30.0+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,662 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.3, version: 2.30.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,662 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,663 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,663 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,663 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,663 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,663 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,663 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,663 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,663 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,663 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_links/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,664 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,664 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,664 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,664 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,665 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,665 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,665 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_expandbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,665 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,665 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,665 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_jaccard/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,665 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.31.1.3, version: 2.31.1.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,665 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,665 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bed12tobed6/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,665 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,665 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,666 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,666 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,666 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,666 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,666 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,666 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,666 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,666 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,666 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,666 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,667 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,667 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,667 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,667 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,667 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_reldistbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,667 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,667 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,667 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,667 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,668 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,668 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,668 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,668 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,668 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/bcftools_plugin_fixploidy/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,668 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/bcftools_convert_to_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,668 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,668 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,668 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/bcftools_plugin_missing2ref/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,668 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,669 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,669 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/bcftools_plugin_counts/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,669 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,669 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,669 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,669 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/bcftools_convert_from_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,669 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/bcftools_plugin_impute_info/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,669 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,669 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,669 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/bcftools_plugin_fill_an_ac/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,670 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bcftools_plugin_fill_tags/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,670 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,670 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,670 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,670 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,670 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,670 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/bcftools_filter/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,670 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/bcftools_csq/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,670 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,670 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/bcftools_plugin_dosage/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,671 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/bcftools_query/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,671 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,671 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcf2tsv/vcf2tsv/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,671 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfaddinfo/vcfaddinfo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,671 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,671 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotate/vcfannotate/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,671 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotategenotypes/vcfannotategenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,671 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbedintersect/vcfbedintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,671 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbreakcreatemulti/vcfbreakcreatemulti/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,671 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcheck/vcfcheck/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,671 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcombine/vcfcombine/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,671 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcommonsamples/vcfcommonsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,672 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffixup/vcffixup/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,672 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfflatten/vcfflatten2/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,672 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgeno2haplo/vcfgeno2haplo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,672 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: 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toolshed.g2.bx.psu.edu/repos/devteam/vcftools_slice/vcftools_slice/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,673 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,673 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,673 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/bcftools_plugin_fixploidy/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,673 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: 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id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,674 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,674 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/bcftools_plugin_counts/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,674 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,674 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: 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tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,675 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,675 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/bcftools_plugin_fill_an_ac/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,675 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bcftools_plugin_fill_tags/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,675 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,675 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,675 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,676 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5, version: 1.15.1+galaxy5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,676 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: 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toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/bcftools_plugin_dosage/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,676 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/bcftools_query/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,677 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,677 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.0.3+galaxy7, version: 1.0.3+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,677 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6, version: 2.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,677 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,677 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,677 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,677 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1, version: 1.28.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,677 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_events/poretools_events/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,677 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_hist/poretools_hist/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,677 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_occupancy/poretools_occupancy/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,678 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualpos/poretools_qualpos/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,678 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_squiggle/poretools_squiggle/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,678 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_yield_plot/poretools_yield_plot/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,678 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3, version: 0.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,678 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_winner/poretools_winner/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,678 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_times/poretools_times/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,679 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_tabular/poretools_tabular/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,679 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_stats/poretools_stats/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,679 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualdist/poretools_qualdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,679 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_nucdist/poretools_nucdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,679 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_extract/poretools_extract/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,679 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.7.2+galaxy1, version: 1.7.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,679 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy1, version: 1.7.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,680 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.4.4+galaxy1, version: 1.4.4+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,680 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.7.2+galaxy0, version: 1.7.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,680 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.43.0+galaxy0, version: 1.43.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,680 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0, version: 0.2.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,680 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,680 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,680 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,680 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,680 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: wig_to_bigWig, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,680 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: liftOver1, version: 1.0.6 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,681 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,681 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,681 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19, version: 4.5covid19 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,681 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,681 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/ivar_filtervariants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,681 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_getmasked/ivar_getmasked/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,681 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,681 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,681 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,682 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,682 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/ivar_filtervariants/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,682 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.4.3+galaxy1, version: 1.4.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,682 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: wiggle2simple1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,682 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,682 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,682 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Extract genomic DNA 1, version: 2.2.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,682 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,682 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,683 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,683 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,683 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,683 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,683 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,683 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,683 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,683 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,683 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,683 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.12.0+galaxy1, version: 3.12.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,683 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3+galaxy0, version: 0.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,683 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.4.13, version: 1.4.13 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,684 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3_r179+galaxy1, version: 0.3_r179+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,684 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1, version: 1.5.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,684 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0, version: 1.3.6+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,684 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.15.5+galaxy2, version: 3.15.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,684 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1, version: 5.2.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,684 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy4, version: 2.17+galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,684 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0, version: 2.4.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,685 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4, version: 0.7.17.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,685 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1, version: 0.7.17.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,685 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.2, version: 0.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,685 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,685 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,685 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-2, version: 2.5.2b-2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,685 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.5, version: 0.7.17.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,685 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2, version: 0.7.17.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,685 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1, version: 2.5.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,686 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.18, version: 0.7.18 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,686 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.18, version: 0.7.18 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,686 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.7+galaxy0, version: 0.2.7+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,686 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.04.22+galaxy0, version: 1.04.22+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,686 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.04.22+galaxy0, version: 1.04.22+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,686 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,686 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,686 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,686 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,687 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,687 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,687 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,687 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_genesets/snpSift_geneSets/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,687 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_dbnsfp/snpSift_dbnsfp/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,687 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,687 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_get_chr_names/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,687 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy4, version: 4.3+T.galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,687 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,688 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1, version: 4.3+T.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,688 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_caseControl/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,688 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_annotate/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,688 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_vcfCheck/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,688 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,688 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,688 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_int/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,688 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpsift_vartype/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,688 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_rmInfo/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,688 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/1.0.12+galaxy0, version: 1.0.12+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,688 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jasminesv/jasminesv/1.0.11+galaxy1, version: 1.0.11+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,689 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2, version: 2.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,689 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0, version: 1.3.6+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,689 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.6, version: 1.3.6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,689 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy5, version: 4.3+T.galaxy5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,689 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,689 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,689 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,690 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,690 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,690 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,690 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy6, version: 4.3+T.galaxy6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,690 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy3, version: 2.1.5+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,690 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.8+galaxy0, version: 1.3.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,690 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.8, version: 1.3.8 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,690 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/5.2+galaxy0, version: 5.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,691 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_get_chr_names/5.2+galaxy0, version: 5.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,691 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/5.2+galaxy0, version: 5.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,691 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/5.2+galaxy0, version: 5.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,691 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/5.2+galaxy0, version: 5.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,691 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/2.4+galaxy1, version: 2.4+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,691 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1, version: 1.3.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,691 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1, version: 0.46.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,691 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.46.0.4, version: 0.46.0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,692 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1, version: 2.11.40.6+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,692 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.38.3+galaxy3, version: 3.38.3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,692 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.24.1+galaxy1, version: 3.24.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,692 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.10.1.1, version: 0.10.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,692 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy7, version: 2.1.0+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,692 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,692 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,692 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.1+galaxy2, version: 2.0.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,692 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1, version: 2.2.1+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,693 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3, version: 2.2.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,693 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deg_annotate/deg_annotate/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,693 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea/1.20.0, version: 1.20.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,693 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fgsea/fgsea/1.8.0+galaxy1, version: 1.8.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,693 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.10.1+galaxy2, version: 1.10.1+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,693 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.48.0+galaxy1, version: 0.48.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,693 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.48.0+galaxy1, version: 0.48.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,694 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.2.3+galaxy0, version: 2.2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,694 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0, version: 2.2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,694 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2, version: 2.0.3+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,694 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/brew3r_r/brew3r_r/1.0.2+galaxy0, version: 1.0.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,694 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.6+galaxy0, version: 2.0.6+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,694 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.4, version: 2.2.1.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,694 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/brew3r_r/brew3r_r/1.0.2+galaxy1, version: 1.0.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,694 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/seurat/seurat/4.3.0.1+galaxy1, version: 4.3.0.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,694 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq/1.48.0+galaxy0, version: 1.48.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,694 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq_count/1.48.0+galaxy0, version: 1.48.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,694 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dexseq/plotdexseq/1.48.0+galaxy0, version: 1.48.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,694 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,694 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,694 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,695 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,695 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,695 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,695 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,695 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,695 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,695 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,695 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,695 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,695 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,695 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_david, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,695 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,695 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_pass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,696 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_gpass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,696 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_beam, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,696 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_lps, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,696 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,696 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,696 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,696 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,696 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,696 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,696 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,696 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,696 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,696 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,697 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,697 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,697 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,697 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,697 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.3, version: 2.18.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,697 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,697 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_artifact_metrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,697 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,697 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,697 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,698 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,698 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,698 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,698 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ValidateSamFile/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,698 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,698 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeBamAlignment/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,698 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,698 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,698 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectHsMetrics/2.18.2, version: 2.18.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,698 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_EstimateLibraryComplexity/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,698 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,699 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,699 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,699 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,699 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,699 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,699 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,700 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,700 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,700 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,700 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,700 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,700 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,700 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,700 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,701 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,701 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,701 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_artifact_metrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,701 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,701 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,701 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,701 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,701 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,702 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,702 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ValidateSamFile/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,702 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,702 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeBamAlignment/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,702 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,702 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: 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panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,703 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/pharmcat/pharmcat/1.3.1+galaxy0, version: 1.3.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,703 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/pharmcat/pharmcat/1.7.0+galaxy0, version: 1.7.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,703 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/10x_bamtofastq/10x_bamtofastq/1.4.1, version: 1.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,703 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,703 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_export/anndata_export/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,703 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,703 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a, version: 1.5.a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,704 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,704 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: 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version: 1.12.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,706 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_pca/scater_plot_pca/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,706 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.7.1+galaxy0, version: 1.7.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,706 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.7.1+galaxy0, version: 1.7.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,706 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.7.1+galaxy0, version: 1.7.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,706 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.7.1+galaxy0, version: 1.7.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,706 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1, version: 1.7.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,706 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_remove_confounders/scanpy_remove_confounders/1.7.1+galaxy0, version: 1.7.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,706 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_parameter_iterator/scanpy_parameter_iterator/0.0.1+galaxy0, version: 0.0.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,706 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/droplet_barcode_plot/_dropletBarcodePlot/1.6.1+galaxy2, version: 1.6.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,707 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_read_10x/scanpy_read_10x/1.4.3+galaxy10, version: 1.4.3+galaxy10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,707 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/gtf2gene_list/_ensembl_gtf2gene_list/1.42.1+galaxy6, version: 1.42.1+galaxy6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,707 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/salmon_kallisto_mtx_to_10x/_salmon_kallisto_mtx_to_10x/0.0.1+galaxy6, version: 0.0.1+galaxy6 into tool 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DEBUG 2024-12-30 00:51:02,707 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/music_construct_eset/music_construct_eset/0.1.1+galaxy0, version: 0.1.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,708 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_read_10x/scanpy_read_10x/1.6.0+galaxy0, version: 1.6.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,708 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.6.0+galaxy1, version: 1.6.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,708 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.8.1+3+galaxy0, version: 1.8.1+3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 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DEBUG 2024-12-30 00:51:02,711 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_export/anndata_export/0.7.5+galaxy1, version: 0.7.5+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,711 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1, version: 0.7.5+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,711 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1, version: 0.7.5+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,711 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,712 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+galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,713 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,713 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,713 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_enrichment/deeptools_plot_enrichment/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,714 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,714 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,714 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,714 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,714 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,715 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,715 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,715 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/deeptools_bam_pe_fragmentsize/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,715 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: 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[pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,716 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,716 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,716 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_enrichment/deeptools_plot_enrichment/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,716 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,716 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,716 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,717 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/3.5.4+galaxy0, version: 3.5.4+galaxy0 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DEBUG 2024-12-30 00:51:02,721 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__procrustes_analysis/qiime2__diversity__procrustes_analysis/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,721 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__mantel/qiime2__diversity__mantel/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,721 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__beta/qiime2__diversity__beta/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,721 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: 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[pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__composition__da_barplot/qiime2__composition__da_barplot/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,736 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__composition__ancombc/qiime2__composition__ancombc/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,736 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__cutadapt__trim_single/qiime2__cutadapt__trim_single/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,736 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: 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[pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__emp_single/qiime2__demux__emp_single/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,737 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__summarize/qiime2__demux__summarize/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,737 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__tabulate_read_counts/qiime2__demux__tabulate_read_counts/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,738 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: 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[pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity_lib__beta_phylogenetic_meta_passthrough/qiime2__diversity_lib__beta_phylogenetic_meta_passthrough/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,742 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity_lib__alpha_passthrough/qiime2__diversity_lib__alpha_passthrough/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,742 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity_lib__shannon_entropy/qiime2__diversity_lib__shannon_entropy/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,743 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toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage2/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,770 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_NVC/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,770 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_clipping_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,770 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_FPKM_count/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,771 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage/2.6.4.3, version: 2.6.4.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,771 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_deletion_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,771 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RPKM_saturation/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,771 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RNA_fragment_size/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,771 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,771 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_annotation/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,771 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_tin/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,771 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,771 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_mismatch_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,772 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_inner_distance/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,772 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_quality/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,772 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_hexamer/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,772 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_insertion_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,772 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam2wig/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,772 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam_stat/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,772 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_GC/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,772 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_saturation/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,772 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage2/2.6.4.2, version: 2.6.4.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,773 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RPKM_saturation/2.6.4.2, version: 2.6.4.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,773 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,773 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_duplication/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,773 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_saturation/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,773 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_tin/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,773 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_clipping_profile/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,774 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_inner_distance/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,774 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage2/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,774 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_annotation/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,774 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_FPKM_count/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,774 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam_stat/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,774 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_GC/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,774 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_quality/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,775 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_insertion_profile/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,775 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,775 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RPKM_saturation/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,775 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,775 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RNA_fragment_size/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,775 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam2wig/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,776 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_hexamer/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,776 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_NVC/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,776 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_deletion_profile/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,776 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_mismatch_profile/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,776 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Summary_Statistics1, version: 1.1.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,777 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Count1, version: 1.0.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,777 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,777 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0, version: 1.34.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,777 [pN:job_handler_0,p:8,tN:MainThread] Skipping tool panel addition of hidden tool: qual_stats_boxplot, version: 1.0.1 +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,777 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.views.edam DEBUG 2024-12-30 00:51:02,777 [pN:job_handler_0,p:8,tN:MainThread] Loading EDAM tool panel finished (158.121 ms) +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,783 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,783 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,783 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1, version: 2.7.8a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,784 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy1, version: 2.7.11a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,784 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy0, version: 2.7.11a+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,784 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy1, version: 2.7.11a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,784 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.50.1+galaxy0, version: 3.50.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,784 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.7+galaxy2, version: 2.11.40.7+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,784 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.50.0+galaxy0, version: 1.50.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,784 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.8+galaxy0, version: 2.11.40.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,785 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.58.1+galaxy0, version: 3.58.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,785 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.36.0+galaxy5, version: 3.36.0+galaxy5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,785 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, version: 1.10.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,785 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/cite_seq_count/cite_seq_count/1.4.4+galaxy0, version: 1.4.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,785 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1, version: 4.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,785 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1, version: 4.9+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,785 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.4+galaxy0, version: 2.9.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,786 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.5+galaxy0, version: 2.9.5+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,786 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, version: 0.4.8.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,786 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.1+galaxy0, version: 0.5.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,786 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0, version: 2.28+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,787 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,787 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,787 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,787 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,787 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy1, version: 1.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,787 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3, version: 1.0+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,787 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,787 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,788 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,788 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,788 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,788 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,788 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,788 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,788 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,788 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,788 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,788 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.6, version: 0.0.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,789 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,789 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,789 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,789 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,789 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,789 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,789 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,789 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,789 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,790 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,790 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,790 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,790 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,790 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,790 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,790 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,790 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,790 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,791 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,791 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,791 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1, version: 2.7.8a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,791 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy1, version: 2.7.11a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,791 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy0, version: 2.7.11a+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,791 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy1, version: 2.7.11a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,791 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, version: 1.10.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,791 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/cite_seq_count/cite_seq_count/1.4.4+galaxy0, version: 1.4.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,792 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy0, version: 1.8+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,792 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy1, version: 1.8+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,792 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Summary_Statistics1, version: 1.1.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,792 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,792 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,792 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,792 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,792 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,792 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,793 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,793 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0, version: 1.2.0.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,793 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5+galaxy2, version: 1.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,793 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5+galaxy2, version: 1.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,793 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.5+galaxy2, version: 1.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,793 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.5+galaxy2, version: 1.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,794 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy1, version: 1.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,794 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3, version: 1.0+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,794 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,794 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,794 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,794 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,795 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,795 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,795 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,795 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,795 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,795 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,795 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,795 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,795 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,795 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,796 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,796 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,796 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,796 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,796 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,796 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,796 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,796 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,796 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,797 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,797 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,797 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.5+galaxy0, version: 0.2.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,797 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy1, version: 2.11.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,797 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,797 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,797 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0, version: 0.2.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,797 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: upload1, version: 1.1.7 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,797 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,797 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,798 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,798 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,798 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: intermine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,798 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: flymine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,798 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: modmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,798 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: mousemine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,798 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ratmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,798 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: yeastmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,798 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,798 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: wormbase, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,798 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,798 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: eupathdb, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,798 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hbvar, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,799 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: export_remote, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,799 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,799 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,799 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0, version: 0.2.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,800 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: param_value_from_file, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,800 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,800 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,800 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0, version: 0.5.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,800 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0, version: 5.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,800 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2, version: 0.5.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,800 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0, version: 0.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,800 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,800 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,800 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,800 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __FILTER_EMPTY_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,800 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,801 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,801 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,801 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,801 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,801 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __TAG_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,801 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __APPLY_RULES__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,801 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __BUILD_LIST__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,801 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __EXTRACT_DATASET__, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,801 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/diff/diff/3.7+galaxy0, version: 3.7+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,801 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,801 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,801 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6, version: 1.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,801 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,802 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.12.0, version: 3.12.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,802 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,802 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,802 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,802 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/0.9.2, version: 0.9.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,802 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.4, version: 0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,802 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0, version: 0.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,802 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,802 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,802 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,802 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,802 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,803 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,803 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,803 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0, version: 0.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,803 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,803 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,803 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,803 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,803 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,803 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,803 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,803 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,804 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,804 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,804 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,804 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_melt/melt/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,804 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_cast/cast/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,804 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jq/jq/1.0, version: 1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,804 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gff3_rebase/gff3.rebase/1.2, version: 1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,804 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,804 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_order_header_sort/column_order_header_sort/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,804 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,804 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: addValue, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,805 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: cat1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,805 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Condense characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,805 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,805 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,805 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: createInterval, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,805 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Cut1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,805 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,805 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Paste1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,805 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,805 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: random_lines1, version: 2.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,805 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Show beginning1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,805 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Show tail1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,805 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: trimmer, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,805 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,805 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: secure_hash_message_digest, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,805 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0, version: 3.3.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,806 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1, version: 3.14.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,806 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0, version: 2.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,806 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0, version: 1.2.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,806 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4, version: 1.1.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,806 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1, version: 0.1.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,806 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0+galaxy0, version: 1.1.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,806 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.16.0+galaxy1, version: 3.16.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,806 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,806 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.3.1, version: 3.3.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,806 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2, version: 3.3.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,806 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1, version: 2.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,807 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/3.2.1, version: 3.2.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,807 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.18.0+galaxy0, version: 3.18.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,807 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3, version: 1.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,807 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3, version: 1.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,807 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.6, version: 0.6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,807 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,807 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,807 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,807 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,807 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,807 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,807 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,807 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/nl/9.3+galaxy1, version: 9.3+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,808 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,808 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,808 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,808 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,808 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,808 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,808 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,808 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,808 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,808 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,808 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy2, version: 9.3+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,809 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,809 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/1.0, version: 1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,809 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Filter1, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,809 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: sort1, version: 1.2.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,809 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Grep1, version: 1.0.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,809 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,809 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,809 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,809 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,809 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: join1, version: 2.1.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,809 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: comp1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,809 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Grouping1, version: 2.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,809 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,810 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,810 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,810 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,810 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,810 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.8, version: 1.16.8 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,810 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,810 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/flash/flash/1.2.11.4, version: 1.2.11.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,810 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.3, version: 0.6.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,810 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,810 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,810 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,811 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,811 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.7, version: 0.2.7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,811 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/length_and_gc_content/0.1.2, version: 0.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,811 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.7+galaxy0, version: 0.6.7+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,811 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.4, version: 1.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,811 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.5+galaxy1, version: 1.1.5+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,811 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.5+galaxy1, version: 1.1.5+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,811 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.9, version: 0.2.9 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,812 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,812 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0, version: 0.20.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,812 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1, version: 0.72+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,812 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1, version: 0.38.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,812 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0, version: 1.11+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,812 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0, version: 0.73+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,812 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1, version: 1.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,812 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0, version: 0.23.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,812 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0, version: 1.24.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,813 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1, version: 0.23.4+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,813 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1, version: 0.74+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,813 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy2, version: 0.23.4+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,813 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.39+galaxy2, version: 0.39+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,813 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/pileup_interval/pileup_interval/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,813 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3, version: 2.2.2d+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,813 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3, version: 1.9+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,813 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0.1+galaxy1, version: 2.0.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,813 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,813 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.4.0.0, version: 2.4.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,813 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamtools_split/2.4.0, version: 2.4.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,813 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam2interval/sam2interval/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,813 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_multi_bamqc/qualimap_multi_bamqc/2.2.2d, version: 2.2.2d into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,814 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,814 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,814 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2, version: 1.9+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,814 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,814 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,814 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,814 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2, version: 2.0.2+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,814 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,814 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,814 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,814 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,814 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8+galaxy1, version: 1.8+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,815 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,815 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,815 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.4, version: 2.1.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,815 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,815 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1, version: 2.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,815 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,816 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,816 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,816 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/boris/filter_on_md/MDtag_filter/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,816 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.2.0, version: 1.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,816 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.2, version: 2.0.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,816 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,816 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,816 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,817 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy1, version: 2.5.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,817 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,817 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lldelisle/revertr2orientationinbam/revertR2orientationInBam/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,817 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.3+galaxy0, version: 2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,817 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3, version: 1.20+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,817 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0.3, version: 2.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,817 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.2+galaxy2, version: 2.5.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,817 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamtools_split/2.5.2+galaxy0, version: 2.5.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,818 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_multi_bamqc/qualimap_multi_bamqc/2.3+galaxy0, version: 2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,818 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,818 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,818 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,818 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,818 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.15.1+galaxy2, version: 1.15.1+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,818 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,818 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,818 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,819 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,819 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,819 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,819 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,819 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.7, version: 2.1.7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,819 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,819 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy2, version: 2.5.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,819 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.2, version: 2.1.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,819 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.3, version: 2.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,819 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,820 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,820 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,820 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,820 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,820 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,820 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,820 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,820 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,820 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,820 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,821 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,821 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_links/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,821 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,821 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_expandbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,821 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,821 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,821 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,821 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_jaccard/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,821 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,822 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,822 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,822 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_reldistbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,822 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,822 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bed12tobed6/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,822 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,822 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,822 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,822 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.2, version: 2.30.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,822 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,823 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,823 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,823 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,823 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,823 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,823 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,823 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,823 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,823 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,824 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0+galaxy2, version: 2.30.0+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,824 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.3, version: 2.30.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,824 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,824 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,824 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,824 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,824 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,824 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,825 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,825 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,825 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,825 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_links/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,825 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,825 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,825 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,825 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,825 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,826 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,826 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_expandbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,826 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,826 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,826 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_jaccard/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,826 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.31.1.3, version: 2.31.1.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,826 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,826 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bed12tobed6/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,826 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,827 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,827 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,827 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,827 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,827 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,827 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,827 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,827 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,827 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,828 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,828 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,828 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,828 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,828 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,828 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,828 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_reldistbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,828 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,829 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,829 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,829 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,829 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,829 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,829 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,829 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,829 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/bcftools_plugin_fixploidy/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,829 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/bcftools_convert_to_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,830 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,830 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,830 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/bcftools_plugin_missing2ref/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,830 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,830 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,830 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/bcftools_plugin_counts/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,830 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,830 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,830 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,830 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/bcftools_convert_from_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,831 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/bcftools_plugin_impute_info/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,831 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,831 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,831 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/bcftools_plugin_fill_an_ac/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,831 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bcftools_plugin_fill_tags/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,831 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,831 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,831 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,831 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,831 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,831 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/bcftools_filter/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,832 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/bcftools_csq/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,832 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,832 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/bcftools_plugin_dosage/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,832 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/bcftools_query/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,832 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,832 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcf2tsv/vcf2tsv/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,832 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfaddinfo/vcfaddinfo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,832 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,832 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotate/vcfannotate/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,832 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotategenotypes/vcfannotategenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,832 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbedintersect/vcfbedintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,833 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbreakcreatemulti/vcfbreakcreatemulti/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,833 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcheck/vcfcheck/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,833 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcombine/vcfcombine/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,833 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcommonsamples/vcfcommonsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,833 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffixup/vcffixup/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,833 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfflatten/vcfflatten2/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,833 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgeno2haplo/vcfgeno2haplo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,833 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgenotypes/vcfgenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,833 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfhethom/vcfhethom/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,833 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfleftalign/vcfleftalign/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,833 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfprimers/vcfprimers/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,834 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfrandomsample/vcfrandomsample/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,834 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfsort/vcfsort/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,834 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,834 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfselectsamples/vcfselectsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,834 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfdistance/vcfdistance/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,834 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffilter/vcffilter2/1.0.0_rc3+galaxy3, version: 1.0.0_rc3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,834 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/vcfdistance/vcfdistance/1.0.0_rc1+galaxy0, version: 1.0.0_rc1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,834 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_annotate/vcftools_annotate/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,834 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_slice/vcftools_slice/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,834 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,834 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,834 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/bcftools_plugin_fixploidy/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,834 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/bcftools_convert_to_vcf/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,835 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,835 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,835 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/bcftools_plugin_missing2ref/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,835 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,835 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,835 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/bcftools_plugin_counts/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,835 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,835 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,835 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,835 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/bcftools_convert_from_vcf/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,835 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/bcftools_plugin_impute_info/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,835 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,836 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,836 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/bcftools_plugin_fill_an_ac/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,836 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bcftools_plugin_fill_tags/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,836 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,836 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,836 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,836 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5, version: 1.15.1+galaxy5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,836 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,836 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/bcftools_filter/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,836 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/bcftools_csq/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,836 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,836 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/bcftools_plugin_dosage/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,837 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/bcftools_query/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,837 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,837 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.0.3+galaxy7, version: 1.0.3+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,837 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6, version: 2.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,837 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,837 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,837 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,837 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1, version: 1.28.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,837 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_events/poretools_events/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,837 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_hist/poretools_hist/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,837 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_occupancy/poretools_occupancy/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,837 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualpos/poretools_qualpos/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,837 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_squiggle/poretools_squiggle/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,837 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_yield_plot/poretools_yield_plot/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,838 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3, version: 0.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,838 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_winner/poretools_winner/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,838 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_times/poretools_times/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,838 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_tabular/poretools_tabular/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,838 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_stats/poretools_stats/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,838 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualdist/poretools_qualdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,838 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_nucdist/poretools_nucdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,838 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_extract/poretools_extract/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,838 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.7.2+galaxy1, version: 1.7.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,838 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy1, version: 1.7.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,838 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.4.4+galaxy1, version: 1.4.4+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,839 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.7.2+galaxy0, version: 1.7.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,839 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.43.0+galaxy0, version: 1.43.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,839 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0, version: 0.2.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,839 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,839 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,839 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,839 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,839 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,839 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,839 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: wig_to_bigWig, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,839 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: bed_to_bigBed, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,839 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: liftOver1, version: 1.0.6 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,840 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,840 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,840 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19, version: 4.5covid19 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,840 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,840 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/ivar_filtervariants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,840 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_getmasked/ivar_getmasked/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,840 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,840 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,840 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,840 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,841 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/ivar_filtervariants/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,841 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.4.3+galaxy1, version: 1.4.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,841 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: wiggle2simple1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,841 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,841 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,841 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Extract genomic DNA 1, version: 2.2.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,841 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,841 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,841 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,841 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,841 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,841 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,842 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,842 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,842 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,842 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,842 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,842 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.12.0+galaxy1, version: 3.12.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,842 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3+galaxy0, version: 0.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,842 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.4.13, version: 1.4.13 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,842 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3_r179+galaxy1, version: 0.3_r179+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,842 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1, version: 1.5.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,842 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0, version: 1.3.6+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,843 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.15.5+galaxy2, version: 3.15.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,843 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1, version: 5.2.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,843 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy4, version: 2.17+galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,843 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0, version: 2.4.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,843 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4, version: 0.7.17.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,843 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1, version: 0.7.17.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,843 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.2, version: 0.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,843 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,843 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,843 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-2, version: 2.5.2b-2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,844 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.5, version: 0.7.17.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,844 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2, version: 0.7.17.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,844 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1, version: 2.5.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,844 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.18, version: 0.7.18 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,844 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.18, version: 0.7.18 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,845 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.7+galaxy0, version: 0.2.7+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,845 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.04.22+galaxy0, version: 1.04.22+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,845 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.04.22+galaxy0, version: 1.04.22+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,845 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,845 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,845 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,845 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,845 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,846 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,846 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,846 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_genesets/snpSift_geneSets/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,846 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_dbnsfp/snpSift_dbnsfp/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,846 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,846 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_get_chr_names/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,846 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy4, version: 4.3+T.galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,846 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,846 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1, version: 4.3+T.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,846 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_caseControl/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,846 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_annotate/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,847 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_vcfCheck/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,847 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,847 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,847 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_int/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,847 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpsift_vartype/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,847 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_rmInfo/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,847 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/1.0.12+galaxy0, version: 1.0.12+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,847 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jasminesv/jasminesv/1.0.11+galaxy1, version: 1.0.11+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,847 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2, version: 2.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,848 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0, version: 1.3.6+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,848 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.6, version: 1.3.6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,848 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy5, version: 4.3+T.galaxy5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,848 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,848 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,848 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,848 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,848 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,848 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,849 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy6, version: 4.3+T.galaxy6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,849 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy3, version: 2.1.5+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,849 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.8+galaxy0, version: 1.3.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,849 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.8, version: 1.3.8 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,849 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/5.2+galaxy0, version: 5.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,849 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_get_chr_names/5.2+galaxy0, version: 5.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,849 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/5.2+galaxy0, version: 5.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,849 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/5.2+galaxy0, version: 5.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,849 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/5.2+galaxy0, version: 5.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,850 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/2.4+galaxy1, version: 2.4+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,850 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1, version: 1.3.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,850 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1, version: 0.46.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,850 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.46.0.4, version: 0.46.0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,850 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1, version: 2.11.40.6+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,850 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.38.3+galaxy3, version: 3.38.3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,850 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.24.1+galaxy1, version: 3.24.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,850 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.10.1.1, version: 0.10.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,850 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy7, version: 2.1.0+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,851 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,851 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,851 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.1+galaxy2, version: 2.0.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,851 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1, version: 2.2.1+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,851 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3, version: 2.2.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,851 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deg_annotate/deg_annotate/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,851 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea/1.20.0, version: 1.20.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,851 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fgsea/fgsea/1.8.0+galaxy1, version: 1.8.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,852 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.10.1+galaxy2, version: 1.10.1+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,852 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.48.0+galaxy1, version: 0.48.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,852 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.48.0+galaxy1, version: 0.48.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,852 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.2.3+galaxy0, version: 2.2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,852 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0, version: 2.2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,852 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2, version: 2.0.3+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,852 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/brew3r_r/brew3r_r/1.0.2+galaxy0, version: 1.0.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,852 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.6+galaxy0, version: 2.0.6+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,852 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.4, version: 2.2.1.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,852 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/brew3r_r/brew3r_r/1.0.2+galaxy1, version: 1.0.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,853 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/seurat/seurat/4.3.0.1+galaxy1, version: 4.3.0.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,853 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq/1.48.0+galaxy0, version: 1.48.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,853 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq_count/1.48.0+galaxy0, version: 1.48.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,853 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dexseq/plotdexseq/1.48.0+galaxy0, version: 1.48.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,853 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,853 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,853 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,853 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,853 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,853 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,853 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,853 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,853 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,854 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,854 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,854 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,854 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,854 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_david, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,854 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,854 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_pass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,854 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_gpass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,854 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_beam, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,854 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_lps, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,854 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,854 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,854 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,855 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,855 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,855 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,855 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,855 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,855 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,855 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,855 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,855 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,855 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,856 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,856 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.3, version: 2.18.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,856 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,856 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_artifact_metrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,856 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,856 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,856 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,856 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,856 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,856 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,857 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ValidateSamFile/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,857 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,857 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeBamAlignment/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,857 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,857 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,857 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectHsMetrics/2.18.2, version: 2.18.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,857 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_EstimateLibraryComplexity/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,857 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,857 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,858 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,858 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,858 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,858 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,858 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,858 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,858 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,859 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,859 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,859 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,859 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,859 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,859 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,859 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,859 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,859 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_artifact_metrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,860 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,860 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,860 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,860 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,860 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,860 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,860 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ValidateSamFile/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,860 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,861 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeBamAlignment/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,861 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,861 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,861 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectHsMetrics/3.1.1, version: 3.1.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,861 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_EstimateLibraryComplexity/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,861 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,861 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,861 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/pharmcat/pharmcat/1.3.1+galaxy0, version: 1.3.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,861 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/pharmcat/pharmcat/1.7.0+galaxy0, version: 1.7.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,862 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/10x_bamtofastq/10x_bamtofastq/1.4.1, version: 1.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,862 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,862 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_export/anndata_export/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,862 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,862 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a, version: 1.5.a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,862 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,862 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/modify_loom/modify_loom/0.7.5+galaxy1, version: 0.7.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,862 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_read_10x/dropletutils_read_10x/1.0.4+galaxy0, version: 1.0.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,862 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_empty_drops/dropletutils_empty_drops/1.0.4+galaxy0, version: 1.0.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,862 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspectclusters/raceid_inspectclusters/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,862 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_filtnormconf/raceid_filtnormconf/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,863 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_clustering/raceid_clustering/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,863 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_trajectory/raceid_trajectory/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,863 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspecttrajectory/raceid_inspecttrajectory/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,863 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.5.1+galaxy0, version: 1.5.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,863 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmonquantmerge/salmonquantmerge/1.5.1+galaxy0, version: 1.5.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,863 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/imgteam/slice_image/ip_slice_image/0.3, version: 0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,863 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_create_qcmetric_ready_sce/scater_create_qcmetric_ready_sce/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,863 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_tsne/scater_plot_tsne/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,863 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_filter/scater_filter/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,863 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_normalize/scater_normalize/1.12.2, version: 1.12.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,863 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_dist_scatter/scater_plot_dist_scatter/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,863 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_exprs_freq/scater_plot_exprs_freq/1.12.2, version: 1.12.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,863 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_pca/scater_plot_pca/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,863 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.7.1+galaxy0, version: 1.7.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,864 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.7.1+galaxy0, version: 1.7.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,864 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.7.1+galaxy0, version: 1.7.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,864 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.7.1+galaxy0, version: 1.7.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,864 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1, version: 1.7.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,864 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_remove_confounders/scanpy_remove_confounders/1.7.1+galaxy0, version: 1.7.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,864 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_parameter_iterator/scanpy_parameter_iterator/0.0.1+galaxy0, version: 0.0.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,864 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/droplet_barcode_plot/_dropletBarcodePlot/1.6.1+galaxy2, version: 1.6.1+galaxy2 into 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[pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2022.11.1+dist.h2bda5906.2, version: 2022.11.1+dist.h2bda5906.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,873 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__alignment__mafft_add/qiime2__alignment__mafft_add/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,873 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__alignment__mafft/qiime2__alignment__mafft/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,873 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__alignment__mask/qiime2__alignment__mask/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,873 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__composition__add_pseudocount/qiime2__composition__add_pseudocount/2022.11.2+q2galaxy.2022.11.1.2, version: 2022.11.2+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,873 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__composition__ancombc/qiime2__composition__ancombc/2022.11.2+q2galaxy.2022.11.1.2, version: 2022.11.2+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,874 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: 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toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__subsample_single/qiime2__demux__subsample_single/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,875 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__summarize/qiime2__demux__summarize/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,875 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__filter_samples/qiime2__demux__filter_samples/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,875 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__emp_single/qiime2__demux__emp_single/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,875 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__beta_correlation/qiime2__diversity__beta_correlation/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,875 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__adonis/qiime2__diversity__adonis/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,876 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__umap/qiime2__diversity__umap/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,876 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__pcoa/qiime2__diversity__pcoa/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,876 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__bioenv/qiime2__diversity__bioenv/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,876 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__pcoa_biplot/qiime2__diversity__pcoa_biplot/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,876 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__tsne/qiime2__diversity__tsne/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,876 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__beta_group_significance/qiime2__diversity__beta_group_significance/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,876 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__procrustes_analysis/qiime2__diversity__procrustes_analysis/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,876 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__mantel/qiime2__diversity__mantel/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,876 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__beta/qiime2__diversity__beta/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,877 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_group_significance/qiime2__diversity__alpha_group_significance/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,877 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__core_metrics_phylogenetic/qiime2__diversity__core_metrics_phylogenetic/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,877 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__core_metrics/qiime2__diversity__core_metrics/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,877 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_correlation/qiime2__diversity__alpha_correlation/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,877 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: 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DEBUG 2024-12-30 00:51:02,880 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__classify_consensus_vsearch/qiime2__feature_classifier__classify_consensus_vsearch/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,880 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__blast/qiime2__feature_classifier__blast/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,880 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__find_consensus_annotation/qiime2__feature_classifier__find_consensus_annotation/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... 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DEBUG 2024-12-30 00:51:02,888 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__vsearch__uchime_ref/qiime2__vsearch__uchime_ref/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,888 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__vsearch__cluster_features_de_novo/qiime2__vsearch__cluster_features_de_novo/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,888 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import_fastq/qiime2_core__tools__import_fastq/2024.10.0+dist.h3d8a7e27, version: 2024.10.0+dist.h3d8a7e27 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,889 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: 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into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,889 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__alignment__mafft/qiime2__alignment__mafft/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,889 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__composition__ancom/qiime2__composition__ancom/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,889 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__composition__add_pseudocount/qiime2__composition__add_pseudocount/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,889 [pN:job_handler_0,p:8,tN:MainThread] Loaded 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[pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__beta/qiime2__diversity__beta/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,895 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__partial_procrustes/qiime2__diversity__partial_procrustes/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,895 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha/qiime2__diversity__alpha/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,896 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: 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[pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity_lib__beta_phylogenetic_meta_passthrough/qiime2__diversity_lib__beta_phylogenetic_meta_passthrough/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,898 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity_lib__alpha_passthrough/qiime2__diversity_lib__alpha_passthrough/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,898 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity_lib__shannon_entropy/qiime2__diversity_lib__shannon_entropy/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,898 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity_lib__weighted_unifrac/qiime2__diversity_lib__weighted_unifrac/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,898 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity_lib__jaccard/qiime2__diversity_lib__jaccard/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,898 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity_lib__faith_pd/qiime2__diversity_lib__faith_pd/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,899 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: 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+galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,924 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage/2.6.4.3, version: 2.6.4.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,924 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_deletion_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,925 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RPKM_saturation/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,925 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RNA_fragment_size/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,925 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,925 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_annotation/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,925 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_tin/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,925 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,925 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_mismatch_profile/2.6.4, version: 2.6.4 into 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+galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,926 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RPKM_saturation/2.6.4.2, version: 2.6.4.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,926 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,926 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_duplication/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,926 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_saturation/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,927 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DEBUG 2024-12-30 00:51:02,928 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RNA_fragment_size/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,928 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam2wig/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,929 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_hexamer/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,929 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_NVC/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,929 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_deletion_profile/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,929 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_mismatch_profile/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,929 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Count1, version: 1.0.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,929 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,929 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0, version: 1.34.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,930 [pN:job_handler_0,p:8,tN:MainThread] Skipping tool panel addition of hidden tool: qual_stats_boxplot, version: 1.0.1 +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:51:02,930 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.views.edam DEBUG 2024-12-30 00:51:02,930 [pN:job_handler_0,p:8,tN:MainThread] Loading EDAM tool panel finished (152.045 ms) +galaxy.tool_util.toolbox.integrated_panel DEBUG 2024-12-30 00:51:02,930 [pN:job_handler_0,p:8,tN:MainThread] Writing integrated tool panel config file to '/galaxy/server/config/mutable/integrated_tool_panel.xml' +galaxy.tool_util.deps.installable WARNING 2024-12-30 00:51:02,948 [pN:job_handler_0,p:8,tN:MainThread] Conda not installed and auto-installation disabled. +galaxy.tool_util.deps.installable WARNING 2024-12-30 00:51:02,953 [pN:job_handler_0,p:8,tN:MainThread] Conda not installed and auto-installation disabled. +galaxy.tool_util.deps.containers DEBUG 2024-12-30 00:51:02,954 [pN:job_handler_0,p:8,tN:MainThread] Loading container resolution config from file '/galaxy/server/config/container_resolvers_conf.xml' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,975 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'ucsc_bam' for datatype 'bam', inherit=False. +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,976 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'ensembl_bam' for datatype 'bam', inherit=False. +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,976 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igv_bam' for datatype 'bam', inherit=False. +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,977 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igb_bam' for datatype 'bam', inherit=False. +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,977 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'iobio_bam' for datatype 'bam', inherit=False. +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,977 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igb_bed' for datatype 'bed', inherit=False. +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,977 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igb_bedgraph' for datatype 'bedgraph', inherit=False. +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,979 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'ucsc_bigbed' for datatype 'bigbed', inherit=False. +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,979 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igb_bb' for datatype 'bigbed', inherit=False. +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,980 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'ucsc_bigwig' for datatype 'bigwig', inherit=False. +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,981 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igb_bigwig' for datatype 'bigwig', inherit=False. +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,981 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igv_bigwig' for datatype 'bigwig', inherit=False. +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,982 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'intermine_simple' for datatype 'intermine_tabular', inherit=False. +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,982 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igv_fasta' for datatype 'fasta', inherit=True. +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,983 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'ensembl_gff' for datatype 'gff', inherit=True. +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,984 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igv_gff' for datatype 'gff', inherit=True. +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,984 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igb_gtf' for datatype 'gtf', inherit=False. +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,985 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'ensembl_interval' for datatype 'interval', inherit=True. +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,986 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'gbrowse_interval_as_bed' for datatype 'interval', inherit=True. +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,986 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'rviewer_interval' for datatype 'interval', inherit=True. +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,987 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igv_interval_as_bed' for datatype 'interval', inherit=True. +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,987 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'avivator' for datatype 'ome.tiff', inherit=False. +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,987 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'q2view' for datatype 'qza', inherit=False. +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,988 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'q2view' for datatype 'qzv', inherit=False. +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,989 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'ucsc_maf_customtrack' for datatype 'mafcustomtrack', inherit=False. +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,991 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'ucsc_vcf' for datatype 'vcf', inherit=False. +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,991 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igv_vcf' for datatype 'vcf', inherit=False. +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,992 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'rviewer_vcf' for datatype 'vcf', inherit=True. +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,992 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'iobio_vcf' for datatype 'vcf', inherit=False. +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,992 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igb_wig' for datatype 'wig', inherit=False. +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,993 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igv_vcf' for datatype 'vcf_bgzip', inherit=False. +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,994 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igv_genbank' for datatype 'genbank', inherit=False. +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,994 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'biom_simple' for datatype 'biom1', inherit=False. +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,994 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'icn3d_simple' for datatype 'sdf', inherit=False. +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,995 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'icn3d_simple' for datatype 'mol2', inherit=False. +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,995 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'icn3d_simple' for datatype 'pdb', inherit=False. +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,995 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'ucsc_trackhub' for datatype 'trackhub', inherit=False. +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,995 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bed' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,995 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,995 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bed' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,995 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bed' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,995 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bedgraph' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,995 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedgraph' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,995 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bedgraph' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,996 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bedgraph' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,996 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bedstrict' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,996 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedstrict' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,996 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bedstrict' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,996 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bedstrict' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,996 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bed6' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,996 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed6' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,996 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bed6' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,996 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bed6' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,996 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bed12' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,996 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed12' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,996 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bed12' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,996 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bed12' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,996 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'probed' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,996 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'probed' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,996 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'probed' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,996 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'probed' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,996 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'chrint' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,996 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'chrint' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,997 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'chrint' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,997 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'chrint' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,997 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_fasta' to datatype 'fasta.gz' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,997 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_gff' to datatype 'gff3' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,997 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_gff' to datatype 'gff3' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,997 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_gff' to datatype 'gff3.gz' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,997 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_gff' to datatype 'gff3.gz' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,997 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_gff' to datatype 'gff3.bz2' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,997 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_gff' to datatype 'gff3.bz2' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,997 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_gff' to datatype 'gtf' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,997 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_gff' to datatype 'gtf' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,998 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'encodepeak' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,998 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'encodepeak' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,998 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'encodepeak' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,998 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'encodepeak' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,998 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_fasta' to datatype 'sequences' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,999 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'interval_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,999 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'interval_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,999 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'interval_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,999 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'interval_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,999 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'juicer_medium_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,999 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'juicer_medium_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,999 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'juicer_medium_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,999 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'juicer_medium_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,999 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bed_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,999 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,999 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bed_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,999 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bed_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,999 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'gff_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,999 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'gff_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,999 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'gff_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:02,999 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'gff_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,000 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_fasta' to datatype 'mothur.align' +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,002 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,003 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,004 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,005 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,005 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,006 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,007 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_Bam_Bai_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,007 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,008 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,009 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,010 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bam_to_coodinate_sorted_bam +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,010 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,011 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_cram_to_bam_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,012 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bed_to_gff_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,013 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,014 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,015 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,016 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bed_to_fli_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,017 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bedgraph_to_bigwig +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,017 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_len_to_linecount +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,018 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_parquet_to_csv +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,020 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: bigwigtowig +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,021 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,022 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,023 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,023 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: csv_to_tabular +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,024 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: tabular_to_csv +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,025 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_fasta_to_tabular +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,025 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_fasta_to_bowtie_base_index +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,026 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_fasta_to_bowtie_color_index +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,026 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_fasta_to_2bit +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,027 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_fasta_to_len +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,027 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_fasta_to_fai +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,028 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,029 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,030 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,030 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,031 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,031 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,032 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,034 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,035 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,036 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,037 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,038 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,038 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,039 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,040 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,041 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,041 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,042 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,044 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,045 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,046 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,047 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,047 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gff_to_bed_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,048 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gff_to_interval_index_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,049 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,049 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gff_to_fli_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,050 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,051 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,052 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,053 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,054 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,054 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gff_to_interval_index_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,055 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,056 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bed_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,057 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bedstrict_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,058 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bed6_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,059 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bed12_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,060 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,061 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,062 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,062 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_picard_interval_list_to_bed6 +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,063 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_tar_to_directory +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,064 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,065 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,065 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,066 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,067 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,067 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,068 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_maf_to_fasta_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,069 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_maf_to_interval_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,070 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,071 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,072 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,073 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,074 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,074 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_sam_to_unsorted_bam +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,075 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bam_to_coodinate_sorted_bam +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,076 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,076 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_sam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,077 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: tabular_to_dbnsfp +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,078 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: tabular_to_csv +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,079 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,080 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,081 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,082 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,082 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,083 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,084 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,085 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bcf_uncompressed_to_bcf +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,086 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bcf_uncompressed_to_bcf +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,087 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_wig_to_bigwig +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,088 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_wiggle_to_interval_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,088 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,089 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,090 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: lped2fpedconvert +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,091 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: lped2pbedconvert +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,091 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: pbed2lpedconvert +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,092 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: pbed2ldindepconvert +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,093 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,094 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,095 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_biom +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,096 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_biom +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,097 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,098 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,099 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,100 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_SMILES_to_MOL +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,102 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,103 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_smiles_to_smiles +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,104 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,105 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,106 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,107 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,108 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,109 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,110 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_inchi_to_mol +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,112 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,114 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,115 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,117 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,118 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,120 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,121 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,123 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,125 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,126 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,127 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_mol2_to_mol +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,128 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,129 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_cml_to_smiles +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,130 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,131 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,132 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,133 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_Pdb_to_Gro_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,134 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,135 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,136 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,136 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,137 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,138 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,139 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_Gro_to_Pdb_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,139 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_ref_to_seq_taxomony +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,140 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_neostorezip_to_neostore +galaxy.datatypes.registry DEBUG 2024-12-30 00:51:03,141 [pN:job_handler_0,p:8,tN:MainThread] Loaded external metadata tool: __SET_METADATA__ +galaxy.tools.special_tools DEBUG 2024-12-30 00:51:03,143 [pN:job_handler_0,p:8,tN:MainThread] Loaded history export tool: __EXPORT_HISTORY__ +galaxy.tools.special_tools DEBUG 2024-12-30 00:51:03,143 [pN:job_handler_0,p:8,tN:MainThread] Loaded history export to uri tool: __EXPORT_HISTORY_TO_URI__ +galaxy.tools.special_tools DEBUG 2024-12-30 00:51:03,144 [pN:job_handler_0,p:8,tN:MainThread] Loaded history import tool: __IMPORT_HISTORY__ +galaxy.tools.special_tools DEBUG 2024-12-30 00:51:03,145 [pN:job_handler_0,p:8,tN:MainThread] Loaded data fetch tool: __DATA_FETCH__ +sqlitedict DEBUG 2024-12-30 00:51:03,148 [pN:job_handler_0,p:8,tN:MainThread] closing SqliteDict(/cvmfs/cloud.galaxyproject.org/var/tool_cache/cache.sqlite) +sqlitedict.SqliteMultithread DEBUG 2024-12-30 00:51:03,148 [pN:job_handler_0,p:8,tN:Thread-2] received: --close--, send: --no more-- +sqlitedict DEBUG 2024-12-30 00:51:03,149 [pN:job_handler_0,p:8,tN:MainThread] opening Sqlite table 'unnamed' in '/cvmfs/cloud.galaxyproject.org/var/tool_cache/cache.sqlite' +galaxy.visualization.plugins.registry INFO 2024-12-30 00:51:03,154 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: PCA_3Dplot +galaxy.visualization.plugins.registry INFO 2024-12-30 00:51:03,154 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: aequatus +galaxy.visualization.plugins.registry INFO 2024-12-30 00:51:03,155 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: annotate_image +galaxy.visualization.plugins.config_parser INFO 2024-12-30 00:51:03,155 [pN:job_handler_0,p:8,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2024-12-30 00:51:03,156 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: chiraviz +galaxy.visualization.plugins.config_parser INFO 2024-12-30 00:51:03,156 [pN:job_handler_0,p:8,tN:MainThread] Visualizations plugin disabled: Circster. Skipping... +galaxy.visualization.plugins.config_parser INFO 2024-12-30 00:51:03,157 [pN:job_handler_0,p:8,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2024-12-30 00:51:03,157 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: csg +galaxy.visualization.plugins.registry INFO 2024-12-30 00:51:03,158 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: cytoscape +galaxy.visualization.plugins.registry INFO 2024-12-30 00:51:03,158 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: drawrna +galaxy.visualization.plugins.registry INFO 2024-12-30 00:51:03,159 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: editor +galaxy.visualization.plugins.registry INFO 2024-12-30 00:51:03,160 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: example +galaxy.visualization.plugins.config_parser INFO 2024-12-30 00:51:03,160 [pN:job_handler_0,p:8,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2024-12-30 00:51:03,160 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: fits_image_viewer +galaxy.visualization.plugins.config_parser INFO 2024-12-30 00:51:03,161 [pN:job_handler_0,p:8,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2024-12-30 00:51:03,161 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: graphviz +galaxy.visualization.plugins.registry INFO 2024-12-30 00:51:03,162 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: h5web +galaxy.visualization.plugins.registry INFO 2024-12-30 00:51:03,164 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: heatmap_cluster +galaxy.visualization.plugins.registry INFO 2024-12-30 00:51:03,166 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: heatmap_default +galaxy.visualization.plugins.config_parser INFO 2024-12-30 00:51:03,166 [pN:job_handler_0,p:8,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2024-12-30 00:51:03,166 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: hivtrace +galaxy.visualization.plugins.config_parser INFO 2024-12-30 00:51:03,167 [pN:job_handler_0,p:8,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2024-12-30 00:51:03,167 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: hyphyvision +galaxy.visualization.plugins.registry INFO 2024-12-30 00:51:03,169 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_bar +galaxy.visualization.plugins.registry INFO 2024-12-30 00:51:03,170 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_box +galaxy.visualization.plugins.registry INFO 2024-12-30 00:51:03,172 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_histogram +galaxy.visualization.plugins.registry INFO 2024-12-30 00:51:03,174 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_line +galaxy.visualization.plugins.registry INFO 2024-12-30 00:51:03,175 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_scatter +galaxy.visualization.plugins.config_parser INFO 2024-12-30 00:51:03,176 [pN:job_handler_0,p:8,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2024-12-30 00:51:03,176 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: audio_player +galaxy.visualization.plugins.config_parser INFO 2024-12-30 00:51:03,177 [pN:job_handler_0,p:8,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2024-12-30 00:51:03,177 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: video_player +galaxy.visualization.plugins.registry INFO 2024-12-30 00:51:03,177 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: msa +galaxy.visualization.plugins.config_parser INFO 2024-12-30 00:51:03,178 [pN:job_handler_0,p:8,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2024-12-30 00:51:03,178 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: mvpapp +galaxy.visualization.plugins.registry INFO 2024-12-30 00:51:03,179 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: ngl +galaxy.visualization.plugins.registry INFO 2024-12-30 00:51:03,180 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nora +galaxy.visualization.plugins.registry INFO 2024-12-30 00:51:03,182 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_bar +galaxy.visualization.plugins.registry INFO 2024-12-30 00:51:03,183 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_bar_stacked +galaxy.visualization.plugins.registry INFO 2024-12-30 00:51:03,185 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_histogram +galaxy.visualization.plugins.registry INFO 2024-12-30 00:51:03,186 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_histogram_discrete +galaxy.visualization.plugins.registry INFO 2024-12-30 00:51:03,188 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_horizontal +galaxy.visualization.plugins.registry INFO 2024-12-30 00:51:03,190 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_horizontal_stacked +galaxy.visualization.plugins.registry INFO 2024-12-30 00:51:03,192 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_line +galaxy.visualization.plugins.registry INFO 2024-12-30 00:51:03,193 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_line_focus +galaxy.visualization.plugins.registry INFO 2024-12-30 00:51:03,194 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_pie +galaxy.visualization.plugins.registry INFO 2024-12-30 00:51:03,196 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_scatter +galaxy.visualization.plugins.registry INFO 2024-12-30 00:51:03,199 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_stackedarea +galaxy.visualization.plugins.registry INFO 2024-12-30 00:51:03,201 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_stackedarea_full +galaxy.visualization.plugins.registry INFO 2024-12-30 00:51:03,203 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_stackedarea_stream +galaxy.visualization.plugins.registry INFO 2024-12-30 00:51:03,203 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: openlayers +galaxy.visualization.plugins.registry INFO 2024-12-30 00:51:03,204 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: openseadragon +galaxy.visualization.plugins.registry INFO 2024-12-30 00:51:03,204 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: phylocanvas +galaxy.visualization.plugins.registry INFO 2024-12-30 00:51:03,205 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: phyloviz +galaxy.visualization.plugins.registry INFO 2024-12-30 00:51:03,206 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: pv +galaxy.visualization.plugins.registry INFO 2024-12-30 00:51:03,206 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: scatterplot +galaxy.visualization.plugins.config_parser INFO 2024-12-30 00:51:03,207 [pN:job_handler_0,p:8,tN:MainThread] Visualizations plugin disabled: Sweepster. Skipping... +galaxy.visualization.plugins.registry INFO 2024-12-30 00:51:03,207 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: trackster +galaxy.visualization.plugins.registry INFO 2024-12-30 00:51:03,208 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: ts_visjs +galaxy.visualization.plugins.config_parser INFO 2024-12-30 00:51:03,208 [pN:job_handler_0,p:8,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2024-12-30 00:51:03,208 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: unipept +galaxy.visualization.plugins.registry INFO 2024-12-30 00:51:03,209 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: venn +galaxy.tours._impl INFO 2024-12-30 00:51:03,222 [pN:job_handler_0,p:8,tN:MainThread] Loaded tour 'core.deferred' +galaxy.tours._impl INFO 2024-12-30 00:51:03,231 [pN:job_handler_0,p:8,tN:MainThread] Loaded tour 'core.history' +galaxy.tours._impl INFO 2024-12-30 00:51:03,238 [pN:job_handler_0,p:8,tN:MainThread] Loaded tour 'core.windows' +galaxy.tours._impl INFO 2024-12-30 00:51:03,254 [pN:job_handler_0,p:8,tN:MainThread] Loaded tour 'core.galaxy_ui' +galaxy.jobs.manager DEBUG 2024-12-30 00:51:03,259 [pN:job_handler_0,p:8,tN:MainThread] Initializing job handler +galaxy.jobs INFO 2024-12-30 00:51:03,259 [pN:job_handler_0,p:8,tN:MainThread] Handler 'job_handler_0' will load all configured runner plugins +galaxy.jobs.runners DEBUG 2024-12-30 00:51:03,260 [pN:job_handler_0,p:8,tN:MainThread] Loading KubernetesRunner with params: {'k8s_cleanup_job': 'onsuccess', 'k8s_fs_group_id': '101', 'k8s_galaxy_instance_id': 'prod-24-12-30-00-37-1-galaxy', 'k8s_interactivetools_ingress_annotations': '\nnginx.ingress.kubernetes.io/auth-tls-pass-certificate-to-upstream: "true"\nnginx.ingress.kubernetes.io/auth-tls-secret: \'prod-24-12-30-00-37-1/ca-secret\'\nnginx.ingress.kubernetes.io/auth-tls-verify-client: "on"\nnginx.ingress.kubernetes.io/auth-tls-verify-depth: "1"\nnginx.ingress.kubernetes.io/proxy-body-size: 10G\nnginx.ingress.kubernetes.io/proxy-read-timeout: "600"\nnginx.ingress.kubernetes.io/ssl-redirect: "true"\n', 'k8s_interactivetools_use_ssl': True, 'k8s_job_ttl_secs_after_finished': 90, 'k8s_namespace': 'prod-24-12-30-00-37-1', 'k8s_node_selector': 'cloud.google.com/gke-nodepool: default-pool', 'k8s_persistent_volume_claims': 'prod-24-12-30-00-37-1-galaxy-galaxy-pvc:/galaxy/server/database,prod-24-12-30-00-37-1-galaxy-refdata-gxy-pvc/data.galaxyproject.org:/cvmfs/data.galaxyproject.org,prod-24-12-30-00-37-1-galaxy-galaxy-pvc/cvmfsclone:/cvmfs/cloud.galaxyproject.org', 'k8s_pod_priority_class': 'prod-24-12-30-00-37-1-priority-class', 'k8s_pull_policy': 'IfNotPresent', 'k8s_supplemental_group_id': '101', 'k8s_use_service_account': True} +galaxy.jobs.runners.state_handler_factory DEBUG 2024-12-30 00:51:03,261 [pN:job_handler_0,p:8,tN:MainThread] Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit +galaxy.jobs.runners.util.pykube_util ERROR 2024-12-30 00:51:03,262 [pN:job_handler_0,p:8,tN:MainThread] Galaxy instance [prod-24-12-30-00-37-1-galaxy] is either too long (>20 characters) or it includes non DNS acceptable characters, ignoring it. +galaxy.jobs DEBUG 2024-12-30 00:51:03,262 [pN:job_handler_0,p:8,tN:MainThread] Loaded job runner 'galaxy.jobs.runners.kubernetes:KubernetesJobRunner' as 'k8s' +galaxy.jobs.runners.state_handler_factory DEBUG 2024-12-30 00:51:03,263 [pN:job_handler_0,p:8,tN:MainThread] Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit +galaxy.jobs DEBUG 2024-12-30 00:51:03,263 [pN:job_handler_0,p:8,tN:MainThread] Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local' +galaxy.jobs.handler DEBUG 2024-12-30 00:51:03,263 [pN:job_handler_0,p:8,tN:MainThread] Loaded job runners plugins: k8s:local +galaxy.jobs.runners DEBUG 2024-12-30 00:51:03,269 [pN:job_handler_0,p:8,tN:MainThread] Starting 4 KubernetesRunner workers +galaxy.jobs.runners DEBUG 2024-12-30 00:51:03,271 [pN:job_handler_0,p:8,tN:MainThread] Starting 4 LocalRunner workers +galaxy.jobs.handler DEBUG 2024-12-30 00:51:03,272 [pN:job_handler_0,p:8,tN:MainThread] Handler queue starting for jobs assigned to handler: job_handler_0 +galaxy.jobs.handler INFO 2024-12-30 00:51:03,285 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Handler job grabber initialized with 'db-skip-locked' assignment method for handler 'job_handler_0', tag(s): _default_ +galaxy.jobs.handler INFO 2024-12-30 00:51:03,287 [pN:job_handler_0,p:8,tN:MainThread] job handler queue started +galaxy.jobs.handler INFO 2024-12-30 00:51:03,288 [pN:job_handler_0,p:8,tN:MainThread] job handler stop queue started +galaxy.web_stack.handlers DEBUG 2024-12-30 00:51:03,307 [pN:job_handler_0,p:8,tN:MainThread] Read definition for handler 'workflow_scheduler0' +galaxy.web_stack.handlers DEBUG 2024-12-30 00:51:03,307 [pN:job_handler_0,p:8,tN:MainThread] Read definition for handler 'workflow_scheduler0' +galaxy.web_stack.handlers DEBUG 2024-12-30 00:51:03,307 [pN:job_handler_0,p:8,tN:MainThread] default set to child with id or tag 'schedulers' +galaxy.web_stack.handlers INFO 2024-12-30 00:51:03,322 [pN:job_handler_0,p:8,tN:MainThread] WorkflowSchedulingManager: No job handler assignment method is set, defaulting to 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED', set the `assign_with` attribute on to override the default +galaxy.workflow.scheduling_manager INFO 2024-12-30 00:51:03,322 [pN:job_handler_0,p:8,tN:MainThread] Workflow scheduling handler assignment method(s): db-skip-locked +galaxy.workflow.scheduling_manager INFO 2024-12-30 00:51:03,322 [pN:job_handler_0,p:8,tN:MainThread] Tag [schedulers] handlers: workflow_scheduler0 +galaxy.web_stack.handlers DEBUG 2024-12-30 00:51:03,322 [pN:job_handler_0,p:8,tN:MainThread] default set to child with id or tag 'schedulers' +galaxy.queue_worker INFO 2024-12-30 00:51:03,334 [pN:job_handler_0,p:8,tN:MainThread] Binding and starting galaxy control worker for job_handler_0 +galaxy.queue_worker INFO 2024-12-30 00:51:03,336 [pN:job_handler_0,p:8,tN:MainThread] Queuing async task rebuild_toolbox_search_index for job_handler_0. +galaxy.model.database_heartbeat DEBUG 2024-12-30 00:51:03,352 [pN:job_handler_0,p:8,tN:database_heartbeart_job_handler_0.thread] job_handler_0 is config watcher +galaxy.app INFO 2024-12-30 00:51:03,366 [pN:job_handler_0,p:8,tN:MainThread] Galaxy app startup finished (18445.781 ms) +galaxy.web_stack INFO 2024-12-30 00:51:03,367 [pN:job_handler_0,p:8,tN:MainThread] Galaxy server instance 'job_handler_0' is running +galaxy.queue_worker INFO 2024-12-30 00:51:03,377 [pN:job_handler_0,p:8,tN:Thread-1] Instance 'job_handler_0' received 'rebuild_toolbox_search_index' task, executing now. +galaxy.queue_worker DEBUG 2024-12-30 00:51:03,377 [pN:job_handler_0,p:8,tN:Thread-1] App is not a webapp, not building a search index +galaxy.model.database_heartbeat DEBUG 2024-12-30 00:52:03,364 [pN:job_handler_0,p:8,tN:database_heartbeart_job_handler_0.thread] job_handler_0 is not config watcher +galaxy.jobs.handler DEBUG 2024-12-30 00:53:26,403 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 1 +tpv.rules.gateway INFO 2024-12-30 00:53:26,437 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] loading tpv rules from: ['https://raw.githubusercontent.com/galaxyproject/tpv-shared-database/main/tools.yml', 'lib/galaxy/jobs/rules/tpv_rules_local.yml', 'https://gist.githubusercontent.com/afgane/68d1dbbe0af2468ba347dc74b6d3f7fa/raw/20edda50161bdcb74ff38935e7f76d79bfdaf303/tvp_rules_tests.yml'] +tpv.rules.gateway INFO 2024-12-30 00:53:26,915 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Watching for changes in file: lib/galaxy/jobs/rules/tpv_rules_local.yml +tpv.core.entities DEBUG 2024-12-30 00:53:27,015 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 00:53:27,016 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (1) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 00:53:27,032 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (1) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 00:53:27,055 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (1) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 00:53:27,100 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (1) Working directory for job is: /galaxy/server/database/jobs_directory/000/1 +galaxy.jobs.runners DEBUG 2024-12-30 00:53:27,110 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [1] queued (78.080 ms) +galaxy.jobs.handler INFO 2024-12-30 00:53:27,117 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (1) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 00:53:27,122 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 1 +galaxy.jobs DEBUG 2024-12-30 00:53:27,282 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [1] prepared (141.068 ms) +galaxy.jobs.command_factory INFO 2024-12-30 00:53:27,310 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/1/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/1/registry.xml' '/galaxy/server/database/jobs_directory/000/1/upload_params.json' '1:/galaxy/server/database/objects/f/8/d/dataset_f8d2e3ae-0730-4f57-8e66-88b71398734c_files:/galaxy/server/database/objects/f/8/d/dataset_f8d2e3ae-0730-4f57-8e66-88b71398734c.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 00:53:27,329 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (1) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/1/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/1/galaxy_1.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 00:53:47,040 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 1: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 00:53:51,886 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 1 finished +galaxy.model.metadata DEBUG 2024-12-30 00:53:51,950 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 1 +galaxy.jobs INFO 2024-12-30 00:53:51,995 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 1 in /galaxy/server/database/jobs_directory/000/1 +galaxy.jobs DEBUG 2024-12-30 00:53:52,050 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 1 executed (134.650 ms) +galaxy.jobs.handler DEBUG 2024-12-30 00:53:52,683 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 2 +tpv.core.entities DEBUG 2024-12-30 00:53:52,729 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 00:53:52,729 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (2) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 00:53:52,736 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (2) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 00:53:52,753 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (2) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 00:53:52,778 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (2) Working directory for job is: /galaxy/server/database/jobs_directory/000/2 +galaxy.jobs.runners DEBUG 2024-12-30 00:53:52,789 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [2] queued (52.769 ms) +galaxy.jobs.handler INFO 2024-12-30 00:53:52,793 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (2) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 00:53:52,796 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 2 +galaxy.jobs DEBUG 2024-12-30 00:53:52,883 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [2] prepared (69.780 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 00:53:52,883 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 00:53:52,884 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5+galaxy2: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.mulled.util DEBUG 2024-12-30 00:53:52,886 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Querying https://quay.io/api/v1/repository for repos within biocontainers +galaxy.queue_worker INFO 2024-12-30 00:54:16,349 [pN:job_handler_0,p:8,tN:Thread-1] Instance 'job_handler_0' received 'reload_toolbox' task, executing now. +galaxy.queue_worker DEBUG 2024-12-30 00:54:16,349 [pN:job_handler_0,p:8,tN:Thread-1] Executing toolbox reload on 'job_handler_0' +galaxy.util WARNING 2024-12-30 00:54:16,394 [pN:job_handler_0,p:8,tN:Thread-1] directory not found: /galaxy/server/lib/galaxy/util/../../../config/plugins/activities +galaxy.tools WARNING 2024-12-30 00:54:16,402 [pN:job_handler_0,p:8,tN:Thread-1] The default shed tool config file (/galaxy/server/config/mutable/editable_shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2024-12-30 00:54:16,402 [pN:job_handler_0,p:8,tN:Thread-1] Parsing the tool configuration /galaxy/server/config/tool_conf.xml +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,403 [pN:job_handler_0,p:8,tN:Thread-1] Tool path for tool configuration /galaxy/server/config/tool_conf.xml is None +galaxy.tool_util.toolbox.base ERROR 2024-12-30 00:54:16,404 [pN:job_handler_0,p:8,tN:Thread-1] Error reading tool configuration file from path 'genomespace/genomespace_importer.xml': [Errno 2] No such file or directory +galaxy.tool_util.toolbox.base ERROR 2024-12-30 00:54:16,404 [pN:job_handler_0,p:8,tN:Thread-1] Error reading tool configuration file from path 'genomespace/genomespace_push.xml': [Errno 2] No such file or directory +galaxy.tool_util.toolbox.base ERROR 2024-12-30 00:54:16,406 [pN:job_handler_0,p:8,tN:Thread-1] Error reading tool configuration file from path 'evolution/codingSnps.xml': [Errno 2] No such file or directory +galaxy.tool_util.toolbox.base ERROR 2024-12-30 00:54:16,406 [pN:job_handler_0,p:8,tN:Thread-1] Error reading tool configuration file from path 'evolution/add_scores.xml': [Errno 2] No such file or directory +galaxy.tool_util.toolbox.base ERROR 2024-12-30 00:54:16,408 [pN:job_handler_0,p:8,tN:Thread-1] Error reading tool from path: phenotype_association/sift.xml +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/tool_util/toolbox/base.py", line 865, in _load_tool_tag_set + tool = self.load_tool(concrete_path, use_cached=False, tool_cache_data_dir=tool_cache_data_dir) + File "/galaxy/server/lib/galaxy/tool_util/toolbox/base.py", line 1092, in load_tool + tool = self.create_tool( + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 530, in create_tool + return self._create_tool_from_source(tool_source, config_file=config_file, **kwds) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 546, in _create_tool_from_source + return create_tool_from_source(self.app, tool_source, **kwds) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 340, in create_tool_from_source + tool = ToolClass(config_file, tool_source, app, **kwds) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 802, in __init__ + raise e + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 799, in __init__ + self.parse(tool_source, guid=guid, dynamic=dynamic) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1123, in parse + self.parse_inputs(self.tool_source) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1414, in parse_inputs + inputs = self.parse_input_elem(page_source, enctypes) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1609, in parse_input_elem + param = self.parse_param_elem(input_source, enctypes, context) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1622, in parse_param_elem + param = ToolParameter.build(self, input_source) + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 319, in build + return parameter_types[param_type](tool, input_source) + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 2044, in __init__ + super().__init__(tool, input_source, trans) + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 1832, in __init__ + super().__init__(tool, input_source) + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 178, in __init__ + self.validators.append(validation.Validator.from_element(self, elem)) + File "/galaxy/server/lib/galaxy/tools/parameters/validation.py", line 50, in from_element + return validator_types[_type].from_element(param, elem) + File "/galaxy/server/lib/galaxy/tools/parameters/validation.py", line 727, in from_element + assert os.path.exists(filename), f"File {filename} specified by the 'filename' attribute not found" +AssertionError: File /galaxy/server/database/tool-data/sift_db.loc specified by the 'filename' attribute not found +galaxy.tools WARNING 2024-12-30 00:54:16,409 [pN:job_handler_0,p:8,tN:Thread-1] The default shed tool config file (/galaxy/server/config/mutable/editable_shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2024-12-30 00:54:16,409 [pN:job_handler_0,p:8,tN:Thread-1] Parsing the tool configuration /cvmfs/cloud.galaxyproject.org/config/shed_tool_conf.xml +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,430 [pN:job_handler_0,p:8,tN:Thread-1] Tool path for shed tool configuration /cvmfs/cloud.galaxyproject.org/config/shed_tool_conf.xml is /cvmfs/cloud.galaxyproject.org/tools +galaxy.tool_util.toolbox.base WARNING 2024-12-30 00:54:16,481 [pN:job_handler_0,p:8,tN:Thread-1] Attempted to load tool shed tool, but the repository with name 'gfastats' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +sqlitedict DEBUG 2024-12-30 00:54:16,481 [pN:job_handler_0,p:8,tN:Thread-1] opening Sqlite table 'unnamed' in '/cvmfs/cloud.galaxyproject.org/var/tool_cache/cache.sqlite' +galaxy.tool_util.toolbox.base ERROR 2024-12-30 00:54:16,498 [pN:job_handler_0,p:8,tN:Thread-1] Error reading tool from path: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/f4a3eff8ab85/gfastats/gfastats.xml +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/tool_util/toolbox/base.py", line 857, in _load_tool_tag_set + tool = self.load_tool( + File "/galaxy/server/lib/galaxy/tool_util/toolbox/base.py", line 1092, in load_tool + tool = self.create_tool( + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 530, in create_tool + return self._create_tool_from_source(tool_source, config_file=config_file, **kwds) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 546, in _create_tool_from_source + return create_tool_from_source(self.app, tool_source, **kwds) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 340, in create_tool_from_source + tool = ToolClass(config_file, tool_source, app, **kwds) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 802, in __init__ + raise e + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 799, in __init__ + self.parse(tool_source, guid=guid, dynamic=dynamic) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1000, in parse + raise Exception(message) +Exception: The tool [toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0] targets version 23.2 of Galaxy, you should upgrade Galaxy to ensure proper functioning of this tool. +galaxy.tools WARNING 2024-12-30 00:54:16,535 [pN:job_handler_0,p:8,tN:Thread-1] The default shed tool config file (/galaxy/server/config/mutable/editable_shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2024-12-30 00:54:16,535 [pN:job_handler_0,p:8,tN:Thread-1] Parsing the tool configuration /galaxy/server/config/mutable/editable_shed_tool_conf.xml +galaxy.tool_util.toolbox.base INFO 2024-12-30 00:54:16,535 [pN:job_handler_0,p:8,tN:Thread-1] Shed-enabled tool configuration file does not exist, but will be created on demand: /galaxy/server/config/mutable/editable_shed_tool_conf.xml +galaxy.tools WARNING 2024-12-30 00:54:16,535 [pN:job_handler_0,p:8,tN:Thread-1] The default shed tool config file (/galaxy/server/config/mutable/editable_shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2024-12-30 00:54:16,535 [pN:job_handler_0,p:8,tN:Thread-1] Parsing the tool configuration /galaxy/server/config/migrated_tools_conf.xml +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,535 [pN:job_handler_0,p:8,tN:Thread-1] Tool path for shed tool configuration /galaxy/server/config/migrated_tools_conf.xml is /galaxy/server/database/shed_tools +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,535 [pN:job_handler_0,p:8,tN:Thread-1] Reading tools from config files finished (133.390 ms) +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,536 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Get Data +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,536 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,536 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,536 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,536 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.5+galaxy0, version: 0.2.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,536 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy1, version: 2.11.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,536 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,537 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,537 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,537 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,537 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,537 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0, version: 0.2.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,537 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: upload1, version: 1.1.7 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,537 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,537 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,537 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,538 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,538 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: intermine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,538 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: flymine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,538 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,538 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: mousemine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,538 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ratmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,538 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: yeastmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,538 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,538 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wormbase, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,538 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,539 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: eupathdb, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,539 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hbvar, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,539 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Send Data +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,539 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: export_remote, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,539 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Send Data +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,539 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Expression Tools +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,539 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,539 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,539 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0, version: 0.2.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,539 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: param_value_from_file, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,539 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Collection Operations +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,539 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,540 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,540 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0, version: 0.5.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,540 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0, version: 5.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,540 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2, version: 0.5.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,540 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0, version: 0.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,540 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,540 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,540 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,540 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_EMPTY_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,540 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,540 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,541 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,541 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,541 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,541 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __TAG_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,541 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __APPLY_RULES__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,541 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __BUILD_LIST__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,541 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __EXTRACT_DATASET__, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,541 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Text Manipulation +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,541 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/diff/diff/3.7+galaxy0, version: 3.7+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,541 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,541 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,542 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6, version: 1.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,542 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,542 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.12.0, version: 3.12.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,542 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,542 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,542 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,542 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/0.9.2, version: 0.9.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,542 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.4, version: 0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,542 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0, version: 0.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,543 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,543 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,543 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,543 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,543 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,543 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,543 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,543 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0, version: 0.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,543 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,544 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,544 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,544 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,544 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,544 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,544 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,544 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,544 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,544 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,545 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,545 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_melt/melt/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,545 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_cast/cast/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,545 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jq/jq/1.0, version: 1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,545 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gff3_rebase/gff3.rebase/1.2, version: 1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,545 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,545 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_order_header_sort/column_order_header_sort/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,545 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,545 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: addValue, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,545 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: cat1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,546 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Condense characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,546 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,546 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,546 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: createInterval, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,546 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Cut1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,546 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,546 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Paste1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,546 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,546 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: random_lines1, version: 2.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,546 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Show beginning1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,546 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Show tail1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,546 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: trimmer, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,547 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,547 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: secure_hash_message_digest, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,547 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0, version: 3.3.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,547 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1, version: 3.14.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,547 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0, version: 2.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,547 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0, version: 1.2.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,547 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4, version: 1.1.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,547 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1, version: 0.1.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,548 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0+galaxy0, version: 1.1.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,548 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.16.0+galaxy1, version: 3.16.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,548 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,548 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.3.1, version: 3.3.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,548 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2, version: 3.3.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,548 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1, version: 2.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,548 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/3.2.1, version: 3.2.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,548 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.18.0+galaxy0, version: 3.18.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,549 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3, version: 1.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,549 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3, version: 1.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,549 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.6, version: 0.6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,549 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,549 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,549 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,549 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,549 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,549 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,549 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,549 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/nl/9.3+galaxy1, version: 9.3+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,550 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,550 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,550 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,550 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,550 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,550 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,550 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,550 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,550 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,551 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,551 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy2, version: 9.3+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,551 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,551 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/1.0, version: 1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,551 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Filter and Sort +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,551 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Filter1, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,551 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: sort1, version: 1.2.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,551 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Grep1, version: 1.0.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,551 [pN:job_handler_0,p:8,tN:Thread-1] Loaded label: GFF +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,551 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,552 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,552 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,552 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,552 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Join, Subtract and Group +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,552 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: join1, version: 2.1.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,552 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: comp1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,552 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Grouping1, version: 2.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,552 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Datamash +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,552 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,552 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,552 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,552 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,553 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,553 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy1, version: 1.8+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,553 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,554 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: FASTA/FASTQ +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,554 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.8, version: 1.16.8 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,557 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,558 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,558 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,558 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,558 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,558 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0, version: 1.2.0.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,558 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/flash/flash/1.2.11.4, version: 1.2.11.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,558 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.3, version: 0.6.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,558 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,558 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,559 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1, version: 4.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,559 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,560 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,560 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.7, version: 0.2.7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,560 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/length_and_gc_content/0.1.2, version: 0.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,560 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1, version: 4.9+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,561 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.7+galaxy0, version: 0.6.7+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,561 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5+galaxy2, version: 1.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,561 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5+galaxy2, version: 1.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,561 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.5+galaxy2, version: 1.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,561 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.4, version: 1.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,561 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.5+galaxy2, version: 1.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,561 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.5+galaxy1, version: 1.1.5+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,561 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.5+galaxy1, version: 1.1.5+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,561 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.9, version: 0.2.9 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,562 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: FASTQ Quality Control +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,562 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,562 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0, version: 0.20.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,562 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1, version: 0.72+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,563 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1, version: 0.38.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,563 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0, version: 1.11+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,563 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0, version: 0.73+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,563 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1, version: 1.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,563 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0, version: 0.23.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,563 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0, version: 1.24.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,564 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1, version: 0.23.4+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,564 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1, version: 0.74+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,564 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy2, version: 0.23.4+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,564 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.39+galaxy2, version: 0.39+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,564 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: SAM/BAM +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,565 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/pileup_interval/pileup_interval/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,565 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3, version: 2.2.2d+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,565 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3, version: 1.9+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,565 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0.1+galaxy1, version: 2.0.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,565 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,565 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.4.0.0, version: 2.4.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,565 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamtools_split/2.4.0, version: 2.4.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,565 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam2interval/sam2interval/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,566 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_multi_bamqc/qualimap_multi_bamqc/2.2.2d, version: 2.2.2d into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,566 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,566 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,566 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2, version: 1.9+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,566 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,566 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,566 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,566 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2, version: 2.0.2+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,566 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,566 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,567 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,567 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,567 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8+galaxy1, version: 1.8+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,567 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,567 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,567 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.4, version: 2.1.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,567 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,567 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1, version: 2.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,568 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,568 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,568 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,568 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/boris/filter_on_md/MDtag_filter/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,568 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.2.0, version: 1.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,568 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.2, version: 2.0.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,568 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,568 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,568 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,569 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy1, version: 2.5.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,569 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,569 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lldelisle/revertr2orientationinbam/revertR2orientationInBam/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,569 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.3+galaxy0, version: 2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,569 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3, version: 1.20+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,569 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0.3, version: 2.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,570 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.2+galaxy2, version: 2.5.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,570 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamtools_split/2.5.2+galaxy0, version: 2.5.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,570 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_multi_bamqc/qualimap_multi_bamqc/2.3+galaxy0, version: 2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,570 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,570 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,570 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,570 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,570 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.15.1+galaxy2, version: 1.15.1+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,570 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,571 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,571 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,571 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,571 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,571 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,571 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,571 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.7, version: 2.1.7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,571 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,571 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy2, version: 2.5.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,572 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.2, version: 2.1.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,572 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.3, version: 2.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,572 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: BED +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,572 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,572 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,572 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,572 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,572 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,572 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,572 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,573 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,573 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,573 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,573 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,573 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,573 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_links/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,573 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,573 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_expandbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,573 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,574 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,574 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,574 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_jaccard/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,574 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,574 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,574 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,574 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_reldistbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,574 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,574 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bed12tobed6/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,575 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,575 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,575 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,575 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.2, version: 2.30.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,575 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,575 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,575 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,575 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,575 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,576 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,576 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,576 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,576 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,576 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,576 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0+galaxy2, version: 2.30.0+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,576 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.3, version: 2.30.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,576 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,576 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,577 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,577 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,577 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,577 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,577 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,577 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,577 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,577 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_links/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,577 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,578 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,578 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,578 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,578 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,578 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,578 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_expandbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,578 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,578 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,578 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_jaccard/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,579 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.31.1.3, version: 2.31.1.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,579 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,579 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bed12tobed6/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,579 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,579 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,579 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,579 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,579 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,580 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,581 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,581 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,581 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,581 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,581 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,581 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,581 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,581 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,582 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,582 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,582 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_reldistbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,582 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,582 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,582 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,582 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,583 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,583 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,583 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: VCF/BCF +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,583 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,583 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,583 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/bcftools_plugin_fixploidy/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,584 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/bcftools_convert_to_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,584 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,584 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,584 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/bcftools_plugin_missing2ref/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,584 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,584 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,584 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/bcftools_plugin_counts/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,584 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,584 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,584 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,584 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/bcftools_convert_from_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,584 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/bcftools_plugin_impute_info/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,584 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,585 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,585 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/bcftools_plugin_fill_an_ac/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,585 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bcftools_plugin_fill_tags/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,585 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,585 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,585 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,585 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,585 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,585 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/bcftools_filter/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,585 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/bcftools_csq/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,585 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,585 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/bcftools_plugin_dosage/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,585 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/bcftools_query/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,586 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,586 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcf2tsv/vcf2tsv/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,586 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfaddinfo/vcfaddinfo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,586 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,586 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotate/vcfannotate/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,586 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotategenotypes/vcfannotategenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,586 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbedintersect/vcfbedintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,586 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbreakcreatemulti/vcfbreakcreatemulti/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,586 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcheck/vcfcheck/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,586 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcombine/vcfcombine/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,586 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcommonsamples/vcfcommonsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,586 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffixup/vcffixup/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,586 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfflatten/vcfflatten2/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,586 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgeno2haplo/vcfgeno2haplo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,587 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgenotypes/vcfgenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,587 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfhethom/vcfhethom/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,587 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfleftalign/vcfleftalign/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,587 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfprimers/vcfprimers/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,587 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfrandomsample/vcfrandomsample/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,587 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfsort/vcfsort/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,587 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,587 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfselectsamples/vcfselectsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,587 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfdistance/vcfdistance/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,588 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffilter/vcffilter2/1.0.0_rc3+galaxy3, version: 1.0.0_rc3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,588 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/vcfdistance/vcfdistance/1.0.0_rc1+galaxy0, version: 1.0.0_rc1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,588 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_annotate/vcftools_annotate/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,588 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_slice/vcftools_slice/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,588 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,588 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,588 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/bcftools_plugin_fixploidy/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,588 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/bcftools_convert_to_vcf/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,588 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,588 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,589 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/bcftools_plugin_missing2ref/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,589 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,589 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,589 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/bcftools_plugin_counts/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,589 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,590 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,590 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,590 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/bcftools_convert_from_vcf/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,590 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/bcftools_plugin_impute_info/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,590 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,590 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,590 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/bcftools_plugin_fill_an_ac/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,590 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bcftools_plugin_fill_tags/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,590 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,591 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,591 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,591 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5, version: 1.15.1+galaxy5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,591 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,591 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/bcftools_filter/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,591 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/bcftools_csq/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,591 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,591 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/bcftools_plugin_dosage/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,591 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/bcftools_query/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,592 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,592 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Nanopore +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,592 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.0.3+galaxy7, version: 1.0.3+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,592 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6, version: 2.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,592 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,592 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,592 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,592 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1, version: 1.28.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,592 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_events/poretools_events/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,593 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_hist/poretools_hist/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,593 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_occupancy/poretools_occupancy/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,593 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualpos/poretools_qualpos/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,593 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_squiggle/poretools_squiggle/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,593 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_yield_plot/poretools_yield_plot/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,593 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3, version: 0.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,593 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_winner/poretools_winner/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,593 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_times/poretools_times/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,593 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_tabular/poretools_tabular/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,593 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_stats/poretools_stats/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,594 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualdist/poretools_qualdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,594 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_nucdist/poretools_nucdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,594 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_extract/poretools_extract/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,594 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.7.2+galaxy1, version: 1.7.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,594 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.4+galaxy0, version: 2.9.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,594 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy1, version: 1.7.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,594 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.4.4+galaxy1, version: 1.4.4+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,594 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.7.2+galaxy0, version: 1.7.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,594 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.43.0+galaxy0, version: 1.43.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,594 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0, version: 0.2.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,595 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.5+galaxy0, version: 2.9.5+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,595 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Convert Formats +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,595 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,595 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,595 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,595 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,595 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,595 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,596 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wig_to_bigWig, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,596 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: bed_to_bigBed, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,596 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Lift-Over +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,596 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: liftOver1, version: 1.0.6 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,596 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Virology +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,596 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,596 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,597 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19, version: 4.5covid19 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,597 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,597 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/ivar_filtervariants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,597 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_getmasked/ivar_getmasked/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,597 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,597 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,597 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,597 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,597 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/ivar_filtervariants/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,598 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.4.3+galaxy1, version: 1.4.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,598 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Operate on Genomic Intervals +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,598 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wiggle2simple1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,598 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,598 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,598 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Fetch Sequences/Alignments +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,598 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Extract genomic DNA 1, version: 2.2.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,598 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,598 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,598 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,598 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,598 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,598 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,599 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,599 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,599 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,599 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,599 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,599 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Assembly +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,599 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, version: 0.4.8.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,599 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.12.0+galaxy1, version: 3.12.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,599 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3+galaxy0, version: 0.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,599 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.4.13, version: 1.4.13 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,599 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.1+galaxy0, version: 0.5.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,599 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3_r179+galaxy1, version: 0.3_r179+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,600 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1, version: 1.5.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,600 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0, version: 1.3.6+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,600 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.15.5+galaxy2, version: 3.15.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,600 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1, version: 5.2.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,600 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Annotation +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,600 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Mapping +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,600 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy4, version: 2.17+galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,600 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0, version: 2.4.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,600 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4, version: 0.7.17.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,600 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1, version: 0.7.17.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,601 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.2, version: 0.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,601 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,601 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,601 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,601 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,601 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1, version: 2.7.8a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,602 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.5, version: 0.7.17.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,602 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2, version: 0.7.17.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,602 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0, version: 2.28+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,602 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1, version: 2.5.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,602 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.18, version: 0.7.18 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,602 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.18, version: 0.7.18 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,602 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.7+galaxy0, version: 0.2.7+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,602 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.04.22+galaxy0, version: 1.04.22+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,603 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.04.22+galaxy0, version: 1.04.22+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,603 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy1, version: 2.7.11a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,603 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy0, version: 2.7.11a+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,603 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy1, version: 2.7.11a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,603 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Variant Calling +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,603 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,603 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,603 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,603 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,603 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,603 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,604 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,604 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_genesets/snpSift_geneSets/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,604 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_dbnsfp/snpSift_dbnsfp/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,604 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,604 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_get_chr_names/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,604 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy4, version: 4.3+T.galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,604 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,604 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1, version: 4.3+T.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,605 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_caseControl/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,605 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_annotate/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,605 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_vcfCheck/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,605 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,605 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,605 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_int/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,605 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpsift_vartype/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,605 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_rmInfo/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,605 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy1, version: 1.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,605 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/1.0.12+galaxy0, version: 1.0.12+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,606 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jasminesv/jasminesv/1.0.11+galaxy1, version: 1.0.11+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,606 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3, version: 1.0+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,606 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2, version: 2.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,606 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0, version: 1.3.6+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,606 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.6, version: 1.3.6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,606 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy5, version: 4.3+T.galaxy5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,606 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,606 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,607 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,607 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,607 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,607 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,607 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy6, version: 4.3+T.galaxy6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,607 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy3, version: 2.1.5+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,607 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.8+galaxy0, version: 1.3.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,607 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.8, version: 1.3.8 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,608 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/5.2+galaxy0, version: 5.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,608 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_get_chr_names/5.2+galaxy0, version: 5.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,608 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/5.2+galaxy0, version: 5.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,608 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/5.2+galaxy0, version: 5.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,608 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/5.2+galaxy0, version: 5.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,608 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/2.4+galaxy1, version: 2.4+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,608 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: ChIP-seq +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,608 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: RNA-seq +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,608 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1, version: 1.3.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,608 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1, version: 0.46.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,609 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.46.0.4, version: 0.46.0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,609 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1, version: 2.11.40.6+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,609 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.38.3+galaxy3, version: 3.38.3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,609 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.24.1+galaxy1, version: 3.24.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,609 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.10.1.1, version: 0.10.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,609 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy7, version: 2.1.0+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,609 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,609 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,610 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.1+galaxy2, version: 2.0.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,610 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.50.1+galaxy0, version: 3.50.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,610 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1, version: 2.2.1+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,610 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.7+galaxy2, version: 2.11.40.7+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,610 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3, version: 2.2.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,610 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deg_annotate/deg_annotate/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,610 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.50.0+galaxy0, version: 1.50.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,611 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea/1.20.0, version: 1.20.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,611 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fgsea/fgsea/1.8.0+galaxy1, version: 1.8.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,611 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.10.1+galaxy2, version: 1.10.1+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,611 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.48.0+galaxy1, version: 0.48.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,611 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.48.0+galaxy1, version: 0.48.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,611 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.8+galaxy0, version: 2.11.40.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,611 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.58.1+galaxy0, version: 3.58.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,611 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.36.0+galaxy5, version: 3.36.0+galaxy5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,612 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.2.3+galaxy0, version: 2.2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,612 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0, version: 2.2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,612 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2, version: 2.0.3+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,612 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/brew3r_r/brew3r_r/1.0.2+galaxy0, version: 1.0.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,612 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.6+galaxy0, version: 2.0.6+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,612 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.4, version: 2.2.1.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,612 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/brew3r_r/brew3r_r/1.0.2+galaxy1, version: 1.0.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,612 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/seurat/seurat/4.3.0.1+galaxy1, version: 4.3.0.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,612 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq/1.48.0+galaxy0, version: 1.48.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,612 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq_count/1.48.0+galaxy0, version: 1.48.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,613 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dexseq/plotdexseq/1.48.0+galaxy0, version: 1.48.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,613 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Multiple Alignments +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,613 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,613 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,613 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,613 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,613 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,613 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,613 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,614 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,614 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,614 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,614 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,614 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,614 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Phenotype Association +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,614 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,614 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_david, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,615 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,615 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_pass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,615 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_gpass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,615 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_beam, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,615 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_lps, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,615 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,615 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Regional Variation +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,615 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: STR-FM: Microsatellite Analysis +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,615 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Motif +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,616 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Chromosome Conformation +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,616 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Metagenomic Analysis +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,616 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Mothur +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,616 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Picard +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,616 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,616 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,617 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,617 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,617 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,617 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,617 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,617 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,617 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,617 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,617 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,618 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,618 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,618 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.3, version: 2.18.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,618 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,618 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_artifact_metrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,618 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,618 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,618 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,618 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,618 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,619 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,619 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ValidateSamFile/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,619 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,619 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeBamAlignment/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,620 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,620 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,620 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectHsMetrics/2.18.2, version: 2.18.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,620 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_EstimateLibraryComplexity/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,620 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,620 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,621 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,621 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,621 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,621 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,621 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,622 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,622 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,622 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,622 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,622 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,622 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,622 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,622 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,622 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,623 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,623 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_artifact_metrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,623 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,623 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,623 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,623 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,623 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,623 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,623 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ValidateSamFile/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,624 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,624 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeBamAlignment/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,624 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,624 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,624 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectHsMetrics/3.1.1, version: 3.1.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,624 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_EstimateLibraryComplexity/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,624 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,624 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,624 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Pharmacology +galaxy.tool_util.toolbox.base DEBUG 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[pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/modify_loom/modify_loom/0.7.5+galaxy1, version: 0.7.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,626 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, version: 1.10.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,626 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_read_10x/dropletutils_read_10x/1.0.4+galaxy0, version: 1.0.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,627 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_empty_drops/dropletutils_empty_drops/1.0.4+galaxy0, version: 1.0.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,627 [pN:job_handler_0,p:8,tN:Thread-1] 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+galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,638 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,638 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_enrichment/deeptools_plot_enrichment/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,638 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,638 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,638 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,639 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,639 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: EMBOSS +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,639 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: GATK +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,639 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: NCBI BLAST+ +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,639 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: 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into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,658 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__composition__ancom/qiime2__composition__ancom/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,658 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__composition__add_pseudocount/qiime2__composition__add_pseudocount/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,658 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__composition__tabulate/qiime2__composition__tabulate/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,658 [pN:job_handler_0,p:8,tN:Thread-1] Loaded 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+galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,661 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__emp_paired/qiime2__demux__emp_paired/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,661 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__filter_samples/qiime2__demux__filter_samples/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,661 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__tsne/qiime2__diversity__tsne/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,661 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,689 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_NVC/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,690 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_deletion_profile/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,690 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_mismatch_profile/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,690 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: MiModD +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,690 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Du Novo +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,690 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Seqtk +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,690 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: TRANSIT +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,690 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Statistics +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,690 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Summary_Statistics1, version: 1.1.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,690 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Count1, version: 1.0.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,690 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Graph/Display Data +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,690 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.6, version: 3.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,690 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,691 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,691 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,691 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,691 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,691 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,691 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,691 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,691 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,691 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,691 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,691 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,691 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,692 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,692 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,692 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,692 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0, version: 1.34.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,692 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.1.3+galaxy0, version: 3.1.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,692 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.5, version: 0.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,692 [pN:job_handler_0,p:8,tN:Thread-1] Skipping tool panel addition of hidden tool: qual_stats_boxplot, version: 1.0.1 +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,693 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,693 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: RNA Analysis (deprecated) +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,693 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: CloudMap (deprecated) +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,693 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Metagenomic Analysis (deprecated) +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,693 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Text Manipulation +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,693 [pN:job_handler_0,p:8,tN:Thread-1] Loading tool panel finished (157.365 ms) +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,700 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,700 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,701 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1, version: 2.7.8a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,701 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0, version: 2.28+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,701 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy1, version: 2.7.11a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,701 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy0, version: 2.7.11a+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,701 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy1, version: 2.7.11a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,701 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,701 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,702 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,702 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,702 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,702 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1, version: 4.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,702 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1, version: 4.9+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,702 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5+galaxy2, version: 1.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,702 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.5+galaxy2, version: 1.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,703 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.4+galaxy0, version: 2.9.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,703 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.5+galaxy0, version: 2.9.5+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,703 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, version: 0.4.8.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,703 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.1+galaxy0, version: 0.5.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,704 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.50.1+galaxy0, version: 3.50.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,704 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.50.0+galaxy0, version: 1.50.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,704 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.58.1+galaxy0, version: 3.58.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,704 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.36.0+galaxy5, version: 3.36.0+galaxy5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,704 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, version: 1.10.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,705 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/imgteam/slice_image/ip_slice_image/0.3-4, version: 0.3-4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,705 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,705 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,705 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,705 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,706 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,706 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,706 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: bed_to_bigBed, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,706 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,706 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,706 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,706 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,706 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,706 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,706 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,707 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,707 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,707 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,707 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,707 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: upload1, version: 1.1.7 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,707 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,707 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,707 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,708 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,708 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: intermine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,708 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: flymine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,708 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,708 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: mousemine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,708 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ratmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,708 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: yeastmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,708 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,708 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wormbase, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,708 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,708 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: eupathdb, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,708 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hbvar, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,708 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,709 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,709 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,709 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_EMPTY_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,709 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,709 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,709 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,709 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,709 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,709 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __TAG_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,709 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __APPLY_RULES__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,709 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __BUILD_LIST__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,709 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __EXTRACT_DATASET__, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,709 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: addValue, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,710 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: cat1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,710 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Cut1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,710 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Show beginning1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,710 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Filter1, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,710 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: sort1, version: 1.2.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,710 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Grep1, version: 1.0.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,710 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: comp1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,710 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,710 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,711 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0, version: 1.2.0.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,711 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5+galaxy2, version: 1.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,711 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.5+galaxy2, version: 1.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,711 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy1, version: 1.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,711 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3, version: 1.0+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,711 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, version: 1.10.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,711 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,712 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,712 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,712 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,712 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,712 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,712 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,712 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,712 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,712 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,713 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.7+galaxy2, version: 2.11.40.7+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,713 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.8+galaxy0, version: 2.11.40.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,713 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,713 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,713 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.6, version: 0.0.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,714 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,714 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,714 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,714 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,714 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,714 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.5+galaxy0, version: 0.2.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,714 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy1, version: 2.11.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,714 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,714 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,715 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0, version: 0.2.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,715 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: export_remote, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,715 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,715 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,715 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0, version: 0.2.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,715 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: param_value_from_file, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,715 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,715 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,715 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0, version: 0.5.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,715 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0, version: 5.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,716 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2, version: 0.5.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,716 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0, version: 0.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,716 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/diff/diff/3.7+galaxy0, version: 3.7+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,716 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,716 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,716 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6, version: 1.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,716 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,716 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.12.0, version: 3.12.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,716 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,716 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,717 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,717 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/0.9.2, version: 0.9.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,717 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.4, version: 0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,717 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0, version: 0.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,717 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,717 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,717 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,717 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,717 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,717 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,718 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,718 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0, version: 0.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,718 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,718 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,718 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,718 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,718 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,718 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,718 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,718 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,719 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,719 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,719 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,719 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_melt/melt/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,719 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_cast/cast/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,719 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jq/jq/1.0, version: 1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,719 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gff3_rebase/gff3.rebase/1.2, version: 1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,719 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,719 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_order_header_sort/column_order_header_sort/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,719 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,719 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Condense characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,720 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,720 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,720 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: createInterval, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,720 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,720 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Paste1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,720 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,720 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: random_lines1, version: 2.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,720 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Show tail1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,720 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: trimmer, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,720 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,720 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: secure_hash_message_digest, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,720 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0, version: 3.3.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,721 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1, version: 3.14.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,721 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0, version: 2.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,721 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0, version: 1.2.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,721 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4, version: 1.1.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,721 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1, version: 0.1.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,721 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0+galaxy0, version: 1.1.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,721 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.16.0+galaxy1, version: 3.16.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,721 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,722 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.3.1, version: 3.3.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,722 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2, version: 3.3.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,722 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1, version: 2.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,722 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/3.2.1, version: 3.2.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,722 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.18.0+galaxy0, version: 3.18.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,722 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3, version: 1.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,722 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3, version: 1.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,722 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.6, version: 0.6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,722 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,722 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,723 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,723 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,723 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,723 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,723 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,723 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/nl/9.3+galaxy1, version: 9.3+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,723 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,723 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,723 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,723 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,724 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,724 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,724 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,724 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,724 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,724 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,724 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy2, version: 9.3+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,724 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,724 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/1.0, version: 1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,725 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,725 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,725 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,725 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,725 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: join1, version: 2.1.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,725 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Grouping1, version: 2.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,725 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,725 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,725 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,725 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,725 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,726 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy1, version: 1.8+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,726 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,726 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.8, version: 1.16.8 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,726 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,726 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/flash/flash/1.2.11.4, version: 1.2.11.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,726 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.3, version: 0.6.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,726 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,726 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,727 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,727 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,727 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.7, version: 0.2.7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,728 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/length_and_gc_content/0.1.2, version: 0.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,728 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.7+galaxy0, version: 0.6.7+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,728 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.4, version: 1.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,728 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.5+galaxy1, version: 1.1.5+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,728 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.5+galaxy1, version: 1.1.5+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,728 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.9, version: 0.2.9 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,728 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,729 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0, version: 0.20.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,729 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1, version: 0.72+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,729 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1, version: 0.38.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,729 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0, version: 1.11+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,729 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0, version: 0.73+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,729 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1, version: 1.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,730 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0, version: 0.23.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,730 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0, version: 1.24.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,730 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1, version: 0.23.4+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,730 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1, version: 0.74+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,730 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy2, version: 0.23.4+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,730 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.39+galaxy2, version: 0.39+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,730 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/pileup_interval/pileup_interval/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,730 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3, version: 2.2.2d+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,730 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3, version: 1.9+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,731 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0.1+galaxy1, version: 2.0.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,731 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,731 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.4.0.0, version: 2.4.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,731 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamtools_split/2.4.0, version: 2.4.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,731 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam2interval/sam2interval/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,731 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_multi_bamqc/qualimap_multi_bamqc/2.2.2d, version: 2.2.2d into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,731 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,731 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,731 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2, version: 1.9+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,731 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,731 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,732 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,732 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2, version: 2.0.2+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,732 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,732 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,732 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,732 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,732 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8+galaxy1, version: 1.8+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,732 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,732 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,733 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.4, version: 2.1.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,733 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,733 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1, version: 2.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,733 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,733 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,733 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,733 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/boris/filter_on_md/MDtag_filter/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,733 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.2.0, version: 1.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,733 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.2, version: 2.0.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,733 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,734 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,734 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,734 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy1, version: 2.5.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,734 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,734 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lldelisle/revertr2orientationinbam/revertR2orientationInBam/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,734 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.3+galaxy0, version: 2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,734 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3, version: 1.20+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,734 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0.3, version: 2.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,735 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.2+galaxy2, version: 2.5.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,735 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamtools_split/2.5.2+galaxy0, version: 2.5.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,735 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_multi_bamqc/qualimap_multi_bamqc/2.3+galaxy0, version: 2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,735 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,735 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,735 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,735 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,735 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.15.1+galaxy2, version: 1.15.1+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,735 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,736 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,736 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,736 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,736 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,736 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,736 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,736 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.7, version: 2.1.7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,737 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,737 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy2, version: 2.5.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,737 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.2, version: 2.1.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,737 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.3, version: 2.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,737 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,737 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,737 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,737 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,737 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,737 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,738 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,738 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,738 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,738 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,738 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,738 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,738 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_links/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,738 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,738 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_expandbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,739 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,739 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,739 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,739 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_jaccard/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,739 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,739 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,739 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,739 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_reldistbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,739 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,739 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bed12tobed6/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,740 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,740 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,740 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,740 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.2, version: 2.30.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,740 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,740 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,740 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,740 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,740 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,740 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,741 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,741 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,741 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,741 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,741 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0+galaxy2, version: 2.30.0+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,741 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.3, version: 2.30.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,741 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,741 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,742 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,742 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,742 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,742 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,742 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,742 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,742 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,742 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_links/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,742 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,743 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,743 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,743 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,743 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,743 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,743 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_expandbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,743 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,743 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,743 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_jaccard/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,744 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.31.1.3, version: 2.31.1.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,744 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,744 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bed12tobed6/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,744 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,744 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,744 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,744 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,744 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,744 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,745 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,745 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,745 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,745 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,745 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,745 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,745 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,745 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,745 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,746 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,746 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_reldistbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,746 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,746 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,746 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,746 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,746 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,746 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,746 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,747 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,747 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/bcftools_plugin_fixploidy/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,747 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/bcftools_convert_to_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,747 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,747 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,747 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/bcftools_plugin_missing2ref/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,747 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,747 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,747 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/bcftools_plugin_counts/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,747 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,748 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,748 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,748 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/bcftools_convert_from_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,748 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/bcftools_plugin_impute_info/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,748 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,748 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,748 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/bcftools_plugin_fill_an_ac/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,748 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bcftools_plugin_fill_tags/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,748 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,749 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,749 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,749 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,749 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,749 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/bcftools_filter/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,750 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/bcftools_csq/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,750 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,750 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/bcftools_plugin_dosage/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,750 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/bcftools_query/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,750 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,750 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcf2tsv/vcf2tsv/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,750 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfaddinfo/vcfaddinfo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,750 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,750 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotate/vcfannotate/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,751 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotategenotypes/vcfannotategenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,751 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbedintersect/vcfbedintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,751 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbreakcreatemulti/vcfbreakcreatemulti/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,751 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcheck/vcfcheck/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,751 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcombine/vcfcombine/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,751 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcommonsamples/vcfcommonsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,751 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffixup/vcffixup/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,751 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfflatten/vcfflatten2/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,751 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgeno2haplo/vcfgeno2haplo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,751 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgenotypes/vcfgenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,751 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfhethom/vcfhethom/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,751 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfleftalign/vcfleftalign/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,751 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfprimers/vcfprimers/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,751 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfrandomsample/vcfrandomsample/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,751 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfsort/vcfsort/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,751 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,751 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfselectsamples/vcfselectsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,752 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfdistance/vcfdistance/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,752 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffilter/vcffilter2/1.0.0_rc3+galaxy3, version: 1.0.0_rc3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,752 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/vcfdistance/vcfdistance/1.0.0_rc1+galaxy0, version: 1.0.0_rc1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,752 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_annotate/vcftools_annotate/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,752 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_slice/vcftools_slice/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,752 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,752 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,752 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/bcftools_plugin_fixploidy/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,752 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/bcftools_convert_to_vcf/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,753 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,753 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,753 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/bcftools_plugin_missing2ref/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,753 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,753 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,753 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/bcftools_plugin_counts/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,753 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,754 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,754 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,754 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/bcftools_convert_from_vcf/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,754 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/bcftools_plugin_impute_info/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,754 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,755 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,755 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/bcftools_plugin_fill_an_ac/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,755 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bcftools_plugin_fill_tags/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,755 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,755 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,755 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,755 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5, version: 1.15.1+galaxy5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,755 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,755 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/bcftools_filter/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,756 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/bcftools_csq/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,756 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,756 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/bcftools_plugin_dosage/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,756 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/bcftools_query/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,756 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,756 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.0.3+galaxy7, version: 1.0.3+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,757 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6, version: 2.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,757 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,757 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,757 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,757 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1, version: 1.28.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,757 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_events/poretools_events/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,757 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_hist/poretools_hist/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,758 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_occupancy/poretools_occupancy/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,758 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualpos/poretools_qualpos/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,758 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_squiggle/poretools_squiggle/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,758 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_yield_plot/poretools_yield_plot/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,758 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3, version: 0.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,758 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_winner/poretools_winner/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,758 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_times/poretools_times/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,758 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_tabular/poretools_tabular/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,758 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_stats/poretools_stats/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,758 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualdist/poretools_qualdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,759 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_nucdist/poretools_nucdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,759 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_extract/poretools_extract/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,759 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.7.2+galaxy1, version: 1.7.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,759 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy1, version: 1.7.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,759 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.4.4+galaxy1, version: 1.4.4+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,759 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.7.2+galaxy0, version: 1.7.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,759 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.43.0+galaxy0, version: 1.43.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,759 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0, version: 0.2.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,760 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,760 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,760 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,760 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,760 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wig_to_bigWig, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,760 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: liftOver1, version: 1.0.6 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,760 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,760 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,760 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19, version: 4.5covid19 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,760 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,761 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/ivar_filtervariants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,761 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_getmasked/ivar_getmasked/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,761 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,761 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,761 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,761 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,761 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/ivar_filtervariants/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,761 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.4.3+galaxy1, version: 1.4.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,761 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wiggle2simple1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,762 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,762 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,762 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Extract genomic DNA 1, version: 2.2.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,762 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,762 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,762 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,762 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,762 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,762 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,762 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,762 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,762 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,763 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,763 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,763 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.12.0+galaxy1, version: 3.12.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,763 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3+galaxy0, version: 0.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,763 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.4.13, version: 1.4.13 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,763 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3_r179+galaxy1, version: 0.3_r179+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,763 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1, version: 1.5.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,763 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0, version: 1.3.6+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,763 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.15.5+galaxy2, version: 3.15.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,764 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1, version: 5.2.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,764 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy4, version: 2.17+galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,764 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0, version: 2.4.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,764 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4, version: 0.7.17.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,765 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1, version: 0.7.17.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,765 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.2, version: 0.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,765 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,765 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,765 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-2, version: 2.5.2b-2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,766 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.5, version: 0.7.17.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,766 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2, version: 0.7.17.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,766 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1, version: 2.5.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,766 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.18, version: 0.7.18 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,766 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.18, version: 0.7.18 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,766 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.7+galaxy0, version: 0.2.7+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,766 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.04.22+galaxy0, version: 1.04.22+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,766 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.04.22+galaxy0, version: 1.04.22+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,767 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,767 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,767 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,767 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,767 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,767 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,767 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,767 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_genesets/snpSift_geneSets/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,768 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_dbnsfp/snpSift_dbnsfp/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,768 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,768 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_get_chr_names/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,768 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy4, version: 4.3+T.galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,768 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,768 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1, version: 4.3+T.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,768 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_caseControl/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,768 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_annotate/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,769 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_vcfCheck/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,769 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,769 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,769 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_int/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,769 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpsift_vartype/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,769 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_rmInfo/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,769 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/1.0.12+galaxy0, version: 1.0.12+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,769 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jasminesv/jasminesv/1.0.11+galaxy1, version: 1.0.11+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,769 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2, version: 2.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,770 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0, version: 1.3.6+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,770 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.6, version: 1.3.6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,770 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy5, version: 4.3+T.galaxy5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,770 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,770 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,770 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,771 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,771 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,771 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,771 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy6, version: 4.3+T.galaxy6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,771 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy3, version: 2.1.5+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,771 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.8+galaxy0, version: 1.3.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,771 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.8, version: 1.3.8 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,771 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/5.2+galaxy0, version: 5.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,771 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_get_chr_names/5.2+galaxy0, version: 5.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,771 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/5.2+galaxy0, version: 5.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,772 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/5.2+galaxy0, version: 5.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,772 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/5.2+galaxy0, version: 5.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,772 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/2.4+galaxy1, version: 2.4+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,772 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1, version: 1.3.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,772 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1, version: 0.46.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,772 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.46.0.4, version: 0.46.0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,772 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1, version: 2.11.40.6+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,772 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.38.3+galaxy3, version: 3.38.3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,772 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.24.1+galaxy1, version: 3.24.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,772 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.10.1.1, version: 0.10.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,772 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy7, version: 2.1.0+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,772 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,773 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,773 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.1+galaxy2, version: 2.0.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,773 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1, version: 2.2.1+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,773 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3, version: 2.2.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,773 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deg_annotate/deg_annotate/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,773 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea/1.20.0, version: 1.20.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,773 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fgsea/fgsea/1.8.0+galaxy1, version: 1.8.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,773 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.10.1+galaxy2, version: 1.10.1+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,773 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.48.0+galaxy1, version: 0.48.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,773 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.48.0+galaxy1, version: 0.48.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,773 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.2.3+galaxy0, version: 2.2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,774 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0, version: 2.2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,774 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2, version: 2.0.3+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,774 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/brew3r_r/brew3r_r/1.0.2+galaxy0, version: 1.0.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,774 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.6+galaxy0, version: 2.0.6+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,774 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.4, version: 2.2.1.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,775 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/brew3r_r/brew3r_r/1.0.2+galaxy1, version: 1.0.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,775 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/seurat/seurat/4.3.0.1+galaxy1, version: 4.3.0.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,775 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq/1.48.0+galaxy0, version: 1.48.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,775 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq_count/1.48.0+galaxy0, version: 1.48.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,775 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dexseq/plotdexseq/1.48.0+galaxy0, version: 1.48.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,775 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,776 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,776 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,776 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,776 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,776 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,776 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,776 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,777 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,777 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,777 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,777 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,777 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,777 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_david, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,777 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,777 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_pass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,777 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_gpass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,777 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_beam, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,778 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_lps, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,778 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,778 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,778 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,778 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,778 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,778 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,778 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,778 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,778 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,779 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,779 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,779 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,779 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,779 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,779 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.3, version: 2.18.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,779 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,779 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_artifact_metrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,779 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,780 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,780 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,780 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,780 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,781 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,781 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ValidateSamFile/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,781 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,781 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeBamAlignment/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,781 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,782 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,782 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectHsMetrics/2.18.2, version: 2.18.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,782 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_EstimateLibraryComplexity/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,782 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,782 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,782 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,783 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,783 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,783 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,783 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,783 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,783 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,783 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,785 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,785 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,785 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,785 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,785 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,785 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,786 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,786 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_artifact_metrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,786 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,786 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,787 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,787 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,787 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,787 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,787 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ValidateSamFile/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,787 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,787 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeBamAlignment/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,787 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,791 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,792 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectHsMetrics/3.1.1, version: 3.1.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,792 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_EstimateLibraryComplexity/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,792 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,792 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,792 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/pharmcat/pharmcat/1.3.1+galaxy0, version: 1.3.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,792 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/pharmcat/pharmcat/1.7.0+galaxy0, version: 1.7.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,792 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/10x_bamtofastq/10x_bamtofastq/1.4.1, version: 1.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,793 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,793 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_export/anndata_export/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,793 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,793 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a, version: 1.5.a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,793 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,793 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/modify_loom/modify_loom/0.7.5+galaxy1, version: 0.7.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,793 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_read_10x/dropletutils_read_10x/1.0.4+galaxy0, version: 1.0.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,793 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_empty_drops/dropletutils_empty_drops/1.0.4+galaxy0, version: 1.0.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,793 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspectclusters/raceid_inspectclusters/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,793 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_filtnormconf/raceid_filtnormconf/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,794 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_clustering/raceid_clustering/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,794 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_trajectory/raceid_trajectory/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,794 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspecttrajectory/raceid_inspecttrajectory/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,794 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.5.1+galaxy0, version: 1.5.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,794 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmonquantmerge/salmonquantmerge/1.5.1+galaxy0, version: 1.5.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,794 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/imgteam/slice_image/ip_slice_image/0.3, version: 0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,794 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_create_qcmetric_ready_sce/scater_create_qcmetric_ready_sce/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,794 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_tsne/scater_plot_tsne/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,794 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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[pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,806 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,806 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,807 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gtftobed12/gtftobed12/357, version: 357 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,807 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool 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[pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__beta_group_significance/qiime2__diversity__beta_group_significance/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,811 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__procrustes_analysis/qiime2__diversity__procrustes_analysis/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,811 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__mantel/qiime2__diversity__mantel/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,811 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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DEBUG 2024-12-30 00:54:16,815 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__blast/qiime2__feature_classifier__blast/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,815 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__find_consensus_annotation/qiime2__feature_classifier__find_consensus_annotation/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,815 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__vsearch_global/qiime2__feature_classifier__vsearch_global/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 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00:54:16,833 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__beta_rarefaction/qiime2__diversity__beta_rarefaction/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,833 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity_lib__beta_phylogenetic_passthrough/qiime2__diversity_lib__beta_phylogenetic_passthrough/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,833 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity_lib__beta_passthrough/qiime2__diversity_lib__beta_passthrough/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,833 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity_lib__beta_phylogenetic_meta_passthrough/qiime2__diversity_lib__beta_phylogenetic_meta_passthrough/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,833 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity_lib__alpha_passthrough/qiime2__diversity_lib__alpha_passthrough/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,834 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity_lib__shannon_entropy/qiime2__diversity_lib__shannon_entropy/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,834 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,836 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__classify_consensus_vsearch/qiime2__feature_classifier__classify_consensus_vsearch/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,836 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__makeblastdb/qiime2__feature_classifier__makeblastdb/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,836 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__vsearch_global/qiime2__feature_classifier__vsearch_global/2024.10.0+q2galaxy.2024.10.0, version: 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version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,867 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage2/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,868 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_annotation/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,868 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_FPKM_count/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,868 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam_stat/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,868 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_GC/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,868 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_quality/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,868 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_insertion_profile/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,868 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,868 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RPKM_saturation/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,869 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,869 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RNA_fragment_size/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,869 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam2wig/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,869 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_hexamer/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,869 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_NVC/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,869 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_deletion_profile/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,869 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_mismatch_profile/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,869 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Summary_Statistics1, version: 1.1.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,869 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Count1, version: 1.0.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,870 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,870 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0, version: 1.34.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,870 [pN:job_handler_0,p:8,tN:Thread-1] Skipping tool panel addition of hidden tool: qual_stats_boxplot, version: 1.0.1 +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,870 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.views.edam DEBUG 2024-12-30 00:54:16,870 [pN:job_handler_0,p:8,tN:Thread-1] Loading EDAM tool panel finished (176.955 ms) +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,876 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,877 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,877 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1, version: 2.7.8a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,877 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy1, version: 2.7.11a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,877 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy0, version: 2.7.11a+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,877 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy1, version: 2.7.11a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,877 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.50.1+galaxy0, version: 3.50.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,877 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.7+galaxy2, version: 2.11.40.7+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,877 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.50.0+galaxy0, version: 1.50.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,878 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.8+galaxy0, version: 2.11.40.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,878 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.58.1+galaxy0, version: 3.58.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,878 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.36.0+galaxy5, version: 3.36.0+galaxy5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,878 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, version: 1.10.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,878 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/cite_seq_count/cite_seq_count/1.4.4+galaxy0, version: 1.4.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,878 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1, version: 4.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,878 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1, version: 4.9+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,878 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.4+galaxy0, version: 2.9.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,879 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.5+galaxy0, version: 2.9.5+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,879 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, version: 0.4.8.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,879 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.1+galaxy0, version: 0.5.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,879 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0, version: 2.28+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,880 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,880 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,880 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,880 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,880 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy1, version: 1.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,880 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3, version: 1.0+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,880 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,881 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,881 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,881 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,881 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,882 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,882 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,882 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,882 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,882 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,882 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,882 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.6, version: 0.0.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,882 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,883 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,883 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,883 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,883 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,884 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,884 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,884 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,884 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,884 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,884 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,884 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,885 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,885 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,885 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,885 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,885 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,885 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,885 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,885 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,886 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1, version: 2.7.8a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,886 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy1, version: 2.7.11a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,886 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy0, version: 2.7.11a+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,887 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy1, version: 2.7.11a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,887 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, version: 1.10.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,887 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/cite_seq_count/cite_seq_count/1.4.4+galaxy0, version: 1.4.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,887 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy0, version: 1.8+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,887 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy1, version: 1.8+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,888 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Summary_Statistics1, version: 1.1.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,888 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,888 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,888 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,888 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,888 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,888 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,888 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,888 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0, version: 1.2.0.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,889 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5+galaxy2, version: 1.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,889 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5+galaxy2, version: 1.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,889 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.5+galaxy2, version: 1.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,889 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.5+galaxy2, version: 1.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,889 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy1, version: 1.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,889 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3, version: 1.0+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,890 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,890 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,890 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,890 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,890 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,890 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,891 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,891 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,891 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,891 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,891 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,891 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,891 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,892 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,892 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,892 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,892 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,892 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,892 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,892 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,892 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,892 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,893 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,893 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,893 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,893 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.5+galaxy0, version: 0.2.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,893 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy1, version: 2.11.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,893 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,893 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,893 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0, version: 0.2.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,893 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: upload1, version: 1.1.7 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,893 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,894 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,894 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,894 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,894 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: intermine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,894 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: flymine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,894 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,894 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: mousemine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,894 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ratmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,894 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: yeastmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,894 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,894 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wormbase, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,894 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,894 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: eupathdb, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,894 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hbvar, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,894 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: export_remote, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,895 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,895 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,895 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0, version: 0.2.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,895 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: param_value_from_file, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,895 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,895 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,895 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0, version: 0.5.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,895 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0, version: 5.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,895 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2, version: 0.5.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,895 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0, version: 0.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,895 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,896 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,896 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,896 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_EMPTY_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,896 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,896 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,896 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,896 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,896 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,896 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __TAG_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,896 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __APPLY_RULES__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,896 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __BUILD_LIST__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,896 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __EXTRACT_DATASET__, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,897 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/diff/diff/3.7+galaxy0, version: 3.7+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,897 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,897 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,897 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6, version: 1.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,897 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,897 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.12.0, version: 3.12.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,897 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,897 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,897 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,898 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/0.9.2, version: 0.9.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,898 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.4, version: 0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,898 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0, version: 0.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,898 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,898 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,898 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,898 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,898 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,898 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,898 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,899 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0, version: 0.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,899 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,899 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,899 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,899 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,899 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,899 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,899 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,899 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,899 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,900 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,900 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,900 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_melt/melt/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,900 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_cast/cast/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,900 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jq/jq/1.0, version: 1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,900 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gff3_rebase/gff3.rebase/1.2, version: 1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,900 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,900 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_order_header_sort/column_order_header_sort/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,900 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,900 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: addValue, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,901 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: cat1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,901 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Condense characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,901 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,901 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,901 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: createInterval, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,901 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Cut1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,901 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,901 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Paste1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,901 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,901 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: random_lines1, version: 2.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,901 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Show beginning1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,901 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Show tail1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,902 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: trimmer, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,902 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,902 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: secure_hash_message_digest, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,902 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0, version: 3.3.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,902 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1, version: 3.14.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,902 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0, version: 2.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,902 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0, version: 1.2.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,902 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4, version: 1.1.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,902 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1, version: 0.1.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,903 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0+galaxy0, version: 1.1.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,903 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.16.0+galaxy1, version: 3.16.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,903 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,903 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.3.1, version: 3.3.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,903 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2, version: 3.3.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,904 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1, version: 2.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,904 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/3.2.1, version: 3.2.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,904 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.18.0+galaxy0, version: 3.18.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,904 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3, version: 1.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,904 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3, version: 1.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,904 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.6, version: 0.6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,904 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,904 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,904 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,905 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,905 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,905 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,905 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,905 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/nl/9.3+galaxy1, version: 9.3+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,905 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,905 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,905 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,906 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,906 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,906 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,906 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,906 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,906 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,906 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,906 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy2, version: 9.3+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,907 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,907 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/1.0, version: 1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,907 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Filter1, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,907 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: sort1, version: 1.2.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,907 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Grep1, version: 1.0.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,907 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,907 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,907 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,907 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,907 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: join1, version: 2.1.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,907 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: comp1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,908 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Grouping1, version: 2.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,908 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,908 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,908 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,908 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,908 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,908 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.8, version: 1.16.8 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,908 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,908 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/flash/flash/1.2.11.4, version: 1.2.11.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,909 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.3, version: 0.6.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,909 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,909 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,909 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,909 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,909 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.7, version: 0.2.7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,909 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/length_and_gc_content/0.1.2, version: 0.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,909 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.7+galaxy0, version: 0.6.7+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,910 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.4, version: 1.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,910 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.5+galaxy1, version: 1.1.5+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,910 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.5+galaxy1, version: 1.1.5+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,910 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.9, version: 0.2.9 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,910 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,910 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0, version: 0.20.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,910 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1, version: 0.72+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,910 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1, version: 0.38.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,910 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0, version: 1.11+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,910 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0, version: 0.73+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,911 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1, version: 1.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,911 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0, version: 0.23.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,911 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0, version: 1.24.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,911 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1, version: 0.23.4+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,912 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1, version: 0.74+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,912 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy2, version: 0.23.4+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,912 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.39+galaxy2, version: 0.39+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,912 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/pileup_interval/pileup_interval/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,912 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3, version: 2.2.2d+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,913 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3, version: 1.9+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,913 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0.1+galaxy1, version: 2.0.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,913 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,913 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.4.0.0, version: 2.4.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,913 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamtools_split/2.4.0, version: 2.4.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,913 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam2interval/sam2interval/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,913 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_multi_bamqc/qualimap_multi_bamqc/2.2.2d, version: 2.2.2d into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,913 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,914 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,914 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2, version: 1.9+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,914 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,914 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,914 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,914 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2, version: 2.0.2+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,914 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,914 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,914 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,914 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,914 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8+galaxy1, version: 1.8+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,915 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,915 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,915 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.4, version: 2.1.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,915 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,915 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1, version: 2.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,915 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,915 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,915 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,915 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/boris/filter_on_md/MDtag_filter/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,915 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.2.0, version: 1.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,915 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.2, version: 2.0.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,916 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,916 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,916 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,916 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy1, version: 2.5.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,916 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,916 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lldelisle/revertr2orientationinbam/revertR2orientationInBam/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,916 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.3+galaxy0, version: 2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,916 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3, version: 1.20+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,917 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0.3, version: 2.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,917 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.2+galaxy2, version: 2.5.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,917 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamtools_split/2.5.2+galaxy0, version: 2.5.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,917 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_multi_bamqc/qualimap_multi_bamqc/2.3+galaxy0, version: 2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,917 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,917 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,917 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,917 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,917 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.15.1+galaxy2, version: 1.15.1+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,918 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,918 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,918 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,918 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,918 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,918 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,918 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,918 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.7, version: 2.1.7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,918 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,918 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy2, version: 2.5.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,919 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.2, version: 2.1.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,919 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.3, version: 2.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,919 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,919 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,919 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,919 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,920 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,920 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,920 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,920 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,920 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,920 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,920 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,920 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,921 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_links/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,921 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,921 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_expandbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,921 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,921 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,921 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,921 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_jaccard/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,921 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,921 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,921 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,921 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_reldistbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,921 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,922 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bed12tobed6/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,922 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,922 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,922 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,922 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.2, version: 2.30.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,922 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,922 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,922 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,922 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,923 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,923 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,923 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,923 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,923 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,923 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,923 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0+galaxy2, version: 2.30.0+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,923 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.3, version: 2.30.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,924 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,924 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,924 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,924 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,924 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,924 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,924 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,924 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,924 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,924 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_links/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,925 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,925 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,925 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,925 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,925 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,925 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,925 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_expandbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,925 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,925 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,925 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_jaccard/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,926 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.31.1.3, version: 2.31.1.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,926 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,926 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bed12tobed6/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,926 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,926 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,926 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,926 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,926 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,926 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,927 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,927 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,927 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,928 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,928 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,928 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,928 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,928 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,928 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,929 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,929 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_reldistbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,929 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,929 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,929 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,930 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,930 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,930 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,930 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,930 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,930 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/bcftools_plugin_fixploidy/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,930 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/bcftools_convert_to_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,930 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,930 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,930 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/bcftools_plugin_missing2ref/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,931 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,931 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,931 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/bcftools_plugin_counts/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,931 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,931 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,931 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,931 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/bcftools_convert_from_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,931 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/bcftools_plugin_impute_info/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,931 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,932 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,932 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/bcftools_plugin_fill_an_ac/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,932 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bcftools_plugin_fill_tags/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,932 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,933 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,933 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,933 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,933 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,933 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/bcftools_filter/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,933 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/bcftools_csq/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,933 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,933 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/bcftools_plugin_dosage/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,933 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/bcftools_query/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,934 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,934 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcf2tsv/vcf2tsv/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,934 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfaddinfo/vcfaddinfo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,934 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,934 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotate/vcfannotate/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,934 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotategenotypes/vcfannotategenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,934 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbedintersect/vcfbedintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,934 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbreakcreatemulti/vcfbreakcreatemulti/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,934 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcheck/vcfcheck/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,934 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcombine/vcfcombine/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,935 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcommonsamples/vcfcommonsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,935 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffixup/vcffixup/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,935 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfflatten/vcfflatten2/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,935 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgeno2haplo/vcfgeno2haplo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,935 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgenotypes/vcfgenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,935 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfhethom/vcfhethom/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,935 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfleftalign/vcfleftalign/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,935 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfprimers/vcfprimers/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,935 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfrandomsample/vcfrandomsample/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,935 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfsort/vcfsort/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,936 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,936 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfselectsamples/vcfselectsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,936 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfdistance/vcfdistance/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,936 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffilter/vcffilter2/1.0.0_rc3+galaxy3, version: 1.0.0_rc3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,936 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/vcfdistance/vcfdistance/1.0.0_rc1+galaxy0, version: 1.0.0_rc1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,936 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_annotate/vcftools_annotate/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,936 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,939 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,939 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/bcftools_plugin_fill_an_ac/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,940 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bcftools_plugin_fill_tags/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,940 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,941 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/bcftools_filter/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,941 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/bcftools_csq/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,941 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,941 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/bcftools_plugin_dosage/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,941 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/bcftools_query/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,941 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,941 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.0.3+galaxy7, version: 1.0.3+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,941 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6, version: 2.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,941 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,942 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,942 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,942 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1, version: 1.28.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,942 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_events/poretools_events/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,942 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_hist/poretools_hist/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,942 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_occupancy/poretools_occupancy/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,942 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualpos/poretools_qualpos/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,942 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,943 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_tabular/poretools_tabular/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,943 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_stats/poretools_stats/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,943 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualdist/poretools_qualdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,943 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_nucdist/poretools_nucdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,943 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_extract/poretools_extract/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,943 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.7.2+galaxy1, version: 1.7.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,944 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy1, version: 1.7.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,944 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.4.4+galaxy1, version: 1.4.4+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,944 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.7.2+galaxy0, version: 1.7.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,944 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.43.0+galaxy0, version: 1.43.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,944 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0, version: 0.2.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,944 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,944 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,944 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,944 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,945 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,945 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,945 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wig_to_bigWig, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,945 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: bed_to_bigBed, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,945 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: liftOver1, version: 1.0.6 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,945 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,945 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,945 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19, version: 4.5covid19 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,945 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,945 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/ivar_filtervariants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,945 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_getmasked/ivar_getmasked/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,945 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,946 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,946 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,946 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,946 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/ivar_filtervariants/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,946 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.4.3+galaxy1, version: 1.4.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,946 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wiggle2simple1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,946 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,946 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,946 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Extract genomic DNA 1, version: 2.2.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,946 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,947 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,947 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,947 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,947 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,947 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,947 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,947 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,947 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,947 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,947 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,947 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.12.0+galaxy1, version: 3.12.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,947 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3+galaxy0, version: 0.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,948 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.4.13, version: 1.4.13 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,948 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3_r179+galaxy1, version: 0.3_r179+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,948 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1, version: 1.5.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,948 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0, version: 1.3.6+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,948 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.15.5+galaxy2, version: 3.15.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,948 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1, version: 5.2.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,948 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy4, version: 2.17+galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,948 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0, version: 2.4.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,948 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4, version: 0.7.17.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,949 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1, version: 0.7.17.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,949 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.2, version: 0.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,949 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,949 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,949 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-2, version: 2.5.2b-2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,950 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.5, version: 0.7.17.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,950 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2, version: 0.7.17.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,950 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1, version: 2.5.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,950 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.18, version: 0.7.18 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,950 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.18, version: 0.7.18 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,950 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.7+galaxy0, version: 0.2.7+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,950 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.04.22+galaxy0, version: 1.04.22+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,951 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.04.22+galaxy0, version: 1.04.22+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,951 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,951 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,951 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,951 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,951 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,951 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,952 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,952 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_genesets/snpSift_geneSets/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,952 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_dbnsfp/snpSift_dbnsfp/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,952 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,952 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_get_chr_names/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,952 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy4, version: 4.3+T.galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,952 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,952 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1, version: 4.3+T.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,952 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_caseControl/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,952 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_annotate/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,952 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_vcfCheck/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,953 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,953 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,953 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_int/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,953 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpsift_vartype/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,953 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_rmInfo/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,953 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/1.0.12+galaxy0, version: 1.0.12+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,953 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jasminesv/jasminesv/1.0.11+galaxy1, version: 1.0.11+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,953 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2, version: 2.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,954 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0, version: 1.3.6+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,954 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.6, version: 1.3.6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,954 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy5, version: 4.3+T.galaxy5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,954 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,954 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,954 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,954 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,954 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,955 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,955 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy6, version: 4.3+T.galaxy6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,955 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy3, version: 2.1.5+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,955 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.8+galaxy0, version: 1.3.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,955 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.8, version: 1.3.8 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,955 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/5.2+galaxy0, version: 5.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,955 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_get_chr_names/5.2+galaxy0, version: 5.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,955 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/5.2+galaxy0, version: 5.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,956 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/5.2+galaxy0, version: 5.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,956 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/5.2+galaxy0, version: 5.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,956 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/2.4+galaxy1, version: 2.4+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,956 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1, version: 1.3.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,956 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1, version: 0.46.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,956 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.46.0.4, version: 0.46.0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,956 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1, version: 2.11.40.6+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,956 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.38.3+galaxy3, version: 3.38.3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,957 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.24.1+galaxy1, version: 3.24.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,957 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.10.1.1, version: 0.10.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,957 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy7, version: 2.1.0+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,957 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,957 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,957 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.1+galaxy2, version: 2.0.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,957 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1, version: 2.2.1+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,958 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3, version: 2.2.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,958 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deg_annotate/deg_annotate/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,958 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea/1.20.0, version: 1.20.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,958 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fgsea/fgsea/1.8.0+galaxy1, version: 1.8.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,958 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.10.1+galaxy2, version: 1.10.1+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,958 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.48.0+galaxy1, version: 0.48.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,958 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.48.0+galaxy1, version: 0.48.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,958 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.2.3+galaxy0, version: 2.2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,959 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0, version: 2.2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,959 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2, version: 2.0.3+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,959 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/brew3r_r/brew3r_r/1.0.2+galaxy0, version: 1.0.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,959 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.6+galaxy0, version: 2.0.6+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,959 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.4, version: 2.2.1.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,959 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/brew3r_r/brew3r_r/1.0.2+galaxy1, version: 1.0.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,959 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/seurat/seurat/4.3.0.1+galaxy1, version: 4.3.0.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,959 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq/1.48.0+galaxy0, version: 1.48.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,959 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq_count/1.48.0+galaxy0, version: 1.48.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,960 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dexseq/plotdexseq/1.48.0+galaxy0, version: 1.48.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,960 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,960 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,960 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,960 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,960 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,960 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,960 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,960 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,961 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,961 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,961 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,961 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,961 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,961 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_david, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,961 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,961 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_pass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,961 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_gpass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,962 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_beam, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,962 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_lps, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,962 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,962 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,962 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,962 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,962 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,962 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,962 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,962 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,963 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,963 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,963 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,963 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,963 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,964 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,964 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.3, version: 2.18.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,964 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,964 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_artifact_metrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,964 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,964 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,964 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,964 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,965 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,965 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,965 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ValidateSamFile/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,965 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,965 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeBamAlignment/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,965 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,965 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,965 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectHsMetrics/2.18.2, version: 2.18.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,966 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_EstimateLibraryComplexity/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,966 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,966 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,966 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,966 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,967 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,967 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,967 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,967 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,967 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,967 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,967 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,967 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,968 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,968 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,968 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,968 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,968 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,968 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_artifact_metrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,968 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,968 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,969 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,969 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,969 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,969 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,969 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ValidateSamFile/3.1.1.0, version: 3.1.1.0 into tool panel. 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[pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectHsMetrics/3.1.1, version: 3.1.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,970 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_EstimateLibraryComplexity/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,970 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,970 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,970 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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00:54:16,978 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_read_10x/dropletutils_read_10x/1.0.4+galaxy0, version: 1.0.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,978 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_empty_drops/dropletutils_empty_drops/1.0.4+galaxy0, version: 1.0.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,978 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspectclusters/raceid_inspectclusters/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,978 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_filtnormconf/raceid_filtnormconf/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,978 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_clustering/raceid_clustering/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,979 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_trajectory/raceid_trajectory/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,979 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspecttrajectory/raceid_inspecttrajectory/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,979 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.5.1+galaxy0, version: 1.5.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,979 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmonquantmerge/salmonquantmerge/1.5.1+galaxy0, version: 1.5.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,979 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/imgteam/slice_image/ip_slice_image/0.3, version: 0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,979 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_create_qcmetric_ready_sce/scater_create_qcmetric_ready_sce/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,980 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_tsne/scater_plot_tsne/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,980 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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+galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,981 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1, version: 1.7.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,981 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_remove_confounders/scanpy_remove_confounders/1.7.1+galaxy0, version: 1.7.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,981 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_parameter_iterator/scanpy_parameter_iterator/0.0.1+galaxy0, version: 0.0.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,981 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/droplet_barcode_plot/_dropletBarcodePlot/1.6.1+galaxy2, version: 1.6.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,981 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_read_10x/scanpy_read_10x/1.4.3+galaxy10, version: 1.4.3+galaxy10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,982 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/gtf2gene_list/_ensembl_gtf2gene_list/1.42.1+galaxy6, version: 1.42.1+galaxy6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,982 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/salmon_kallisto_mtx_to_10x/_salmon_kallisto_mtx_to_10x/0.0.1+galaxy6, version: 0.0.1+galaxy6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,982 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/sceasy_convert/sceasy_convert/0.0.5+galaxy1, version: 0.0.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,982 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/0.0.3+galaxy0, version: 0.0.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,982 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/retrieve_scxa/retrieve_scxa/v0.0.2+galaxy2, version: v0.0.2+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,982 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/music_inspect_eset/music_inspect_eset/0.1.1+galaxy0, version: 0.1.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,982 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/music_construct_eset/music_construct_eset/0.1.1+galaxy0, version: 0.1.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,983 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_read_10x/scanpy_read_10x/1.6.0+galaxy0, version: 1.6.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,983 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.6.0+galaxy1, version: 1.6.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,983 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.8.1+3+galaxy0, version: 1.8.1+3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,983 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.6.0+galaxy0, version: 1.6.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,983 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[pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__beta_group_significance/qiime2__diversity__beta_group_significance/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,997 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__procrustes_analysis/qiime2__diversity__procrustes_analysis/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,997 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__mantel/qiime2__diversity__mantel/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:16,997 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,024 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__classify_consensus_vsearch/qiime2__feature_classifier__classify_consensus_vsearch/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,024 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__makeblastdb/qiime2__feature_classifier__makeblastdb/2024.10.0+q2galaxy.2024.10.0, version: 2024.10.0+q2galaxy.2024.10.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,025 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__vsearch_global/qiime2__feature_classifier__vsearch_global/2024.10.0+q2galaxy.2024.10.0, version: 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toolshed.g2.bx.psu.edu/repos/imgteam/slice_image/ip_slice_image/0.3-4, version: 0.3-4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,054 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.10.2+galaxy2, version: 1.10.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,054 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.10.2+galaxy2, version: 1.10.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,054 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.10.2+galaxy1, version: 1.10.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,054 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.10.2+galaxy2, version: 1.10.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,054 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy2, version: 1.10.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,054 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_remove_confounders/scanpy_remove_confounders/1.10.2+galaxy2, version: 1.10.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,054 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_duplication/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,054 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage2/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,054 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_NVC/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,054 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_clipping_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,055 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_FPKM_count/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,055 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage/2.6.4.3, version: 2.6.4.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,055 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_deletion_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,055 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RPKM_saturation/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,055 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RNA_fragment_size/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,055 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,055 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_annotation/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,055 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_tin/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,055 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,055 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_mismatch_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,055 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_inner_distance/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,056 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_quality/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,056 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_hexamer/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,056 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_insertion_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,056 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam2wig/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,056 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam_stat/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,056 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_GC/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,056 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_saturation/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,056 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage2/2.6.4.2, version: 2.6.4.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,057 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RPKM_saturation/2.6.4.2, version: 2.6.4.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,057 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,057 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_duplication/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,057 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_saturation/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,057 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_tin/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,057 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_clipping_profile/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,057 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_inner_distance/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,058 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage2/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,058 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_annotation/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,058 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_FPKM_count/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,058 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam_stat/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,058 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_GC/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,058 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_quality/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,059 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_insertion_profile/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,059 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,059 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RPKM_saturation/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,059 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,059 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RNA_fragment_size/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,059 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam2wig/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,060 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_hexamer/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,060 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_NVC/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,060 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_deletion_profile/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,060 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_mismatch_profile/5.0.3+galaxy0, version: 5.0.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,062 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Count1, version: 1.0.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,062 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,062 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0, version: 1.34.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,062 [pN:job_handler_0,p:8,tN:Thread-1] Skipping tool panel addition of hidden tool: qual_stats_boxplot, version: 1.0.1 +galaxy.tool_util.toolbox.base DEBUG 2024-12-30 00:54:17,062 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.views.edam DEBUG 2024-12-30 00:54:17,063 [pN:job_handler_0,p:8,tN:Thread-1] Loading EDAM tool panel finished (192.133 ms) +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,063 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,063 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,063 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,063 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,063 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,064 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,064 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_Bam_Bai_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,064 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,064 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,064 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,064 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_coodinate_sorted_bam +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,064 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,064 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_cram_to_bam_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,064 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_to_gff_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,065 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,065 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,065 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,065 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_to_fli_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,065 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bedgraph_to_bigwig +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,065 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_len_to_linecount +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,065 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_parquet_to_csv +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,065 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: bigwigtowig +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,065 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,065 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,065 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,065 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: csv_to_tabular +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,065 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: tabular_to_csv +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,065 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_tabular +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,065 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_bowtie_base_index +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,066 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_bowtie_color_index +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,066 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_2bit +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,066 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_len +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,066 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_fai +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,067 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,068 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,068 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,068 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,068 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,068 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,068 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,068 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,068 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,068 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,068 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,068 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,068 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,068 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,069 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,069 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,069 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,069 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,069 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,069 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,069 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,069 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,069 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gff_to_bed_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,069 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gff_to_interval_index_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,069 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,069 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gff_to_fli_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,069 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,069 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,070 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,070 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,070 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,070 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gff_to_interval_index_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,070 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,070 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bed_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,070 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bedstrict_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,070 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bed6_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,070 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bed12_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,070 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,070 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,070 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,070 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_picard_interval_list_to_bed6 +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,071 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_tar_to_directory +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,071 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,071 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,071 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,071 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,071 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,071 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,071 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_maf_to_fasta_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,071 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_maf_to_interval_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,071 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,071 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,071 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,071 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,071 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,072 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_sam_to_unsorted_bam +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,072 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_coodinate_sorted_bam +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,072 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,072 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_sam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,072 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: tabular_to_dbnsfp +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,072 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: tabular_to_csv +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,072 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,072 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,072 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,072 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,072 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,072 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,072 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,073 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bcf_uncompressed_to_bcf +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,073 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bcf_uncompressed_to_bcf +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,073 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_wig_to_bigwig +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,073 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_wiggle_to_interval_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,073 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,073 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,073 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: lped2fpedconvert +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,073 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: lped2pbedconvert +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,073 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: pbed2lpedconvert +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,073 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: pbed2ldindepconvert +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,073 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,073 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,073 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_biom +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,073 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_biom +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,073 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,074 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,074 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,074 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_SMILES_to_MOL +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,074 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,074 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_smiles_to_smiles +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,074 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,074 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,074 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,074 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,074 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,074 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,074 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_inchi_to_mol +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,074 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,074 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,074 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,075 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,075 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,075 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,075 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,075 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,075 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,075 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,075 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mol2_to_mol +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,075 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,075 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_cml_to_smiles +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,076 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,076 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,076 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,076 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_Pdb_to_Gro_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,076 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,076 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,076 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,076 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,076 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,076 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,076 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_Gro_to_Pdb_0 +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,076 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_ref_to_seq_taxomony +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,076 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_neostorezip_to_neostore +galaxy.datatypes.registry DEBUG 2024-12-30 00:54:17,078 [pN:job_handler_0,p:8,tN:Thread-1] Loaded external metadata tool: __SET_METADATA__ +galaxy.tools.special_tools DEBUG 2024-12-30 00:54:17,079 [pN:job_handler_0,p:8,tN:Thread-1] Loaded history export tool: __EXPORT_HISTORY__ +galaxy.tools.special_tools DEBUG 2024-12-30 00:54:17,080 [pN:job_handler_0,p:8,tN:Thread-1] Loaded history export to uri tool: __EXPORT_HISTORY_TO_URI__ +galaxy.tools.special_tools DEBUG 2024-12-30 00:54:17,082 [pN:job_handler_0,p:8,tN:Thread-1] Loaded history import tool: __IMPORT_HISTORY__ +galaxy.tools.special_tools DEBUG 2024-12-30 00:54:17,083 [pN:job_handler_0,p:8,tN:Thread-1] Loaded data fetch tool: __DATA_FETCH__ +galaxy.queue_worker INFO 2024-12-30 00:54:17,083 [pN:job_handler_0,p:8,tN:Thread-1] Queuing async task rebuild_toolbox_search_index for job_handler_0. +galaxy.queue_worker DEBUG 2024-12-30 00:54:17,084 [pN:job_handler_0,p:8,tN:Thread-1] Toolbox reload (735.367 ms) +galaxy.queue_worker INFO 2024-12-30 00:54:17,085 [pN:job_handler_0,p:8,tN:Thread-1] Instance 'job_handler_0' received 'rebuild_toolbox_search_index' task, executing now. +galaxy.queue_worker DEBUG 2024-12-30 00:54:17,085 [pN:job_handler_0,p:8,tN:Thread-1] App is not a webapp, not building a search index +galaxy.tool_util.deps.containers INFO 2024-12-30 00:54:18,600 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyhdfd78af_2,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 00:54:18,627 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/2/tool_script.sh] for tool command [gx-fastq-filter '/galaxy/server/database/objects/f/8/d/dataset_f8d2e3ae-0730-4f57-8e66-88b71398734c.dat' '/galaxy/server/database/jobs_directory/000/2/configs/tmpgn3htfkj' '/galaxy/server/database/objects/e/b/6/dataset_eb67a9a0-727d-4723-9f99-2f4e42a6a3ef.dat' '/galaxy/server/database/objects/e/b/6/dataset_eb67a9a0-727d-4723-9f99-2f4e42a6a3ef_files' 'sanger'] +galaxy.jobs.runners DEBUG 2024-12-30 00:54:18,654 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (2) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/2/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/2/galaxy_2.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 00:54:18,681 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 00:54:18,682 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5+galaxy2: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-12-30 00:54:18,704 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyhdfd78af_2,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 00:54:33,332 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 2: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 00:54:38,461 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 2 finished +galaxy.model.metadata DEBUG 2024-12-30 00:54:38,522 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 2 +galaxy.jobs INFO 2024-12-30 00:54:38,564 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 2 in /galaxy/server/database/jobs_directory/000/2 +galaxy.objectstore CRITICAL 2024-12-30 00:54:38,608 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] None delete error [Errno 13] Permission denied: 'tmpgn3htfkj' +galaxy.jobs DEBUG 2024-12-30 00:54:38,608 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 2 executed (116.840 ms) +galaxy.jobs.handler DEBUG 2024-12-30 00:54:39,875 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 3 +tpv.core.entities DEBUG 2024-12-30 00:54:39,913 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 00:54:39,913 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (3) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 00:54:39,918 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (3) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 00:54:39,934 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (3) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 00:54:39,955 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (3) Working directory for job is: /galaxy/server/database/jobs_directory/000/3 +galaxy.jobs.runners DEBUG 2024-12-30 00:54:39,962 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [3] queued (44.304 ms) +galaxy.jobs.handler INFO 2024-12-30 00:54:39,966 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (3) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 00:54:39,971 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 3 +galaxy.jobs DEBUG 2024-12-30 00:54:40,085 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [3] prepared (94.795 ms) +galaxy.jobs.command_factory INFO 2024-12-30 00:54:40,107 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/3/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/3/registry.xml' '/galaxy/server/database/jobs_directory/000/3/upload_params.json' '3:/galaxy/server/database/objects/d/3/8/dataset_d3801609-721d-49d2-9e61-05088cddce34_files:/galaxy/server/database/objects/d/3/8/dataset_d3801609-721d-49d2-9e61-05088cddce34.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 00:54:40,118 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (3) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/3/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/3/galaxy_3.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 00:54:49,540 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 3: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 00:54:54,488 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 3 finished +galaxy.model.metadata DEBUG 2024-12-30 00:54:54,551 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 3 +galaxy.jobs INFO 2024-12-30 00:54:54,590 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 3 in /galaxy/server/database/jobs_directory/000/3 +galaxy.jobs DEBUG 2024-12-30 00:54:54,652 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 3 executed (133.633 ms) +galaxy.jobs.handler DEBUG 2024-12-30 00:54:55,308 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 4 +tpv.core.entities DEBUG 2024-12-30 00:54:55,347 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 00:54:55,348 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (4) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 00:54:55,354 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (4) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 00:54:55,369 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (4) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 00:54:55,391 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (4) Working directory for job is: /galaxy/server/database/jobs_directory/000/4 +galaxy.jobs.runners DEBUG 2024-12-30 00:54:55,398 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [4] queued (44.748 ms) +galaxy.jobs.handler INFO 2024-12-30 00:54:55,403 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (4) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 00:54:55,407 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 4 +galaxy.jobs DEBUG 2024-12-30 00:54:55,496 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [4] prepared (70.501 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 00:54:55,497 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 00:54:55,497 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5+galaxy2: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-12-30 00:54:55,520 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyhdfd78af_2,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 00:54:55,543 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/4/tool_script.sh] for tool command [gx-fastq-filter '/galaxy/server/database/objects/d/3/8/dataset_d3801609-721d-49d2-9e61-05088cddce34.dat' '/galaxy/server/database/jobs_directory/000/4/configs/tmp_097w_3i' '/galaxy/server/database/objects/3/e/c/dataset_3ec732c7-770b-4b8d-a46d-7d43f979e300.dat' '/galaxy/server/database/objects/3/e/c/dataset_3ec732c7-770b-4b8d-a46d-7d43f979e300_files' 'sanger.gz'] +galaxy.jobs.runners DEBUG 2024-12-30 00:54:55,557 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (4) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/4/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/4/galaxy_4.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 00:54:55,569 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 00:54:55,569 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5+galaxy2: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-12-30 00:54:55,589 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyhdfd78af_2,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 00:55:00,702 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 4: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 00:55:05,915 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 4 finished +galaxy.model.metadata DEBUG 2024-12-30 00:55:05,976 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 4 +galaxy.jobs INFO 2024-12-30 00:55:06,011 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 4 in /galaxy/server/database/jobs_directory/000/4 +galaxy.objectstore CRITICAL 2024-12-30 00:55:06,059 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] None delete error [Errno 13] Permission denied: 'tmp_097w_3i' +galaxy.jobs DEBUG 2024-12-30 00:55:06,059 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 4 executed (116.516 ms) +galaxy.jobs.handler DEBUG 2024-12-30 00:55:07,688 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 5 +tpv.core.entities DEBUG 2024-12-30 00:55:07,728 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 00:55:07,728 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (5) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 00:55:07,735 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (5) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 00:55:07,754 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (5) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 00:55:07,774 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (5) Working directory for job is: /galaxy/server/database/jobs_directory/000/5 +galaxy.jobs.runners DEBUG 2024-12-30 00:55:07,781 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [5] queued (45.727 ms) +galaxy.jobs.handler INFO 2024-12-30 00:55:07,785 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (5) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 00:55:07,790 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 5 +galaxy.jobs DEBUG 2024-12-30 00:55:07,902 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [5] prepared (90.770 ms) +galaxy.jobs.command_factory INFO 2024-12-30 00:55:07,924 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/5/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/5/registry.xml' '/galaxy/server/database/jobs_directory/000/5/upload_params.json' '5:/galaxy/server/database/objects/c/9/d/dataset_c9db4f9c-b880-4f01-9616-a187d6420a33_files:/galaxy/server/database/objects/c/9/d/dataset_c9db4f9c-b880-4f01-9616-a187d6420a33.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 00:55:07,940 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (5) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/5/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/5/galaxy_5.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 00:55:17,924 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 5: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 00:55:22,921 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 5 finished +galaxy.model.metadata DEBUG 2024-12-30 00:55:22,982 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 5 +galaxy.jobs INFO 2024-12-30 00:55:23,019 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 5 in /galaxy/server/database/jobs_directory/000/5 +galaxy.jobs DEBUG 2024-12-30 00:55:23,083 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 5 executed (135.057 ms) +galaxy.jobs.handler DEBUG 2024-12-30 00:55:24,152 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 6 +tpv.core.entities DEBUG 2024-12-30 00:55:24,194 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 00:55:24,195 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (6) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 00:55:24,201 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (6) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 00:55:24,218 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (6) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 00:55:24,240 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (6) Working directory for job is: /galaxy/server/database/jobs_directory/000/6 +galaxy.jobs.runners DEBUG 2024-12-30 00:55:24,249 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [6] queued (47.132 ms) +galaxy.jobs.handler INFO 2024-12-30 00:55:24,253 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (6) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 00:55:24,258 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 6 +galaxy.jobs DEBUG 2024-12-30 00:55:24,348 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [6] prepared (71.023 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 00:55:24,349 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 00:55:24,349 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5+galaxy2: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-12-30 00:55:24,379 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyhdfd78af_2,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 00:55:24,403 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/6/tool_script.sh] for tool command [gx-fastq-filter '/galaxy/server/database/objects/c/9/d/dataset_c9db4f9c-b880-4f01-9616-a187d6420a33.dat' '/galaxy/server/database/jobs_directory/000/6/configs/tmposeccvgh' '/galaxy/server/database/objects/6/7/9/dataset_6792b127-ffc3-4e18-a4b5-67f3c43cfbca.dat' '/galaxy/server/database/objects/6/7/9/dataset_6792b127-ffc3-4e18-a4b5-67f3c43cfbca_files' 'cssanger'] +galaxy.jobs.runners DEBUG 2024-12-30 00:55:24,418 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (6) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/6/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/6/galaxy_6.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 00:55:24,433 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 00:55:24,434 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5+galaxy2: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-12-30 00:55:24,458 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyhdfd78af_2,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 00:55:30,094 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 6: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 00:55:34,925 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 6 finished +galaxy.model.metadata DEBUG 2024-12-30 00:55:34,994 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 6 +galaxy.jobs INFO 2024-12-30 00:55:35,032 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 6 in /galaxy/server/database/jobs_directory/000/6 +galaxy.objectstore CRITICAL 2024-12-30 00:55:35,072 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] None delete error [Errno 13] Permission denied: 'tmposeccvgh' +galaxy.jobs DEBUG 2024-12-30 00:55:35,072 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 6 executed (115.191 ms) +galaxy.jobs.handler DEBUG 2024-12-30 00:55:36,507 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 7 +tpv.core.entities DEBUG 2024-12-30 00:55:36,537 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 00:55:36,537 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (7) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 00:55:36,542 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (7) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 00:55:36,556 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (7) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 00:55:36,573 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (7) Working directory for job is: /galaxy/server/database/jobs_directory/000/7 +galaxy.jobs.runners DEBUG 2024-12-30 00:55:36,580 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [7] queued (38.038 ms) +galaxy.jobs.handler INFO 2024-12-30 00:55:36,584 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (7) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 00:55:36,588 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 7 +galaxy.jobs DEBUG 2024-12-30 00:55:36,699 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [7] prepared (91.944 ms) +galaxy.jobs.command_factory INFO 2024-12-30 00:55:36,720 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/7/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/7/registry.xml' '/galaxy/server/database/jobs_directory/000/7/upload_params.json' '7:/galaxy/server/database/objects/1/c/e/dataset_1ce9bf3a-2cb3-426a-ab53-dad847780695_files:/galaxy/server/database/objects/1/c/e/dataset_1ce9bf3a-2cb3-426a-ab53-dad847780695.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 00:55:36,732 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (7) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/7/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/7/galaxy_7.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 00:55:46,312 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 7: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 00:55:51,198 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 7 finished +galaxy.model.metadata DEBUG 2024-12-30 00:55:51,261 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 7 +galaxy.jobs INFO 2024-12-30 00:55:51,302 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 7 in /galaxy/server/database/jobs_directory/000/7 +galaxy.jobs DEBUG 2024-12-30 00:55:51,365 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 7 executed (136.412 ms) +galaxy.jobs.handler DEBUG 2024-12-30 00:55:51,878 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 8 +tpv.core.entities DEBUG 2024-12-30 00:55:51,914 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 00:55:51,914 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (8) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 00:55:51,918 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (8) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 00:55:51,936 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (8) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 00:55:51,956 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (8) Working directory for job is: /galaxy/server/database/jobs_directory/000/8 +galaxy.jobs.runners DEBUG 2024-12-30 00:55:51,965 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [8] queued (46.538 ms) +galaxy.jobs.handler INFO 2024-12-30 00:55:51,968 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (8) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 00:55:51,973 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 8 +galaxy.jobs DEBUG 2024-12-30 00:55:52,061 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [8] prepared (68.794 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 00:55:52,061 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 00:55:52,062 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5+galaxy2: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-12-30 00:55:52,083 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyhdfd78af_2,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 00:55:52,106 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/8/tool_script.sh] for tool command [gx-fastq-filter '/galaxy/server/database/objects/1/c/e/dataset_1ce9bf3a-2cb3-426a-ab53-dad847780695.dat' '/galaxy/server/database/jobs_directory/000/8/configs/tmpvp0mavwx' '/galaxy/server/database/objects/d/d/0/dataset_dd0fe042-4095-4386-9244-c4fa76ee94c0.dat' '/galaxy/server/database/objects/d/d/0/dataset_dd0fe042-4095-4386-9244-c4fa76ee94c0_files' 'sanger'] +galaxy.jobs.runners DEBUG 2024-12-30 00:55:52,118 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (8) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/8/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/8/galaxy_8.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 00:55:52,132 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 00:55:52,132 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5+galaxy2: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-12-30 00:55:52,152 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyhdfd78af_2,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 00:55:57,443 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 8: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 00:56:02,246 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 8 finished +galaxy.model.metadata DEBUG 2024-12-30 00:56:02,321 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 8 +galaxy.jobs INFO 2024-12-30 00:56:02,381 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 8 in /galaxy/server/database/jobs_directory/000/8 +galaxy.objectstore CRITICAL 2024-12-30 00:56:02,417 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] None delete error [Errno 13] Permission denied: 'tmpvp0mavwx' +galaxy.jobs DEBUG 2024-12-30 00:56:02,417 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 8 executed (145.657 ms) +galaxy.jobs.handler DEBUG 2024-12-30 00:56:04,212 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 9 +tpv.core.entities DEBUG 2024-12-30 00:56:04,247 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 00:56:04,248 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (9) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 00:56:04,253 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (9) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 00:56:04,269 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (9) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 00:56:04,288 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (9) Working directory for job is: /galaxy/server/database/jobs_directory/000/9 +galaxy.jobs.runners DEBUG 2024-12-30 00:56:04,295 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [9] queued (42.490 ms) +galaxy.jobs.handler INFO 2024-12-30 00:56:04,300 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (9) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 00:56:04,305 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 9 +galaxy.jobs DEBUG 2024-12-30 00:56:04,421 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [9] prepared (96.610 ms) +galaxy.jobs.command_factory INFO 2024-12-30 00:56:04,446 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/9/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/9/registry.xml' '/galaxy/server/database/jobs_directory/000/9/upload_params.json' '9:/galaxy/server/database/objects/4/5/0/dataset_450d81ae-b79b-4234-a2bc-e875142f9115_files:/galaxy/server/database/objects/4/5/0/dataset_450d81ae-b79b-4234-a2bc-e875142f9115.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 00:56:04,459 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (9) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/9/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/9/galaxy_9.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 00:56:12,694 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 9: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 00:56:17,692 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 9 finished +galaxy.model.metadata DEBUG 2024-12-30 00:56:17,749 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 9 +galaxy.jobs INFO 2024-12-30 00:56:17,789 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 9 in /galaxy/server/database/jobs_directory/000/9 +galaxy.jobs DEBUG 2024-12-30 00:56:17,848 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 9 executed (128.785 ms) +galaxy.jobs.handler DEBUG 2024-12-30 00:56:18,614 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 10 +tpv.core.entities DEBUG 2024-12-30 00:56:18,652 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 00:56:18,652 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (10) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 00:56:18,657 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (10) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 00:56:18,675 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (10) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 00:56:18,696 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (10) Working directory for job is: /galaxy/server/database/jobs_directory/000/10 +galaxy.jobs.runners DEBUG 2024-12-30 00:56:18,705 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [10] queued (47.888 ms) +galaxy.jobs.handler INFO 2024-12-30 00:56:18,709 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (10) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 00:56:18,713 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 10 +galaxy.jobs DEBUG 2024-12-30 00:56:18,805 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [10] prepared (71.934 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 00:56:18,806 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 00:56:18,806 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5+galaxy2: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-12-30 00:56:18,828 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyhdfd78af_2,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 00:56:18,850 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/10/tool_script.sh] for tool command [gx-fastq-filter '/galaxy/server/database/objects/4/5/0/dataset_450d81ae-b79b-4234-a2bc-e875142f9115.dat' '/galaxy/server/database/jobs_directory/000/10/configs/tmpg4hl57qt' '/galaxy/server/database/objects/0/7/7/dataset_07728230-e91e-43d0-9e77-662897b1674a.dat' '/galaxy/server/database/objects/0/7/7/dataset_07728230-e91e-43d0-9e77-662897b1674a_files' 'sanger'] +galaxy.jobs.runners DEBUG 2024-12-30 00:56:18,865 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (10) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/10/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/10/galaxy_10.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 00:56:18,878 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 00:56:18,878 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5+galaxy2: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-12-30 00:56:18,900 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyhdfd78af_2,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 00:56:23,827 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 10: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 00:56:28,804 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 10 finished +galaxy.model.metadata DEBUG 2024-12-30 00:56:28,862 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 10 +galaxy.jobs INFO 2024-12-30 00:56:28,903 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 10 in /galaxy/server/database/jobs_directory/000/10 +galaxy.objectstore CRITICAL 2024-12-30 00:56:28,958 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] None delete error [Errno 13] Permission denied: 'tmpg4hl57qt' +galaxy.jobs DEBUG 2024-12-30 00:56:28,958 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 10 executed (125.975 ms) +galaxy.jobs.handler DEBUG 2024-12-30 00:56:29,963 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 11 +tpv.core.entities DEBUG 2024-12-30 00:56:29,997 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 00:56:29,998 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (11) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 00:56:30,003 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (11) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 00:56:30,016 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (11) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 00:56:30,035 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (11) Working directory for job is: /galaxy/server/database/jobs_directory/000/11 +galaxy.jobs.runners DEBUG 2024-12-30 00:56:30,042 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [11] queued (38.665 ms) +galaxy.jobs.handler INFO 2024-12-30 00:56:30,047 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (11) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 00:56:30,049 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 11 +galaxy.jobs DEBUG 2024-12-30 00:56:30,159 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [11] prepared (91.390 ms) +galaxy.jobs.command_factory INFO 2024-12-30 00:56:30,182 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/11/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/11/registry.xml' '/galaxy/server/database/jobs_directory/000/11/upload_params.json' '11:/galaxy/server/database/objects/f/5/0/dataset_f50db55d-c71b-4ab2-a1d9-72ab1969d93a_files:/galaxy/server/database/objects/f/5/0/dataset_f50db55d-c71b-4ab2-a1d9-72ab1969d93a.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 00:56:30,196 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (11) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/11/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/11/galaxy_11.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 00:56:39,004 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 11: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 00:56:43,911 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 11 finished +galaxy.model.metadata DEBUG 2024-12-30 00:56:43,973 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 11 +galaxy.jobs INFO 2024-12-30 00:56:44,012 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 11 in /galaxy/server/database/jobs_directory/000/11 +galaxy.jobs DEBUG 2024-12-30 00:56:44,065 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 11 executed (124.878 ms) +galaxy.jobs.handler DEBUG 2024-12-30 00:56:45,350 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 12 +tpv.core.entities DEBUG 2024-12-30 00:56:45,389 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 00:56:45,390 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (12) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 00:56:45,396 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (12) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 00:56:45,413 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (12) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 00:56:45,435 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (12) Working directory for job is: /galaxy/server/database/jobs_directory/000/12 +galaxy.jobs.runners DEBUG 2024-12-30 00:56:45,443 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [12] queued (46.859 ms) +galaxy.jobs.handler INFO 2024-12-30 00:56:45,448 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (12) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 00:56:45,452 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 12 +galaxy.jobs DEBUG 2024-12-30 00:56:45,556 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [12] prepared (82.886 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 00:56:45,556 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 00:56:45,556 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5+galaxy2: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-12-30 00:56:45,580 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyhdfd78af_2,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 00:56:45,603 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/12/tool_script.sh] for tool command [gx-fastq-filter '/galaxy/server/database/objects/f/5/0/dataset_f50db55d-c71b-4ab2-a1d9-72ab1969d93a.dat' '/galaxy/server/database/jobs_directory/000/12/configs/tmprrkywyx7' '/galaxy/server/database/objects/9/a/6/dataset_9a66111a-1137-498d-98f1-593d91e180cf.dat' '/galaxy/server/database/objects/9/a/6/dataset_9a66111a-1137-498d-98f1-593d91e180cf_files' 'sanger'] +galaxy.jobs.runners DEBUG 2024-12-30 00:56:45,617 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (12) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/12/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/12/galaxy_12.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 00:56:45,645 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 00:56:45,645 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5+galaxy2: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-12-30 00:56:45,663 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyhdfd78af_2,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 00:56:51,143 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 12: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 00:56:56,041 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 12 finished +galaxy.model.metadata DEBUG 2024-12-30 00:56:56,099 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 12 +galaxy.jobs INFO 2024-12-30 00:56:56,139 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 12 in /galaxy/server/database/jobs_directory/000/12 +galaxy.objectstore CRITICAL 2024-12-30 00:56:56,180 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] None delete error [Errno 13] Permission denied: 'tmprrkywyx7' +galaxy.jobs DEBUG 2024-12-30 00:56:56,180 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 12 executed (109.578 ms) +galaxy.jobs.handler DEBUG 2024-12-30 00:56:57,701 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 13 +tpv.core.entities DEBUG 2024-12-30 00:56:57,737 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 00:56:57,738 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (13) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 00:56:57,743 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (13) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 00:56:57,760 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (13) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 00:56:57,780 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (13) Working directory for job is: /galaxy/server/database/jobs_directory/000/13 +galaxy.jobs.runners DEBUG 2024-12-30 00:56:57,787 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [13] queued (43.742 ms) +galaxy.jobs.handler INFO 2024-12-30 00:56:57,791 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (13) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 00:56:57,796 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 13 +galaxy.jobs DEBUG 2024-12-30 00:56:57,923 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [13] prepared (104.581 ms) +galaxy.jobs.command_factory INFO 2024-12-30 00:56:57,947 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/13/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/13/registry.xml' '/galaxy/server/database/jobs_directory/000/13/upload_params.json' '13:/galaxy/server/database/objects/6/e/d/dataset_6ed63b4e-ba8f-4ebf-b765-bbf53ef7fa4f_files:/galaxy/server/database/objects/6/e/d/dataset_6ed63b4e-ba8f-4ebf-b765-bbf53ef7fa4f.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 00:56:57,962 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (13) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/13/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/13/galaxy_13.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 00:57:07,411 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 13: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 00:57:12,265 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 13 finished +galaxy.model.metadata DEBUG 2024-12-30 00:57:12,331 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 13 +galaxy.jobs INFO 2024-12-30 00:57:12,376 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 13 in /galaxy/server/database/jobs_directory/000/13 +galaxy.jobs DEBUG 2024-12-30 00:57:12,438 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 13 executed (143.608 ms) +galaxy.jobs.handler DEBUG 2024-12-30 00:57:13,122 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 14 +tpv.core.entities DEBUG 2024-12-30 00:57:13,161 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 00:57:13,162 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (14) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 00:57:13,167 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (14) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 00:57:13,185 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (14) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 00:57:13,207 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (14) Working directory for job is: /galaxy/server/database/jobs_directory/000/14 +galaxy.jobs.runners DEBUG 2024-12-30 00:57:13,215 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [14] queued (47.946 ms) +galaxy.jobs.handler INFO 2024-12-30 00:57:13,219 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (14) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 00:57:13,224 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 14 +galaxy.jobs DEBUG 2024-12-30 00:57:13,310 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [14] prepared (66.963 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 00:57:13,311 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 00:57:13,311 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5+galaxy2: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-12-30 00:57:13,332 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyhdfd78af_2,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 00:57:13,354 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/14/tool_script.sh] for tool command [gx-fastq-filter '/galaxy/server/database/objects/6/e/d/dataset_6ed63b4e-ba8f-4ebf-b765-bbf53ef7fa4f.dat' '/galaxy/server/database/jobs_directory/000/14/configs/tmpsia7llf1' '/galaxy/server/database/objects/4/3/5/dataset_435d0704-31f7-43c7-acb9-19c7906d2791.dat' '/galaxy/server/database/objects/4/3/5/dataset_435d0704-31f7-43c7-acb9-19c7906d2791_files' 'sanger'] +galaxy.jobs.runners DEBUG 2024-12-30 00:57:13,366 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (14) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/14/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/14/galaxy_14.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 00:57:13,380 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 00:57:13,380 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5+galaxy2: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-12-30 00:57:13,400 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyhdfd78af_2,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 00:57:18,539 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 14: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 00:57:23,375 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 14 finished +galaxy.model.metadata DEBUG 2024-12-30 00:57:23,437 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 14 +galaxy.jobs INFO 2024-12-30 00:57:23,475 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 14 in /galaxy/server/database/jobs_directory/000/14 +galaxy.objectstore CRITICAL 2024-12-30 00:57:23,516 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] None delete error [Errno 13] Permission denied: 'tmpsia7llf1' +galaxy.jobs DEBUG 2024-12-30 00:57:23,516 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 14 executed (114.115 ms) +galaxy.jobs.handler DEBUG 2024-12-30 00:57:25,468 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 15 +tpv.core.entities DEBUG 2024-12-30 00:57:25,501 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 00:57:25,501 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (15) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 00:57:25,507 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (15) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 00:57:25,522 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (15) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 00:57:25,538 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (15) Working directory for job is: /galaxy/server/database/jobs_directory/000/15 +galaxy.jobs.runners DEBUG 2024-12-30 00:57:25,546 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [15] queued (38.927 ms) +galaxy.jobs.handler INFO 2024-12-30 00:57:25,550 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (15) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 00:57:25,555 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 15 +galaxy.jobs DEBUG 2024-12-30 00:57:25,687 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [15] prepared (110.931 ms) +galaxy.jobs.command_factory INFO 2024-12-30 00:57:25,709 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/15/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/15/registry.xml' '/galaxy/server/database/jobs_directory/000/15/upload_params.json' '15:/galaxy/server/database/objects/3/2/0/dataset_320d76c1-de48-4c94-ace8-c2b5235754c3_files:/galaxy/server/database/objects/3/2/0/dataset_320d76c1-de48-4c94-ace8-c2b5235754c3.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 00:57:25,740 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (15) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/15/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/15/galaxy_15.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 00:57:33,814 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 15: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 00:57:38,756 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 15 finished +galaxy.model.metadata DEBUG 2024-12-30 00:57:38,819 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 15 +galaxy.jobs INFO 2024-12-30 00:57:38,861 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 15 in /galaxy/server/database/jobs_directory/000/15 +galaxy.jobs DEBUG 2024-12-30 00:57:38,917 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 15 executed (131.653 ms) +galaxy.jobs.handler DEBUG 2024-12-30 00:57:39,951 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 16 +tpv.core.entities DEBUG 2024-12-30 00:57:39,988 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 00:57:39,988 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (16) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 00:57:39,992 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (16) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 00:57:40,008 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (16) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 00:57:40,027 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (16) Working directory for job is: /galaxy/server/database/jobs_directory/000/16 +galaxy.jobs.runners DEBUG 2024-12-30 00:57:40,036 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [16] queued (43.378 ms) +galaxy.jobs.handler INFO 2024-12-30 00:57:40,040 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (16) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 00:57:40,044 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 16 +galaxy.jobs DEBUG 2024-12-30 00:57:40,133 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [16] prepared (68.172 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 00:57:40,133 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 00:57:40,133 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5+galaxy2: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-12-30 00:57:40,157 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyhdfd78af_2,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 00:57:40,179 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/16/tool_script.sh] for tool command [gx-fastq-filter '/galaxy/server/database/objects/3/2/0/dataset_320d76c1-de48-4c94-ace8-c2b5235754c3.dat' '/galaxy/server/database/jobs_directory/000/16/configs/tmptyt7csr4' '/galaxy/server/database/objects/9/0/3/dataset_903aac80-1a35-4adc-b2d4-8f7b04f45fc2.dat' '/galaxy/server/database/objects/9/0/3/dataset_903aac80-1a35-4adc-b2d4-8f7b04f45fc2_files' 'sanger'] +galaxy.jobs.runners DEBUG 2024-12-30 00:57:40,194 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (16) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/16/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/16/galaxy_16.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 00:57:40,208 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 00:57:40,208 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5+galaxy2: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-12-30 00:57:40,226 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyhdfd78af_2,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 00:57:45,050 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 16: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 00:57:49,936 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 16 finished +galaxy.model.metadata DEBUG 2024-12-30 00:57:49,994 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 16 +galaxy.jobs INFO 2024-12-30 00:57:50,031 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 16 in /galaxy/server/database/jobs_directory/000/16 +galaxy.objectstore CRITICAL 2024-12-30 00:57:50,073 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] None delete error [Errno 13] Permission denied: 'tmptyt7csr4' +galaxy.jobs DEBUG 2024-12-30 00:57:50,073 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 16 executed (110.439 ms) +galaxy.jobs.handler DEBUG 2024-12-30 00:57:51,272 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 17 +tpv.core.entities DEBUG 2024-12-30 00:57:51,311 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 00:57:51,312 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (17) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 00:57:51,318 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (17) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 00:57:51,337 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (17) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 00:57:51,360 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (17) Working directory for job is: /galaxy/server/database/jobs_directory/000/17 +galaxy.jobs.runners DEBUG 2024-12-30 00:57:51,368 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [17] queued (49.852 ms) +galaxy.jobs.handler INFO 2024-12-30 00:57:51,372 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (17) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 00:57:51,377 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 17 +galaxy.jobs DEBUG 2024-12-30 00:57:51,488 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [17] prepared (91.118 ms) +galaxy.jobs.command_factory INFO 2024-12-30 00:57:51,509 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/17/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/17/registry.xml' '/galaxy/server/database/jobs_directory/000/17/upload_params.json' '17:/galaxy/server/database/objects/4/0/9/dataset_409e023e-f55e-40eb-87e8-a8a93fb2c569_files:/galaxy/server/database/objects/4/0/9/dataset_409e023e-f55e-40eb-87e8-a8a93fb2c569.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 00:57:51,523 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (17) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/17/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/17/galaxy_17.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 00:57:59,212 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 17: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 00:58:03,999 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 17 finished +galaxy.model.metadata DEBUG 2024-12-30 00:58:04,060 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 17 +galaxy.jobs INFO 2024-12-30 00:58:04,103 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 17 in /galaxy/server/database/jobs_directory/000/17 +galaxy.jobs DEBUG 2024-12-30 00:58:04,159 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 17 executed (131.520 ms) +galaxy.jobs.handler DEBUG 2024-12-30 00:58:04,655 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 18 +tpv.core.entities DEBUG 2024-12-30 00:58:04,696 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 00:58:04,696 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (18) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 00:58:04,702 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (18) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 00:58:04,717 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (18) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 00:58:04,737 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (18) Working directory for job is: /galaxy/server/database/jobs_directory/000/18 +galaxy.jobs.runners DEBUG 2024-12-30 00:58:04,746 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [18] queued (43.572 ms) +galaxy.jobs.handler INFO 2024-12-30 00:58:04,750 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (18) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 00:58:04,755 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 18 +galaxy.jobs DEBUG 2024-12-30 00:58:04,849 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [18] prepared (74.018 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 00:58:04,850 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 00:58:04,850 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5+galaxy2: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-12-30 00:58:04,870 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyhdfd78af_2,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 00:58:04,895 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/18/tool_script.sh] for tool command [gx-fastq-filter '/galaxy/server/database/objects/4/0/9/dataset_409e023e-f55e-40eb-87e8-a8a93fb2c569.dat' '/galaxy/server/database/jobs_directory/000/18/configs/tmpbdkqifwx' '/galaxy/server/database/objects/a/1/6/dataset_a16d7fec-6759-44cd-aac0-775ea89502b2.dat' '/galaxy/server/database/objects/a/1/6/dataset_a16d7fec-6759-44cd-aac0-775ea89502b2_files' 'sanger'] +galaxy.jobs.runners DEBUG 2024-12-30 00:58:04,910 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (18) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/18/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/18/galaxy_18.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 00:58:04,924 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 00:58:04,924 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5+galaxy2: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-12-30 00:58:04,947 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyhdfd78af_2,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 00:58:10,380 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 18: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 00:58:15,329 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 18 finished +galaxy.model.metadata DEBUG 2024-12-30 00:58:15,413 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 18 +galaxy.jobs INFO 2024-12-30 00:58:15,482 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 18 in /galaxy/server/database/jobs_directory/000/18 +galaxy.objectstore CRITICAL 2024-12-30 00:58:15,536 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] None delete error [Errno 13] Permission denied: 'tmpbdkqifwx' +galaxy.jobs DEBUG 2024-12-30 00:58:15,536 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 18 executed (178.038 ms) +galaxy.jobs.handler DEBUG 2024-12-30 00:58:18,045 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 19 +tpv.core.entities DEBUG 2024-12-30 00:58:18,082 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 00:58:18,082 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (19) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 00:58:18,087 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (19) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 00:58:18,106 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (19) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 00:58:18,128 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (19) Working directory for job is: /galaxy/server/database/jobs_directory/000/19 +galaxy.jobs.runners DEBUG 2024-12-30 00:58:18,136 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [19] queued (48.545 ms) +galaxy.jobs.handler INFO 2024-12-30 00:58:18,139 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (19) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 00:58:18,145 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 19 +galaxy.jobs DEBUG 2024-12-30 00:58:18,273 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [19] prepared (106.417 ms) +galaxy.jobs.command_factory INFO 2024-12-30 00:58:18,296 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/19/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/19/registry.xml' '/galaxy/server/database/jobs_directory/000/19/upload_params.json' '19:/galaxy/server/database/objects/9/c/3/dataset_9c358bf5-6246-44f9-b451-9344843dd2df_files:/galaxy/server/database/objects/9/c/3/dataset_9c358bf5-6246-44f9-b451-9344843dd2df.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 00:58:18,310 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (19) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/19/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/19/galaxy_19.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 00:58:26,582 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 19: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 00:58:31,454 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 19 finished +galaxy.model.metadata DEBUG 2024-12-30 00:58:31,522 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 19 +galaxy.jobs INFO 2024-12-30 00:58:31,567 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 19 in /galaxy/server/database/jobs_directory/000/19 +galaxy.jobs DEBUG 2024-12-30 00:58:31,620 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 19 executed (131.270 ms) +galaxy.jobs.handler DEBUG 2024-12-30 00:58:32,458 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 20 +tpv.core.entities DEBUG 2024-12-30 00:58:32,497 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 00:58:32,497 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (20) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 00:58:32,503 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (20) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 00:58:32,517 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (20) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 00:58:32,538 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (20) Working directory for job is: /galaxy/server/database/jobs_directory/000/20 +galaxy.jobs.runners DEBUG 2024-12-30 00:58:32,547 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [20] queued (44.307 ms) +galaxy.jobs.handler INFO 2024-12-30 00:58:32,551 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (20) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 00:58:32,554 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 20 +galaxy.security.object_wrapper WARNING 2024-12-30 00:58:32,616 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Unable to create dynamic subclass SafeStringWrapper__galaxy.model.none_like.None__NoneType__NotImplementedType__Number__SafeStringWrapper__ToolParameterValueWrapper__bool__bytearray__ellipsis for , None: type() doesn't support MRO entry resolution; use types.new_class() +galaxy.jobs DEBUG 2024-12-30 00:58:32,666 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [20] prepared (93.780 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 00:58:32,666 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 00:58:32,666 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3: mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33 +galaxy.tool_util.deps.containers INFO 2024-12-30 00:58:32,857 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 00:58:32,879 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/20/tool_script.sh] for tool command [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/20/outputs/COMMAND_VERSION 2>&1; +addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/9/c/3/dataset_9c358bf5-6246-44f9-b451-9344843dd2df.dat' infile && samtools view -@ $addthreads -b -o outfile infile && samtools sort -@ $addthreads -m $addmemory"M" -T "${TMPDIR:-.}" -O bam -o tmpsam outfile && mv tmpsam outfile] +galaxy.jobs.runners DEBUG 2024-12-30 00:58:32,894 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (20) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/20/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/20/galaxy_20.ec; +if [ -f "/galaxy/server/database/jobs_directory/000/20/working/outfile" ] ; then cp "/galaxy/server/database/jobs_directory/000/20/working/outfile" "/galaxy/server/database/objects/9/1/3/dataset_91316a40-ef40-41cf-b9f3-7f10c5d9601d.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 00:58:32,907 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 00:58:32,907 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3: mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33 +galaxy.tool_util.deps.containers INFO 2024-12-30 00:58:32,927 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 00:58:45,873 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 20: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 00:58:50,814 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 20 finished +galaxy.model.metadata DEBUG 2024-12-30 00:58:50,876 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 20 +galaxy.util WARNING 2024-12-30 00:58:50,937 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/9/1/3/dataset_91316a40-ef40-41cf-b9f3-7f10c5d9601d.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/9/1/3/dataset_91316a40-ef40-41cf-b9f3-7f10c5d9601d.dat' +galaxy.jobs INFO 2024-12-30 00:58:50,969 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 20 in /galaxy/server/database/jobs_directory/000/20 +galaxy.jobs DEBUG 2024-12-30 00:58:51,027 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 20 executed (185.128 ms) +galaxy.jobs.handler DEBUG 2024-12-30 00:58:52,061 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 21, 22 +tpv.core.entities DEBUG 2024-12-30 00:58:52,099 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 00:58:52,100 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (21) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 00:58:52,104 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (21) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 00:58:52,118 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (21) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 00:58:52,140 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (21) Working directory for job is: /galaxy/server/database/jobs_directory/000/21 +galaxy.jobs.runners DEBUG 2024-12-30 00:58:52,146 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [21] queued (42.567 ms) +galaxy.jobs.handler INFO 2024-12-30 00:58:52,151 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (21) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 00:58:52,154 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 21 +tpv.core.entities DEBUG 2024-12-30 00:58:52,168 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 00:58:52,169 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (22) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 00:58:52,176 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (22) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 00:58:52,191 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (22) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 00:58:52,222 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (22) Working directory for job is: /galaxy/server/database/jobs_directory/000/22 +galaxy.jobs.runners DEBUG 2024-12-30 00:58:52,231 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [22] queued (54.592 ms) +galaxy.jobs.handler INFO 2024-12-30 00:58:52,234 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (22) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 00:58:52,247 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 22 +galaxy.jobs DEBUG 2024-12-30 00:58:52,282 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [21] prepared (103.136 ms) +galaxy.jobs.command_factory INFO 2024-12-30 00:58:52,308 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/21/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/21/registry.xml' '/galaxy/server/database/jobs_directory/000/21/upload_params.json' '21:/galaxy/server/database/objects/2/c/9/dataset_2c9607fc-350c-43f5-a46e-7ec3001626b7_files:/galaxy/server/database/objects/2/c/9/dataset_2c9607fc-350c-43f5-a46e-7ec3001626b7.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 00:58:52,323 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (21) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/21/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/21/galaxy_21.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-12-30 00:58:52,388 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [22] prepared (118.921 ms) +galaxy.jobs.command_factory INFO 2024-12-30 00:58:52,411 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/22/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/22/registry.xml' '/galaxy/server/database/jobs_directory/000/22/upload_params.json' '22:/galaxy/server/database/objects/b/6/f/dataset_b6f9f501-2b3c-44d2-893f-59e883837a99_files:/galaxy/server/database/objects/b/6/f/dataset_b6f9f501-2b3c-44d2-893f-59e883837a99.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 00:58:52,425 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (22) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/22/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/22/galaxy_22.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes ERROR 2024-12-30 00:59:01,212 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Could not clean up k8s batch job. Ignoring... +Traceback (most recent call last): + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/http.py", line 437, in raise_for_status + resp.raise_for_status() + File "/galaxy/server/.venv/lib/python3.10/site-packages/requests/models.py", line 1021, in raise_for_status + raise HTTPError(http_error_msg, response=self) +requests.exceptions.HTTPError: 409 Client Error: Conflict for url: https://10.107.32.1:443/apis/batch/v1/namespaces/prod-24-12-30-00-37-1/jobs/gxy-r5c47 + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 817, in _handle_job_failure + self.__cleanup_k8s_job(job) + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 824, in __cleanup_k8s_job + delete_job(job, k8s_cleanup_job) + File "/galaxy/server/lib/galaxy/jobs/runners/util/pykube_util.py", line 107, in delete_job + job.scale(replicas=0) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/mixins.py", line 30, in scale + self.update() + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 165, in update + self.patch(self.obj, subresource=subresource) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 157, in patch + self.api.raise_for_status(r) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/http.py", line 444, in raise_for_status + raise HTTPError(resp.status_code, payload["message"]) +pykube.exceptions.HTTPError: Operation cannot be fulfilled on jobs.batch "gxy-r5c47": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 00:59:01,294 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (22/gxy-r5c47) Terminated at user's request +galaxy.jobs.runners DEBUG 2024-12-30 00:59:02,365 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 21: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 00:59:07,382 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 21 finished +galaxy.model.metadata DEBUG 2024-12-30 00:59:07,445 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 21 +galaxy.jobs INFO 2024-12-30 00:59:07,492 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 21 in /galaxy/server/database/jobs_directory/000/21 +galaxy.jobs DEBUG 2024-12-30 00:59:07,561 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 21 executed (150.687 ms) +galaxy.jobs.handler DEBUG 2024-12-30 00:59:08,618 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 23, 24 +tpv.core.entities DEBUG 2024-12-30 00:59:08,658 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 00:59:08,658 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (23) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 00:59:08,665 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (23) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 00:59:08,683 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (23) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 00:59:08,708 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (23) Working directory for job is: /galaxy/server/database/jobs_directory/000/23 +galaxy.jobs.runners DEBUG 2024-12-30 00:59:08,715 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [23] queued (50.373 ms) +galaxy.jobs.handler INFO 2024-12-30 00:59:08,720 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (23) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 00:59:08,723 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 23 +tpv.core.entities DEBUG 2024-12-30 00:59:08,741 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 00:59:08,742 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (24) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 00:59:08,749 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (24) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 00:59:08,770 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (24) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 00:59:08,806 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (24) Working directory for job is: /galaxy/server/database/jobs_directory/000/24 +galaxy.jobs.runners DEBUG 2024-12-30 00:59:08,814 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [24] queued (65.177 ms) +galaxy.jobs.handler INFO 2024-12-30 00:59:08,820 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (24) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 00:59:08,823 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 24 +galaxy.jobs DEBUG 2024-12-30 00:59:08,866 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [23] prepared (117.624 ms) +galaxy.jobs.command_factory INFO 2024-12-30 00:59:08,901 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/23/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/23/registry.xml' '/galaxy/server/database/jobs_directory/000/23/upload_params.json' '23:/galaxy/server/database/objects/8/2/f/dataset_82f68dc0-4041-44c8-b4d7-afb9e5550e29_files:/galaxy/server/database/objects/8/2/f/dataset_82f68dc0-4041-44c8-b4d7-afb9e5550e29.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 00:59:08,917 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (23) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/23/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/23/galaxy_23.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-12-30 00:59:08,965 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [24] prepared (115.451 ms) +galaxy.jobs.command_factory INFO 2024-12-30 00:59:08,990 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/24/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/24/registry.xml' '/galaxy/server/database/jobs_directory/000/24/upload_params.json' '24:/galaxy/server/database/objects/1/5/1/dataset_15145316-4dbd-405c-8120-95224b22d731_files:/galaxy/server/database/objects/1/5/1/dataset_15145316-4dbd-405c-8120-95224b22d731.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 00:59:09,005 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (24) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/24/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/24/galaxy_24.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 00:59:18,799 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 23: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 00:59:18,824 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 24: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 00:59:23,849 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 24 finished +galaxy.jobs.runners DEBUG 2024-12-30 00:59:23,885 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 23 finished +galaxy.model.metadata DEBUG 2024-12-30 00:59:23,924 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 24 +galaxy.model.metadata DEBUG 2024-12-30 00:59:23,969 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 23 +galaxy.jobs INFO 2024-12-30 00:59:23,975 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 24 in /galaxy/server/database/jobs_directory/000/24 +galaxy.jobs DEBUG 2024-12-30 00:59:24,054 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 24 executed (176.461 ms) +galaxy.jobs INFO 2024-12-30 00:59:24,059 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 23 in /galaxy/server/database/jobs_directory/000/23 +galaxy.jobs DEBUG 2024-12-30 00:59:24,129 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 23 executed (209.397 ms) +galaxy.jobs.handler DEBUG 2024-12-30 00:59:25,201 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 25 +tpv.core.entities DEBUG 2024-12-30 00:59:25,248 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 00:59:25,249 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (25) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 00:59:25,255 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (25) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 00:59:25,275 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (25) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 00:59:25,295 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (25) Working directory for job is: /galaxy/server/database/jobs_directory/000/25 +galaxy.jobs.runners DEBUG 2024-12-30 00:59:25,305 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [25] queued (48.838 ms) +galaxy.jobs.handler INFO 2024-12-30 00:59:25,309 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (25) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 00:59:25,314 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 25 +galaxy.jobs DEBUG 2024-12-30 00:59:25,415 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [25] prepared (78.900 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 00:59:25,415 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 00:59:25,415 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3: mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33 +galaxy.tool_util.deps.containers INFO 2024-12-30 00:59:25,642 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 00:59:25,665 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/25/tool_script.sh] for tool command [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/25/outputs/COMMAND_VERSION 2>&1; +addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/1/5/1/dataset_15145316-4dbd-405c-8120-95224b22d731.dat' reference.fa && samtools faidx reference.fa && ln -s '/galaxy/server/database/objects/8/2/f/dataset_82f68dc0-4041-44c8-b4d7-afb9e5550e29.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/5/b/b/metadata_5bb2679b-65fa-4f8f-b100-2c269866be67.dat' infile.crai && samtools view -@ $addthreads -b -o outfile -T 'reference.fa' -t 'reference.fa.fai' infile && samtools sort -@ $addthreads -m $addmemory"M" -T "${TMPDIR:-.}" -O bam -o tmpsam outfile && mv tmpsam outfile] +galaxy.jobs.runners DEBUG 2024-12-30 00:59:25,681 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (25) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/25/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/25/galaxy_25.ec; +if [ -f "/galaxy/server/database/jobs_directory/000/25/working/outfile" ] ; then cp "/galaxy/server/database/jobs_directory/000/25/working/outfile" "/galaxy/server/database/objects/2/e/f/dataset_2efacf8e-75e1-4748-9d81-6916a7a3fb44.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 00:59:25,694 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 00:59:25,694 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3: mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33 +galaxy.tool_util.deps.containers INFO 2024-12-30 00:59:25,713 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 00:59:30,961 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 25: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 00:59:36,201 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 25 finished +galaxy.model.metadata DEBUG 2024-12-30 00:59:36,271 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 25 +galaxy.util WARNING 2024-12-30 00:59:36,331 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/2/e/f/dataset_2efacf8e-75e1-4748-9d81-6916a7a3fb44.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/2/e/f/dataset_2efacf8e-75e1-4748-9d81-6916a7a3fb44.dat' +galaxy.jobs INFO 2024-12-30 00:59:36,366 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 25 in /galaxy/server/database/jobs_directory/000/25 +galaxy.jobs DEBUG 2024-12-30 00:59:36,428 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 25 executed (197.351 ms) +galaxy.jobs.handler DEBUG 2024-12-30 00:59:37,590 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 26 +tpv.core.entities DEBUG 2024-12-30 00:59:37,627 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 00:59:37,627 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (26) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 00:59:37,633 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (26) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 00:59:37,651 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (26) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 00:59:37,674 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (26) Working directory for job is: /galaxy/server/database/jobs_directory/000/26 +galaxy.jobs.runners DEBUG 2024-12-30 00:59:37,682 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [26] queued (49.241 ms) +galaxy.jobs.handler INFO 2024-12-30 00:59:37,686 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (26) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 00:59:37,692 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 26 +galaxy.jobs DEBUG 2024-12-30 00:59:37,804 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [26] prepared (90.755 ms) +galaxy.jobs.command_factory INFO 2024-12-30 00:59:37,827 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/26/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/26/registry.xml' '/galaxy/server/database/jobs_directory/000/26/upload_params.json' '26:/galaxy/server/database/objects/3/4/c/dataset_34c83c44-d6e9-4318-9a91-53b0c43c419a_files:/galaxy/server/database/objects/3/4/c/dataset_34c83c44-d6e9-4318-9a91-53b0c43c419a.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 00:59:37,843 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (26) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/26/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/26/galaxy_26.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 00:59:47,157 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 26: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 00:59:52,310 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 26 finished +galaxy.model.metadata DEBUG 2024-12-30 00:59:52,377 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 26 +galaxy.jobs INFO 2024-12-30 00:59:52,465 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 26 in /galaxy/server/database/jobs_directory/000/26 +galaxy.jobs DEBUG 2024-12-30 00:59:52,520 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 26 executed (179.286 ms) +galaxy.jobs.handler DEBUG 2024-12-30 00:59:53,033 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 27 +tpv.core.entities DEBUG 2024-12-30 00:59:53,072 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 00:59:53,073 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (27) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 00:59:53,079 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (27) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 00:59:53,097 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (27) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 00:59:53,117 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (27) Working directory for job is: /galaxy/server/database/jobs_directory/000/27 +galaxy.jobs.runners DEBUG 2024-12-30 00:59:53,125 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [27] queued (45.427 ms) +galaxy.jobs.handler INFO 2024-12-30 00:59:53,129 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (27) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 00:59:53,133 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 27 +galaxy.jobs DEBUG 2024-12-30 00:59:53,211 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [27] prepared (56.078 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 00:59:53,212 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 00:59:53,212 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3: mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33 +galaxy.tool_util.deps.containers INFO 2024-12-30 00:59:53,233 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 00:59:53,255 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/27/tool_script.sh] for tool command [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/27/outputs/COMMAND_VERSION 2>&1; +addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/3/4/c/dataset_34c83c44-d6e9-4318-9a91-53b0c43c419a.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/b/1/9/metadata_b1974381-2ba2-4623-88e3-61636470b2bf.dat' infile.bai && samtools view -@ $addthreads -b -o outfile infile] +galaxy.jobs.runners DEBUG 2024-12-30 00:59:53,270 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (27) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/27/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/27/galaxy_27.ec; +if [ -f "/galaxy/server/database/jobs_directory/000/27/working/outfile" ] ; then cp "/galaxy/server/database/jobs_directory/000/27/working/outfile" "/galaxy/server/database/objects/1/b/8/dataset_1b808570-2846-47c5-b673-69d7156cf648.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 00:59:53,283 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 00:59:53,283 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3: mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33 +galaxy.tool_util.deps.containers INFO 2024-12-30 00:59:53,303 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 00:59:59,321 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 27: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:00:04,986 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 27 finished +galaxy.model.metadata DEBUG 2024-12-30 01:00:05,073 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 27 +galaxy.util WARNING 2024-12-30 01:00:05,135 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/1/b/8/dataset_1b808570-2846-47c5-b673-69d7156cf648.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/1/b/8/dataset_1b808570-2846-47c5-b673-69d7156cf648.dat' +galaxy.jobs INFO 2024-12-30 01:00:05,184 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 27 in /galaxy/server/database/jobs_directory/000/27 +galaxy.jobs DEBUG 2024-12-30 01:00:05,261 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 27 executed (236.672 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:00:06,607 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 28 +tpv.core.entities DEBUG 2024-12-30 01:00:06,650 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:00:06,650 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (28) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:00:06,658 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (28) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:00:06,676 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (28) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:00:06,701 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (28) Working directory for job is: /galaxy/server/database/jobs_directory/000/28 +galaxy.jobs.runners DEBUG 2024-12-30 01:00:06,708 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [28] queued (50.091 ms) +galaxy.jobs.handler INFO 2024-12-30 01:00:06,712 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (28) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:00:06,718 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 28 +galaxy.jobs DEBUG 2024-12-30 01:00:06,861 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [28] prepared (119.726 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:00:06,888 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/28/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/28/registry.xml' '/galaxy/server/database/jobs_directory/000/28/upload_params.json' '28:/galaxy/server/database/objects/3/f/1/dataset_3f1a80b0-52ae-464b-ade4-8e8e29d9ec18_files:/galaxy/server/database/objects/3/f/1/dataset_3f1a80b0-52ae-464b-ade4-8e8e29d9ec18.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:00:06,903 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (28) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/28/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/28/galaxy_28.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:00:17,702 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 28: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:00:22,704 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 28 finished +galaxy.model.metadata DEBUG 2024-12-30 01:00:22,768 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 28 +galaxy.jobs INFO 2024-12-30 01:00:22,856 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 28 in /galaxy/server/database/jobs_directory/000/28 +galaxy.jobs DEBUG 2024-12-30 01:00:22,917 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 28 executed (182.582 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:00:24,111 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 29 +tpv.core.entities DEBUG 2024-12-30 01:00:24,154 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:00:24,155 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (29) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:00:24,160 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (29) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:00:24,180 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (29) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:00:24,202 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (29) Working directory for job is: /galaxy/server/database/jobs_directory/000/29 +galaxy.jobs.runners DEBUG 2024-12-30 01:00:24,210 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [29] queued (49.261 ms) +galaxy.jobs.handler INFO 2024-12-30 01:00:24,214 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (29) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:00:24,219 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 29 +galaxy.jobs DEBUG 2024-12-30 01:00:24,314 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [29] prepared (73.888 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:00:24,314 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:00:24,315 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3: mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:00:24,336 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:00:24,363 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/29/tool_script.sh] for tool command [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/29/outputs/COMMAND_VERSION 2>&1; +addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/3/f/1/dataset_3f1a80b0-52ae-464b-ade4-8e8e29d9ec18.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/5/1/6/metadata_51686606-7655-42ce-80b7-29bdb8709f83.dat' infile.bai && samtools view -@ $addthreads -b -o outfile infile] +galaxy.jobs.runners DEBUG 2024-12-30 01:00:24,381 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (29) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/29/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/29/galaxy_29.ec; +if [ -f "/galaxy/server/database/jobs_directory/000/29/working/outfile" ] ; then cp "/galaxy/server/database/jobs_directory/000/29/working/outfile" "/galaxy/server/database/objects/c/9/3/dataset_c93549d3-dc3e-4ef0-9316-3962a786abc9.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:00:24,395 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:00:24,395 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3: mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:00:24,416 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 01:00:29,893 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 29: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:00:34,817 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 29 finished +galaxy.model.metadata DEBUG 2024-12-30 01:00:34,885 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 29 +galaxy.util WARNING 2024-12-30 01:00:34,937 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/c/9/3/dataset_c93549d3-dc3e-4ef0-9316-3962a786abc9.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/c/9/3/dataset_c93549d3-dc3e-4ef0-9316-3962a786abc9.dat' +galaxy.jobs INFO 2024-12-30 01:00:34,979 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 29 in /galaxy/server/database/jobs_directory/000/29 +galaxy.jobs DEBUG 2024-12-30 01:00:35,033 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 29 executed (188.017 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:00:36,486 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 30 +tpv.core.entities DEBUG 2024-12-30 01:00:36,523 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:00:36,523 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (30) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:00:36,529 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (30) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:00:36,545 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (30) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:00:36,566 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (30) Working directory for job is: /galaxy/server/database/jobs_directory/000/30 +galaxy.jobs.runners DEBUG 2024-12-30 01:00:36,572 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [30] queued (43.258 ms) +galaxy.jobs.handler INFO 2024-12-30 01:00:36,576 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (30) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:00:36,580 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 30 +galaxy.jobs DEBUG 2024-12-30 01:00:36,690 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [30] prepared (91.640 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:00:36,714 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/30/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/30/registry.xml' '/galaxy/server/database/jobs_directory/000/30/upload_params.json' '30:/galaxy/server/database/objects/6/f/5/dataset_6f531b03-1517-465e-9632-bbdac4d1fce2_files:/galaxy/server/database/objects/6/f/5/dataset_6f531b03-1517-465e-9632-bbdac4d1fce2.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:00:36,727 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (30) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/30/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/30/galaxy_30.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:00:45,072 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 30: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:00:50,107 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 30 finished +galaxy.model.metadata DEBUG 2024-12-30 01:00:50,172 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 30 +galaxy.jobs INFO 2024-12-30 01:00:50,220 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 30 in /galaxy/server/database/jobs_directory/000/30 +galaxy.jobs DEBUG 2024-12-30 01:00:50,289 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 30 executed (151.141 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:00:50,881 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 31 +tpv.core.entities DEBUG 2024-12-30 01:00:50,912 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:00:50,912 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (31) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:00:50,916 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (31) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:00:50,931 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (31) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:00:50,948 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (31) Working directory for job is: /galaxy/server/database/jobs_directory/000/31 +galaxy.jobs.runners DEBUG 2024-12-30 01:00:50,957 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [31] queued (41.047 ms) +galaxy.jobs.handler INFO 2024-12-30 01:00:50,962 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (31) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:00:50,966 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 31 +galaxy.jobs DEBUG 2024-12-30 01:00:51,044 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [31] prepared (57.231 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:00:51,045 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:00:51,045 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3: mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:00:51,067 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:00:51,089 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/31/tool_script.sh] for tool command [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/31/outputs/COMMAND_VERSION 2>&1; +addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/6/f/5/dataset_6f531b03-1517-465e-9632-bbdac4d1fce2.dat' infile && samtools view -@ $addthreads -b -o outfile infile && samtools sort -@ $addthreads -m $addmemory"M" -T "${TMPDIR:-.}" -O bam -o tmpsam outfile && mv tmpsam outfile] +galaxy.jobs.runners DEBUG 2024-12-30 01:00:51,103 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (31) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/31/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/31/galaxy_31.ec; +if [ -f "/galaxy/server/database/jobs_directory/000/31/working/outfile" ] ; then cp "/galaxy/server/database/jobs_directory/000/31/working/outfile" "/galaxy/server/database/objects/b/7/d/dataset_b7d20c47-3c50-46e8-b2e3-14561bfea4be.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:00:51,117 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:00:51,117 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3: mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:00:51,136 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 01:00:57,207 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 31: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:01:02,209 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 31 finished +galaxy.model.metadata DEBUG 2024-12-30 01:01:02,273 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 31 +galaxy.util WARNING 2024-12-30 01:01:02,313 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/b/7/d/dataset_b7d20c47-3c50-46e8-b2e3-14561bfea4be.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/b/7/d/dataset_b7d20c47-3c50-46e8-b2e3-14561bfea4be.dat' +galaxy.jobs INFO 2024-12-30 01:01:02,355 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 31 in /galaxy/server/database/jobs_directory/000/31 +galaxy.jobs DEBUG 2024-12-30 01:01:02,412 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 31 executed (175.908 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:01:03,344 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 32 +tpv.core.entities DEBUG 2024-12-30 01:01:03,379 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:01:03,380 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (32) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:01:03,384 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (32) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:01:03,400 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (32) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:01:03,418 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (32) Working directory for job is: /galaxy/server/database/jobs_directory/000/32 +galaxy.jobs.runners DEBUG 2024-12-30 01:01:03,425 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [32] queued (40.922 ms) +galaxy.jobs.handler INFO 2024-12-30 01:01:03,429 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (32) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:01:03,434 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 32 +galaxy.jobs DEBUG 2024-12-30 01:01:03,538 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [32] prepared (87.360 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:01:03,562 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/32/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/32/registry.xml' '/galaxy/server/database/jobs_directory/000/32/upload_params.json' '32:/galaxy/server/database/objects/8/6/7/dataset_867f6e65-c516-44bc-ad66-a6c71a93cf2b_files:/galaxy/server/database/objects/8/6/7/dataset_867f6e65-c516-44bc-ad66-a6c71a93cf2b.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:01:03,574 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (32) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/32/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/32/galaxy_32.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:01:12,374 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 32: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:01:17,773 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 32 finished +galaxy.model.metadata DEBUG 2024-12-30 01:01:17,848 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 32 +galaxy.jobs INFO 2024-12-30 01:01:17,896 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 32 in /galaxy/server/database/jobs_directory/000/32 +galaxy.jobs DEBUG 2024-12-30 01:01:17,961 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 32 executed (149.849 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:01:18,807 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 33 +tpv.core.entities DEBUG 2024-12-30 01:01:18,853 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:01:18,854 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (33) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:01:18,862 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (33) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:01:18,883 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (33) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:01:18,907 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (33) Working directory for job is: /galaxy/server/database/jobs_directory/000/33 +galaxy.jobs.runners DEBUG 2024-12-30 01:01:18,916 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [33] queued (53.925 ms) +galaxy.jobs.handler INFO 2024-12-30 01:01:18,921 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (33) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:01:18,926 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 33 +galaxy.jobs DEBUG 2024-12-30 01:01:19,012 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [33] prepared (63.823 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:01:19,012 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:01:19,012 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3: mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:01:19,035 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:01:19,058 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/33/tool_script.sh] for tool command [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/33/outputs/COMMAND_VERSION 2>&1; +addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/8/6/7/dataset_867f6e65-c516-44bc-ad66-a6c71a93cf2b.dat' infile && samtools view -@ $addthreads -h -o outfile infile] +galaxy.jobs.runners DEBUG 2024-12-30 01:01:19,075 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (33) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/33/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/33/galaxy_33.ec; +if [ -f "/galaxy/server/database/jobs_directory/000/33/working/outfile" ] ; then cp "/galaxy/server/database/jobs_directory/000/33/working/outfile" "/galaxy/server/database/objects/6/4/8/dataset_648379be-ae90-4283-9b62-be8ce86ac851.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:01:19,089 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:01:19,090 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3: mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:01:19,109 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 01:01:24,582 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 33: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:01:30,097 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 33 finished +galaxy.model.metadata DEBUG 2024-12-30 01:01:30,170 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 33 +galaxy.util WARNING 2024-12-30 01:01:30,178 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/6/4/8/dataset_648379be-ae90-4283-9b62-be8ce86ac851.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/6/4/8/dataset_648379be-ae90-4283-9b62-be8ce86ac851.dat' +galaxy.jobs INFO 2024-12-30 01:01:30,223 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 33 in /galaxy/server/database/jobs_directory/000/33 +galaxy.jobs DEBUG 2024-12-30 01:01:30,283 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 33 executed (154.878 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:01:31,211 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 34 +tpv.core.entities DEBUG 2024-12-30 01:01:31,253 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:01:31,254 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (34) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:01:31,261 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (34) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:01:31,281 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (34) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:01:31,302 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (34) Working directory for job is: /galaxy/server/database/jobs_directory/000/34 +galaxy.jobs.runners DEBUG 2024-12-30 01:01:31,310 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [34] queued (48.954 ms) +galaxy.jobs.handler INFO 2024-12-30 01:01:31,314 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (34) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:01:31,319 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 34 +galaxy.jobs DEBUG 2024-12-30 01:01:31,454 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [34] prepared (114.221 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:01:31,488 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/34/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/34/registry.xml' '/galaxy/server/database/jobs_directory/000/34/upload_params.json' '34:/galaxy/server/database/objects/c/f/0/dataset_cf08de5f-7c96-43fe-a5fc-5f5fd218e798_files:/galaxy/server/database/objects/c/f/0/dataset_cf08de5f-7c96-43fe-a5fc-5f5fd218e798.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:01:31,511 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (34) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/34/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/34/galaxy_34.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:01:39,769 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 34: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:01:44,891 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 34 finished +galaxy.model.metadata DEBUG 2024-12-30 01:01:44,956 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 34 +galaxy.jobs INFO 2024-12-30 01:01:44,997 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 34 in /galaxy/server/database/jobs_directory/000/34 +galaxy.jobs DEBUG 2024-12-30 01:01:45,047 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 34 executed (127.370 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:01:45,642 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 35 +tpv.core.entities DEBUG 2024-12-30 01:01:45,685 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:01:45,686 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (35) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:01:45,693 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (35) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:01:45,711 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (35) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:01:45,731 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (35) Working directory for job is: /galaxy/server/database/jobs_directory/000/35 +galaxy.jobs.runners DEBUG 2024-12-30 01:01:45,739 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [35] queued (45.921 ms) +galaxy.jobs.handler INFO 2024-12-30 01:01:45,743 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (35) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:01:45,748 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 35 +galaxy.jobs DEBUG 2024-12-30 01:01:45,832 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [35] prepared (62.397 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:01:45,832 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:01:45,832 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3: mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:01:45,852 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:01:45,876 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/35/tool_script.sh] for tool command [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/35/outputs/COMMAND_VERSION 2>&1; +addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/c/f/0/dataset_cf08de5f-7c96-43fe-a5fc-5f5fd218e798.dat' infile && samtools view -@ $addthreads -b -o outfile infile && samtools sort -@ $addthreads -m $addmemory"M" -T "${TMPDIR:-.}" -O bam -o tmpsam outfile && mv tmpsam outfile] +galaxy.jobs.runners DEBUG 2024-12-30 01:01:45,891 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (35) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/35/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/35/galaxy_35.ec; +if [ -f "/galaxy/server/database/jobs_directory/000/35/working/outfile" ] ; then cp "/galaxy/server/database/jobs_directory/000/35/working/outfile" "/galaxy/server/database/objects/c/d/5/dataset_cd54992a-ba21-46dc-b3a8-c99888bd1a6f.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:01:45,904 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:01:45,904 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3: mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:01:45,922 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 01:01:51,894 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 35: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:01:56,838 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 35 finished +galaxy.model.metadata DEBUG 2024-12-30 01:01:56,905 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 35 +galaxy.util WARNING 2024-12-30 01:01:56,955 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/c/d/5/dataset_cd54992a-ba21-46dc-b3a8-c99888bd1a6f.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/c/d/5/dataset_cd54992a-ba21-46dc-b3a8-c99888bd1a6f.dat' +galaxy.jobs INFO 2024-12-30 01:01:56,996 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 35 in /galaxy/server/database/jobs_directory/000/35 +galaxy.jobs DEBUG 2024-12-30 01:01:57,074 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 35 executed (205.263 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:01:58,069 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 36 +tpv.core.entities DEBUG 2024-12-30 01:01:58,108 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:01:58,109 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (36) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:01:58,115 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (36) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:01:58,133 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (36) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:01:58,155 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (36) Working directory for job is: /galaxy/server/database/jobs_directory/000/36 +galaxy.jobs.runners DEBUG 2024-12-30 01:01:58,163 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [36] queued (48.718 ms) +galaxy.jobs.handler INFO 2024-12-30 01:01:58,168 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (36) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:01:58,172 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 36 +galaxy.jobs DEBUG 2024-12-30 01:01:58,285 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [36] prepared (95.732 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:01:58,310 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/36/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/36/registry.xml' '/galaxy/server/database/jobs_directory/000/36/upload_params.json' '36:/galaxy/server/database/objects/f/f/9/dataset_ff9e3630-42b4-416e-acd3-2f51776a3369_files:/galaxy/server/database/objects/f/f/9/dataset_ff9e3630-42b4-416e-acd3-2f51776a3369.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:01:58,322 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (36) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/36/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/36/galaxy_36.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:02:07,102 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 36: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:02:12,143 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 36 finished +galaxy.model.metadata DEBUG 2024-12-30 01:02:12,210 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 36 +galaxy.jobs INFO 2024-12-30 01:02:12,256 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 36 in /galaxy/server/database/jobs_directory/000/36 +galaxy.jobs DEBUG 2024-12-30 01:02:12,315 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 36 executed (142.643 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:02:13,514 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 37 +tpv.core.entities DEBUG 2024-12-30 01:02:13,555 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:02:13,556 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (37) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:02:13,561 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (37) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:02:13,576 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (37) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:02:13,597 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (37) Working directory for job is: /galaxy/server/database/jobs_directory/000/37 +galaxy.jobs.runners DEBUG 2024-12-30 01:02:13,605 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [37] queued (44.470 ms) +galaxy.jobs.handler INFO 2024-12-30 01:02:13,610 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (37) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:02:13,614 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 37 +galaxy.jobs DEBUG 2024-12-30 01:02:13,700 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [37] prepared (64.703 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:02:13,701 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:02:13,701 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3: mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:02:13,723 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:02:13,748 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/37/tool_script.sh] for tool command [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/37/outputs/COMMAND_VERSION 2>&1; +addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/f/f/9/dataset_ff9e3630-42b4-416e-acd3-2f51776a3369.dat' infile && samtools view -@ $addthreads -h -o outfile infile] +galaxy.jobs.runners DEBUG 2024-12-30 01:02:13,764 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (37) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/37/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/37/galaxy_37.ec; +if [ -f "/galaxy/server/database/jobs_directory/000/37/working/outfile" ] ; then cp "/galaxy/server/database/jobs_directory/000/37/working/outfile" "/galaxy/server/database/objects/b/e/1/dataset_be153424-88f0-4307-873b-7a5dd534472e.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:02:13,778 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:02:13,778 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3: mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:02:13,797 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 01:02:19,251 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 37: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:02:24,180 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 37 finished +galaxy.model.metadata DEBUG 2024-12-30 01:02:24,243 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 37 +galaxy.util WARNING 2024-12-30 01:02:24,251 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/b/e/1/dataset_be153424-88f0-4307-873b-7a5dd534472e.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/b/e/1/dataset_be153424-88f0-4307-873b-7a5dd534472e.dat' +galaxy.jobs INFO 2024-12-30 01:02:24,293 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 37 in /galaxy/server/database/jobs_directory/000/37 +galaxy.jobs DEBUG 2024-12-30 01:02:24,362 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 37 executed (152.049 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:02:25,883 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 38 +tpv.core.entities DEBUG 2024-12-30 01:02:25,922 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:02:25,922 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (38) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:02:25,928 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (38) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:02:25,948 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (38) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:02:25,971 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (38) Working directory for job is: /galaxy/server/database/jobs_directory/000/38 +galaxy.jobs.runners DEBUG 2024-12-30 01:02:25,979 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [38] queued (50.635 ms) +galaxy.jobs.handler INFO 2024-12-30 01:02:25,983 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (38) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:02:25,989 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 38 +galaxy.jobs DEBUG 2024-12-30 01:02:26,125 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [38] prepared (111.145 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:02:26,150 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/38/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/38/registry.xml' '/galaxy/server/database/jobs_directory/000/38/upload_params.json' '38:/galaxy/server/database/objects/6/5/8/dataset_65847279-3505-415f-acf6-d92d9038b5c4_files:/galaxy/server/database/objects/6/5/8/dataset_65847279-3505-415f-acf6-d92d9038b5c4.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:02:26,165 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (38) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/38/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/38/galaxy_38.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:02:36,488 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 38: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:02:41,596 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 38 finished +galaxy.model.metadata DEBUG 2024-12-30 01:02:41,664 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 38 +galaxy.jobs INFO 2024-12-30 01:02:41,744 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 38 in /galaxy/server/database/jobs_directory/000/38 +galaxy.jobs DEBUG 2024-12-30 01:02:41,811 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 38 executed (181.804 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:02:42,376 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 39 +tpv.core.entities DEBUG 2024-12-30 01:02:42,419 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:02:42,419 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (39) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:02:42,426 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (39) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:02:42,444 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (39) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:02:42,468 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (39) Working directory for job is: /galaxy/server/database/jobs_directory/000/39 +galaxy.jobs.runners DEBUG 2024-12-30 01:02:42,477 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [39] queued (51.587 ms) +galaxy.jobs.handler INFO 2024-12-30 01:02:42,482 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (39) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:02:42,486 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 39 +galaxy.jobs DEBUG 2024-12-30 01:02:42,573 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [39] prepared (66.170 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:02:42,574 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:02:42,574 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3: mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:02:42,596 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:02:42,622 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/39/tool_script.sh] for tool command [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/39/outputs/COMMAND_VERSION 2>&1; +addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/6/5/8/dataset_65847279-3505-415f-acf6-d92d9038b5c4.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/6/2/0/metadata_62000f91-16f1-4941-a503-c9eddf4de206.dat' infile.bai && samtools view -@ $addthreads -h -o outfile infile] +galaxy.jobs.runners DEBUG 2024-12-30 01:02:42,637 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (39) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/39/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/39/galaxy_39.ec; +if [ -f "/galaxy/server/database/jobs_directory/000/39/working/outfile" ] ; then cp "/galaxy/server/database/jobs_directory/000/39/working/outfile" "/galaxy/server/database/objects/4/b/0/dataset_4b0623b9-1f49-4503-a66c-4b0592c5b92b.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:02:42,651 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:02:42,651 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3: mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:02:42,669 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 01:02:47,676 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 39: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:02:52,652 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 39 finished +galaxy.model.metadata DEBUG 2024-12-30 01:02:52,721 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 39 +galaxy.util WARNING 2024-12-30 01:02:52,733 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/4/b/0/dataset_4b0623b9-1f49-4503-a66c-4b0592c5b92b.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/4/b/0/dataset_4b0623b9-1f49-4503-a66c-4b0592c5b92b.dat' +galaxy.jobs INFO 2024-12-30 01:02:52,768 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 39 in /galaxy/server/database/jobs_directory/000/39 +galaxy.jobs DEBUG 2024-12-30 01:02:52,824 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 39 executed (143.726 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:02:53,869 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 40 +tpv.core.entities DEBUG 2024-12-30 01:02:53,909 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:02:53,909 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (40) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:02:53,916 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (40) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:02:53,936 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (40) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:02:53,958 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (40) Working directory for job is: /galaxy/server/database/jobs_directory/000/40 +galaxy.jobs.runners DEBUG 2024-12-30 01:02:53,967 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [40] queued (50.742 ms) +galaxy.jobs.handler INFO 2024-12-30 01:02:53,971 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (40) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:02:53,976 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 40 +galaxy.jobs DEBUG 2024-12-30 01:02:54,096 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [40] prepared (99.169 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:02:54,121 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/40/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/40/registry.xml' '/galaxy/server/database/jobs_directory/000/40/upload_params.json' '40:/galaxy/server/database/objects/6/0/8/dataset_608664d7-0bf6-47f6-a39a-2a953a90c5a8_files:/galaxy/server/database/objects/6/0/8/dataset_608664d7-0bf6-47f6-a39a-2a953a90c5a8.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:02:54,137 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (40) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/40/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/40/galaxy_40.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:03:03,927 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 40: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:03:09,100 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 40 finished +galaxy.model.metadata DEBUG 2024-12-30 01:03:09,167 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 40 +galaxy.jobs INFO 2024-12-30 01:03:09,250 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 40 in /galaxy/server/database/jobs_directory/000/40 +galaxy.jobs DEBUG 2024-12-30 01:03:09,319 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 40 executed (189.000 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:03:10,355 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 41 +tpv.core.entities DEBUG 2024-12-30 01:03:10,394 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:03:10,395 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (41) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:03:10,401 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (41) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:03:10,417 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (41) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:03:10,435 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (41) Working directory for job is: /galaxy/server/database/jobs_directory/000/41 +galaxy.jobs.runners DEBUG 2024-12-30 01:03:10,443 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [41] queued (41.842 ms) +galaxy.jobs.handler INFO 2024-12-30 01:03:10,447 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (41) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:03:10,452 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 41 +galaxy.jobs DEBUG 2024-12-30 01:03:10,539 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [41] prepared (67.354 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:03:10,540 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:03:10,540 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3: mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:03:10,562 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:03:10,588 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/41/tool_script.sh] for tool command [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/41/outputs/COMMAND_VERSION 2>&1; +addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/6/0/8/dataset_608664d7-0bf6-47f6-a39a-2a953a90c5a8.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/6/9/1/metadata_691152b8-dccd-4549-859c-186d84302395.dat' infile.bai && samtools view -H -o outfile infile] +galaxy.jobs.runners DEBUG 2024-12-30 01:03:10,606 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (41) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/41/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/41/galaxy_41.ec; +if [ -f "/galaxy/server/database/jobs_directory/000/41/working/outfile" ] ; then cp "/galaxy/server/database/jobs_directory/000/41/working/outfile" "/galaxy/server/database/objects/4/0/0/dataset_40039d6c-c7e7-4932-9508-f3f044716876.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:03:10,619 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:03:10,619 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3: mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:03:10,640 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 01:03:16,085 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 41: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:03:20,999 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 41 finished +galaxy.model.metadata DEBUG 2024-12-30 01:03:21,062 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 41 +galaxy.util WARNING 2024-12-30 01:03:21,073 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/4/0/0/dataset_40039d6c-c7e7-4932-9508-f3f044716876.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/4/0/0/dataset_40039d6c-c7e7-4932-9508-f3f044716876.dat' +galaxy.jobs INFO 2024-12-30 01:03:21,103 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 41 in /galaxy/server/database/jobs_directory/000/41 +galaxy.jobs DEBUG 2024-12-30 01:03:21,156 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 41 executed (128.063 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:03:22,718 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 42 +tpv.core.entities DEBUG 2024-12-30 01:03:22,756 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:03:22,756 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (42) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:03:22,761 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (42) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:03:22,780 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (42) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:03:22,800 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (42) Working directory for job is: /galaxy/server/database/jobs_directory/000/42 +galaxy.jobs.runners DEBUG 2024-12-30 01:03:22,808 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [42] queued (46.436 ms) +galaxy.jobs.handler INFO 2024-12-30 01:03:22,813 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (42) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:03:22,815 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 42 +galaxy.jobs DEBUG 2024-12-30 01:03:22,937 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [42] prepared (100.204 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:03:22,960 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/42/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/42/registry.xml' '/galaxy/server/database/jobs_directory/000/42/upload_params.json' '42:/galaxy/server/database/objects/5/b/a/dataset_5ba6f385-5fb8-4ea8-b781-f14cc4ccb78b_files:/galaxy/server/database/objects/5/b/a/dataset_5ba6f385-5fb8-4ea8-b781-f14cc4ccb78b.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:03:22,972 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (42) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/42/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/42/galaxy_42.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes ERROR 2024-12-30 01:03:31,186 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Could not clean up k8s batch job. Ignoring... +Traceback (most recent call last): + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/http.py", line 437, in raise_for_status + resp.raise_for_status() + File "/galaxy/server/.venv/lib/python3.10/site-packages/requests/models.py", line 1021, in raise_for_status + raise HTTPError(http_error_msg, response=self) +requests.exceptions.HTTPError: 409 Client Error: Conflict for url: https://10.107.32.1:443/apis/batch/v1/namespaces/prod-24-12-30-00-37-1/jobs/gxy-7fn4f + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 817, in _handle_job_failure + self.__cleanup_k8s_job(job) + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 824, in __cleanup_k8s_job + delete_job(job, k8s_cleanup_job) + File "/galaxy/server/lib/galaxy/jobs/runners/util/pykube_util.py", line 107, in delete_job + job.scale(replicas=0) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/mixins.py", line 30, in scale + self.update() + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 165, in update + self.patch(self.obj, subresource=subresource) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 157, in patch + self.api.raise_for_status(r) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/http.py", line 444, in raise_for_status + raise HTTPError(resp.status_code, payload["message"]) +pykube.exceptions.HTTPError: Operation cannot be fulfilled on jobs.batch "gxy-7fn4f": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:03:31,237 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (42/gxy-7fn4f) Terminated at user's request +galaxy.jobs.handler DEBUG 2024-12-30 01:03:31,993 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 43 +tpv.core.entities DEBUG 2024-12-30 01:03:32,025 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:03:32,026 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (43) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:03:32,031 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (43) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:03:32,046 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (43) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:03:32,061 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (43) Working directory for job is: /galaxy/server/database/jobs_directory/000/43 +galaxy.jobs.runners DEBUG 2024-12-30 01:03:32,068 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [43] queued (36.803 ms) +galaxy.jobs.handler INFO 2024-12-30 01:03:32,071 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (43) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:03:32,076 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 43 +galaxy.jobs DEBUG 2024-12-30 01:03:32,195 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [43] prepared (100.039 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:03:32,222 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/43/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/43/registry.xml' '/galaxy/server/database/jobs_directory/000/43/upload_params.json' '43:/galaxy/server/database/objects/b/7/5/dataset_b75648cc-5249-4304-8ace-91d5cc9ef736_files:/galaxy/server/database/objects/b/7/5/dataset_b75648cc-5249-4304-8ace-91d5cc9ef736.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:03:32,236 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (43) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/43/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/43/galaxy_43.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:03:42,570 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 43: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:03:47,766 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 43 finished +galaxy.model.metadata DEBUG 2024-12-30 01:03:47,835 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 43 +galaxy.jobs INFO 2024-12-30 01:03:47,923 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 43 in /galaxy/server/database/jobs_directory/000/43 +galaxy.jobs DEBUG 2024-12-30 01:03:47,987 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 43 executed (190.020 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:03:48,438 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 44 +tpv.core.entities DEBUG 2024-12-30 01:03:48,476 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:03:48,476 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (44) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:03:48,481 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (44) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:03:48,494 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (44) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:03:48,511 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (44) Working directory for job is: /galaxy/server/database/jobs_directory/000/44 +galaxy.jobs.runners DEBUG 2024-12-30 01:03:48,520 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [44] queued (39.080 ms) +galaxy.jobs.handler INFO 2024-12-30 01:03:48,523 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (44) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:03:48,529 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 44 +galaxy.jobs DEBUG 2024-12-30 01:03:48,614 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [44] prepared (63.995 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:03:48,614 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:03:48,614 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3: mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:03:48,640 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:03:48,665 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/44/tool_script.sh] for tool command [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/44/outputs/COMMAND_VERSION 2>&1; +addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/b/7/5/dataset_b75648cc-5249-4304-8ace-91d5cc9ef736.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/9/5/f/metadata_95f71871-7671-4ce0-a133-901b41e93fef.dat' infile.bai && samtools view -@ $addthreads -c -o outfile infile] +galaxy.jobs.runners DEBUG 2024-12-30 01:03:48,682 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (44) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/44/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/44/galaxy_44.ec; +if [ -f "/galaxy/server/database/jobs_directory/000/44/working/outfile" ] ; then cp "/galaxy/server/database/jobs_directory/000/44/working/outfile" "/galaxy/server/database/objects/4/2/e/dataset_42e0785c-a848-48fe-a08c-0b862e215d98.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:03:48,697 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:03:48,697 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3: mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:03:48,718 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 01:03:54,754 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 44: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:04:00,393 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 44 finished +galaxy.model.metadata DEBUG 2024-12-30 01:04:00,454 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 44 +galaxy.util WARNING 2024-12-30 01:04:00,463 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/4/2/e/dataset_42e0785c-a848-48fe-a08c-0b862e215d98.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/4/2/e/dataset_42e0785c-a848-48fe-a08c-0b862e215d98.dat' +galaxy.jobs INFO 2024-12-30 01:04:00,494 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 44 in /galaxy/server/database/jobs_directory/000/44 +galaxy.jobs DEBUG 2024-12-30 01:04:00,552 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 44 executed (128.711 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:04:01,875 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 45, 46 +tpv.core.entities DEBUG 2024-12-30 01:04:01,913 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:04:01,914 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (45) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:04:01,919 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (45) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:04:01,935 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (45) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:04:01,954 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (45) Working directory for job is: /galaxy/server/database/jobs_directory/000/45 +galaxy.jobs.runners DEBUG 2024-12-30 01:04:01,960 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [45] queued (41.002 ms) +galaxy.jobs.handler INFO 2024-12-30 01:04:01,965 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (45) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:04:01,972 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 45 +tpv.core.entities DEBUG 2024-12-30 01:04:01,989 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:04:01,989 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (46) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:04:01,996 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (46) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:04:02,018 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (46) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:04:02,057 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (46) Working directory for job is: /galaxy/server/database/jobs_directory/000/46 +galaxy.jobs.runners DEBUG 2024-12-30 01:04:02,064 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [46] queued (67.559 ms) +galaxy.jobs.handler INFO 2024-12-30 01:04:02,071 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (46) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:04:02,075 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 46 +galaxy.jobs DEBUG 2024-12-30 01:04:02,123 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [45] prepared (123.029 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:04:02,158 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/45/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/45/registry.xml' '/galaxy/server/database/jobs_directory/000/45/upload_params.json' '45:/galaxy/server/database/objects/1/8/3/dataset_183c37b0-bee7-4a73-a48e-30ab382a4229_files:/galaxy/server/database/objects/1/8/3/dataset_183c37b0-bee7-4a73-a48e-30ab382a4229.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:04:02,178 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (45) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/45/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/45/galaxy_45.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-12-30 01:04:02,226 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [46] prepared (128.788 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:04:02,255 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/46/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/46/registry.xml' '/galaxy/server/database/jobs_directory/000/46/upload_params.json' '46:/galaxy/server/database/objects/a/1/2/dataset_a12e5adb-c6f6-4c5c-b777-5253dc17e5c5_files:/galaxy/server/database/objects/a/1/2/dataset_a12e5adb-c6f6-4c5c-b777-5253dc17e5c5.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:04:02,271 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (46) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/46/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/46/galaxy_46.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:04:12,140 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 45: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:04:12,166 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 46: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:04:17,766 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 45 finished +galaxy.jobs.runners DEBUG 2024-12-30 01:04:17,791 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 46 finished +galaxy.model.metadata DEBUG 2024-12-30 01:04:17,842 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 45 +galaxy.model.metadata DEBUG 2024-12-30 01:04:17,869 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 46 +galaxy.jobs INFO 2024-12-30 01:04:17,901 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 45 in /galaxy/server/database/jobs_directory/000/45 +galaxy.jobs INFO 2024-12-30 01:04:17,925 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 46 in /galaxy/server/database/jobs_directory/000/46 +galaxy.jobs DEBUG 2024-12-30 01:04:17,971 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 45 executed (175.149 ms) +galaxy.jobs DEBUG 2024-12-30 01:04:17,993 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 46 executed (168.303 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:04:18,609 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 47 +tpv.core.entities DEBUG 2024-12-30 01:04:18,655 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:04:18,656 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (47) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:04:18,662 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (47) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:04:18,679 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (47) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:04:18,702 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (47) Working directory for job is: /galaxy/server/database/jobs_directory/000/47 +galaxy.jobs.runners DEBUG 2024-12-30 01:04:18,712 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [47] queued (49.762 ms) +galaxy.jobs.handler INFO 2024-12-30 01:04:18,718 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (47) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:04:18,720 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 47 +galaxy.jobs DEBUG 2024-12-30 01:04:18,819 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [47] prepared (77.071 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:04:18,820 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:04:18,820 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3: mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:04:18,843 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:04:18,867 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/47/tool_script.sh] for tool command [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/47/outputs/COMMAND_VERSION 2>&1; +addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/a/1/2/dataset_a12e5adb-c6f6-4c5c-b777-5253dc17e5c5.dat' reference.fa && samtools faidx reference.fa && ln -s '/galaxy/server/database/objects/1/8/3/dataset_183c37b0-bee7-4a73-a48e-30ab382a4229.dat' infile && samtools view -@ $addthreads -C -o outfile --output-fmt-option no_ref -T 'reference.fa' -t 'reference.fa.fai' infile] +galaxy.jobs.runners DEBUG 2024-12-30 01:04:18,884 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (47) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/47/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/47/galaxy_47.ec; +if [ -f "/galaxy/server/database/jobs_directory/000/47/working/outfile" ] ; then cp "/galaxy/server/database/jobs_directory/000/47/working/outfile" "/galaxy/server/database/objects/a/9/8/dataset_a9873827-fc02-4b4a-9cb2-b29b6072215a.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:04:18,897 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:04:18,898 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3: mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:04:18,921 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 01:04:25,362 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 47: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:04:30,585 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 47 finished +galaxy.model.metadata DEBUG 2024-12-30 01:04:30,646 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 47 +galaxy.util WARNING 2024-12-30 01:04:30,696 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/a/9/8/dataset_a9873827-fc02-4b4a-9cb2-b29b6072215a.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/a/9/8/dataset_a9873827-fc02-4b4a-9cb2-b29b6072215a.dat' +galaxy.jobs INFO 2024-12-30 01:04:30,730 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 47 in /galaxy/server/database/jobs_directory/000/47 +galaxy.jobs DEBUG 2024-12-30 01:04:30,798 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 47 executed (185.061 ms) +sqlitedict.SqliteMultithread DEBUG 2024-12-30 01:04:31,344 [pN:job_handler_0,p:8,tN:Thread-3] received: --close--, send: --no more-- +galaxy.jobs.handler DEBUG 2024-12-30 01:04:32,375 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 48, 49 +tpv.core.entities DEBUG 2024-12-30 01:04:32,412 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:04:32,413 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (48) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:04:32,419 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (48) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:04:32,438 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (48) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:04:32,460 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (48) Working directory for job is: /galaxy/server/database/jobs_directory/000/48 +galaxy.jobs.runners DEBUG 2024-12-30 01:04:32,468 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [48] queued (48.352 ms) +galaxy.jobs.handler INFO 2024-12-30 01:04:32,472 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (48) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:04:32,477 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 48 +tpv.core.entities DEBUG 2024-12-30 01:04:32,491 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:04:32,492 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (49) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:04:32,499 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (49) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:04:32,518 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (49) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:04:32,553 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (49) Working directory for job is: /galaxy/server/database/jobs_directory/000/49 +galaxy.jobs.runners DEBUG 2024-12-30 01:04:32,562 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [49] queued (62.816 ms) +galaxy.jobs.handler INFO 2024-12-30 01:04:32,567 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (49) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:04:32,571 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 49 +galaxy.jobs DEBUG 2024-12-30 01:04:32,616 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [48] prepared (114.662 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:04:32,650 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/48/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/48/registry.xml' '/galaxy/server/database/jobs_directory/000/48/upload_params.json' '48:/galaxy/server/database/objects/f/9/4/dataset_f9405ae4-38bc-415f-bab2-c96fdb4e7e11_files:/galaxy/server/database/objects/f/9/4/dataset_f9405ae4-38bc-415f-bab2-c96fdb4e7e11.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:04:32,669 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (48) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/48/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/48/galaxy_48.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-12-30 01:04:32,714 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [49] prepared (117.150 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:04:32,743 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/49/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/49/registry.xml' '/galaxy/server/database/jobs_directory/000/49/upload_params.json' '49:/galaxy/server/database/objects/9/d/d/dataset_9dd09f3c-6b61-4cf5-9b57-7f146d6f38a3_files:/galaxy/server/database/objects/9/d/d/dataset_9dd09f3c-6b61-4cf5-9b57-7f146d6f38a3.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:04:32,757 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (49) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/49/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/49/galaxy_49.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:04:41,851 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 48: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:04:41,877 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 49: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:04:47,499 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 48 finished +galaxy.jobs.runners DEBUG 2024-12-30 01:04:47,558 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 49 finished +galaxy.model.metadata DEBUG 2024-12-30 01:04:47,580 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 48 +galaxy.model.metadata DEBUG 2024-12-30 01:04:47,650 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 49 +galaxy.jobs INFO 2024-12-30 01:04:47,687 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 48 in /galaxy/server/database/jobs_directory/000/48 +galaxy.jobs INFO 2024-12-30 01:04:47,701 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 49 in /galaxy/server/database/jobs_directory/000/49 +galaxy.jobs DEBUG 2024-12-30 01:04:47,757 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 48 executed (223.848 ms) +galaxy.jobs DEBUG 2024-12-30 01:04:47,775 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 49 executed (175.095 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:04:49,180 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 50 +tpv.core.entities DEBUG 2024-12-30 01:04:49,230 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:04:49,231 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (50) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:04:49,238 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (50) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:04:49,259 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (50) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:04:49,282 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (50) Working directory for job is: /galaxy/server/database/jobs_directory/000/50 +galaxy.jobs.runners DEBUG 2024-12-30 01:04:49,292 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [50] queued (53.315 ms) +galaxy.jobs.handler INFO 2024-12-30 01:04:49,296 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (50) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:04:49,302 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 50 +galaxy.jobs DEBUG 2024-12-30 01:04:49,412 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [50] prepared (86.602 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:04:49,412 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:04:49,412 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3: mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:04:49,649 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:04:49,675 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/50/tool_script.sh] for tool command [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/50/outputs/COMMAND_VERSION 2>&1; +addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/9/d/d/dataset_9dd09f3c-6b61-4cf5-9b57-7f146d6f38a3.dat' reference.fa && samtools faidx reference.fa && ln -s '/galaxy/server/database/objects/f/9/4/dataset_f9405ae4-38bc-415f-bab2-c96fdb4e7e11.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/2/8/2/metadata_28276a21-5728-4dd1-90cf-15f56bbf1923.dat' infile.bai && samtools view -@ $addthreads -C -o outfile --output-fmt-option no_ref -T 'reference.fa' -t 'reference.fa.fai' infile] +galaxy.jobs.runners DEBUG 2024-12-30 01:04:49,692 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (50) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/50/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/50/galaxy_50.ec; +if [ -f "/galaxy/server/database/jobs_directory/000/50/working/outfile" ] ; then cp "/galaxy/server/database/jobs_directory/000/50/working/outfile" "/galaxy/server/database/objects/b/6/4/dataset_b64148af-5c88-4762-ad1d-81593f749c67.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:04:49,706 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:04:49,706 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3: mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:04:49,730 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 01:04:55,000 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 50: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:05:00,191 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 50 finished +galaxy.model.metadata DEBUG 2024-12-30 01:05:00,255 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 50 +galaxy.util WARNING 2024-12-30 01:05:00,310 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/b/6/4/dataset_b64148af-5c88-4762-ad1d-81593f749c67.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/b/6/4/dataset_b64148af-5c88-4762-ad1d-81593f749c67.dat' +galaxy.jobs INFO 2024-12-30 01:05:00,341 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 50 in /galaxy/server/database/jobs_directory/000/50 +galaxy.jobs DEBUG 2024-12-30 01:05:00,399 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 50 executed (177.509 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:05:01,605 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 52, 51 +tpv.core.entities DEBUG 2024-12-30 01:05:01,645 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:05:01,645 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (51) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:05:01,650 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (51) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:05:01,667 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (51) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:05:01,690 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (51) Working directory for job is: /galaxy/server/database/jobs_directory/000/51 +galaxy.jobs.runners DEBUG 2024-12-30 01:05:01,698 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [51] queued (47.615 ms) +galaxy.jobs.handler INFO 2024-12-30 01:05:01,702 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (51) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:05:01,707 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 51 +tpv.core.entities DEBUG 2024-12-30 01:05:01,721 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:05:01,722 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (52) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:05:01,729 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (52) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:05:01,750 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (52) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:05:01,786 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (52) Working directory for job is: /galaxy/server/database/jobs_directory/000/52 +galaxy.jobs.runners DEBUG 2024-12-30 01:05:01,796 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [52] queued (66.210 ms) +galaxy.jobs.handler INFO 2024-12-30 01:05:01,801 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (52) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:05:01,808 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 52 +galaxy.jobs DEBUG 2024-12-30 01:05:01,851 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [51] prepared (117.198 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:05:01,890 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/51/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/51/registry.xml' '/galaxy/server/database/jobs_directory/000/51/upload_params.json' '51:/galaxy/server/database/objects/d/0/2/dataset_d027d03b-d98a-428c-b9b0-fb69149577f8_files:/galaxy/server/database/objects/d/0/2/dataset_d027d03b-d98a-428c-b9b0-fb69149577f8.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:05:01,908 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (51) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/51/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/51/galaxy_51.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-12-30 01:05:01,948 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [52] prepared (114.072 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:05:01,974 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/52/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/52/registry.xml' '/galaxy/server/database/jobs_directory/000/52/upload_params.json' '52:/galaxy/server/database/objects/4/2/5/dataset_425bbfb2-986a-4fcb-98e6-07eaae34e0a7_files:/galaxy/server/database/objects/4/2/5/dataset_425bbfb2-986a-4fcb-98e6-07eaae34e0a7.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:05:01,991 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (52) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/52/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/52/galaxy_52.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:05:11,375 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 52: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:05:12,543 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 51: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:05:16,943 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 52 finished +galaxy.model.metadata DEBUG 2024-12-30 01:05:17,023 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 52 +galaxy.jobs INFO 2024-12-30 01:05:17,074 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 52 in /galaxy/server/database/jobs_directory/000/52 +galaxy.jobs DEBUG 2024-12-30 01:05:17,143 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 52 executed (165.206 ms) +galaxy.jobs.runners DEBUG 2024-12-30 01:05:17,974 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 51 finished +galaxy.model.metadata DEBUG 2024-12-30 01:05:18,043 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 51 +galaxy.jobs INFO 2024-12-30 01:05:18,130 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 51 in /galaxy/server/database/jobs_directory/000/51 +galaxy.jobs DEBUG 2024-12-30 01:05:18,205 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 51 executed (200.242 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:05:19,215 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 53 +tpv.core.entities DEBUG 2024-12-30 01:05:19,257 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:05:19,257 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (53) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:05:19,262 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (53) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:05:19,279 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (53) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:05:19,299 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (53) Working directory for job is: /galaxy/server/database/jobs_directory/000/53 +galaxy.jobs.runners DEBUG 2024-12-30 01:05:19,309 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [53] queued (47.063 ms) +galaxy.jobs.handler INFO 2024-12-30 01:05:19,314 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (53) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:05:19,319 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 53 +galaxy.jobs DEBUG 2024-12-30 01:05:19,417 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [53] prepared (78.887 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:05:19,417 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:05:19,418 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3: mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:05:19,443 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:05:19,468 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/53/tool_script.sh] for tool command [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/53/outputs/COMMAND_VERSION 2>&1; +addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/4/2/5/dataset_425bbfb2-986a-4fcb-98e6-07eaae34e0a7.dat' reference.fa && samtools faidx reference.fa && ln -s '/galaxy/server/database/objects/d/0/2/dataset_d027d03b-d98a-428c-b9b0-fb69149577f8.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/e/e/b/metadata_eebd7975-99dd-4822-91ab-d287b5a0a2fc.dat' infile.bai && samtools view -@ $addthreads -C -o outfile --output-fmt-option no_ref -T 'reference.fa' -t 'reference.fa.fai' infile 'CHROMOSOME_I'] +galaxy.jobs.runners DEBUG 2024-12-30 01:05:19,486 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (53) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/53/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/53/galaxy_53.ec; +if [ -f "/galaxy/server/database/jobs_directory/000/53/working/outfile" ] ; then cp "/galaxy/server/database/jobs_directory/000/53/working/outfile" "/galaxy/server/database/objects/e/3/6/dataset_e3610e5b-0553-4f20-bebc-891c929483ea.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:05:19,499 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:05:19,500 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3: mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:05:19,522 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 01:05:25,694 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 53: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:05:30,794 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 53 finished +galaxy.model.metadata DEBUG 2024-12-30 01:05:30,855 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 53 +galaxy.util WARNING 2024-12-30 01:05:30,903 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/e/3/6/dataset_e3610e5b-0553-4f20-bebc-891c929483ea.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/e/3/6/dataset_e3610e5b-0553-4f20-bebc-891c929483ea.dat' +galaxy.jobs INFO 2024-12-30 01:05:30,932 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 53 in /galaxy/server/database/jobs_directory/000/53 +galaxy.jobs DEBUG 2024-12-30 01:05:30,992 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 53 executed (171.192 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:05:31,593 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 54 +tpv.core.entities DEBUG 2024-12-30 01:05:31,634 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:05:31,634 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (54) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:05:31,639 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (54) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:05:31,657 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (54) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:05:31,678 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (54) Working directory for job is: /galaxy/server/database/jobs_directory/000/54 +galaxy.jobs.runners DEBUG 2024-12-30 01:05:31,686 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [54] queued (46.909 ms) +galaxy.jobs.handler INFO 2024-12-30 01:05:31,690 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (54) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:05:31,694 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 54 +galaxy.jobs DEBUG 2024-12-30 01:05:31,800 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [54] prepared (88.694 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:05:31,821 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/54/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/54/registry.xml' '/galaxy/server/database/jobs_directory/000/54/upload_params.json' '54:/galaxy/server/database/objects/4/6/d/dataset_46dd4fb2-6af8-4022-a912-e17351796ee0_files:/galaxy/server/database/objects/4/6/d/dataset_46dd4fb2-6af8-4022-a912-e17351796ee0.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:05:31,836 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (54) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/54/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/54/galaxy_54.ec; sh -c "exit $return_code" +galaxy.jobs.handler DEBUG 2024-12-30 01:05:32,692 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 55 +tpv.core.entities DEBUG 2024-12-30 01:05:32,728 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:05:32,729 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (55) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:05:32,733 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (55) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:05:32,749 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (55) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:05:32,770 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (55) Working directory for job is: /galaxy/server/database/jobs_directory/000/55 +galaxy.jobs.runners DEBUG 2024-12-30 01:05:32,777 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [55] queued (44.086 ms) +galaxy.jobs.handler INFO 2024-12-30 01:05:32,783 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (55) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:05:32,785 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 55 +galaxy.jobs DEBUG 2024-12-30 01:05:32,898 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [55] prepared (92.613 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:05:32,922 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/55/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/55/registry.xml' '/galaxy/server/database/jobs_directory/000/55/upload_params.json' '55:/galaxy/server/database/objects/4/f/c/dataset_4fcc00dc-751e-4498-8317-f1cb142787bc_files:/galaxy/server/database/objects/4/f/c/dataset_4fcc00dc-751e-4498-8317-f1cb142787bc.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:05:32,935 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (55) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/55/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/55/galaxy_55.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:05:41,004 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 54: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:05:41,049 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 55: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:05:46,502 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 54 finished +galaxy.model.metadata DEBUG 2024-12-30 01:05:46,577 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 54 +galaxy.jobs.runners DEBUG 2024-12-30 01:05:46,638 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 55 finished +galaxy.jobs INFO 2024-12-30 01:05:46,656 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 54 in /galaxy/server/database/jobs_directory/000/54 +galaxy.model.metadata DEBUG 2024-12-30 01:05:46,710 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 55 +galaxy.jobs DEBUG 2024-12-30 01:05:46,745 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 54 executed (208.313 ms) +galaxy.jobs INFO 2024-12-30 01:05:46,763 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 55 in /galaxy/server/database/jobs_directory/000/55 +galaxy.jobs DEBUG 2024-12-30 01:05:46,831 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 55 executed (159.261 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:05:48,191 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 56 +tpv.core.entities DEBUG 2024-12-30 01:05:48,238 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:05:48,239 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (56) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:05:48,245 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (56) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:05:48,262 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (56) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:05:48,284 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (56) Working directory for job is: /galaxy/server/database/jobs_directory/000/56 +galaxy.jobs.runners DEBUG 2024-12-30 01:05:48,293 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [56] queued (47.543 ms) +galaxy.jobs.handler INFO 2024-12-30 01:05:48,298 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (56) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:05:48,300 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 56 +galaxy.jobs DEBUG 2024-12-30 01:05:48,385 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [56] prepared (64.957 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:05:48,385 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:05:48,385 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3: mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:05:48,410 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:05:48,434 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/56/tool_script.sh] for tool command [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/56/outputs/COMMAND_VERSION 2>&1; +addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/4/f/c/dataset_4fcc00dc-751e-4498-8317-f1cb142787bc.dat' reference.fa && samtools faidx reference.fa && ln -s '/galaxy/server/database/objects/4/6/d/dataset_46dd4fb2-6af8-4022-a912-e17351796ee0.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/1/1/6/metadata_116d9fab-db82-45f6-93df-576f1b775a6b.dat' infile.crai && samtools view -@ $addthreads -b -o outfile -T 'reference.fa' -t 'reference.fa.fai' infile 'CHROMOSOME_I' && samtools sort -@ $addthreads -m $addmemory"M" -T "${TMPDIR:-.}" -O bam -o tmpsam outfile && mv tmpsam outfile] +galaxy.jobs.runners DEBUG 2024-12-30 01:05:48,452 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (56) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/56/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/56/galaxy_56.ec; +if [ -f "/galaxy/server/database/jobs_directory/000/56/working/outfile" ] ; then cp "/galaxy/server/database/jobs_directory/000/56/working/outfile" "/galaxy/server/database/objects/3/0/4/dataset_304191dc-360c-4fbb-b4e9-2f6b31cbd005.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:05:48,466 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:05:48,466 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3: mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:05:48,488 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 01:05:53,181 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 56: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:05:58,416 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 56 finished +galaxy.model.metadata DEBUG 2024-12-30 01:05:58,486 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 56 +galaxy.util WARNING 2024-12-30 01:05:58,543 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/3/0/4/dataset_304191dc-360c-4fbb-b4e9-2f6b31cbd005.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/3/0/4/dataset_304191dc-360c-4fbb-b4e9-2f6b31cbd005.dat' +galaxy.jobs INFO 2024-12-30 01:05:58,578 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 56 in /galaxy/server/database/jobs_directory/000/56 +galaxy.jobs DEBUG 2024-12-30 01:05:58,636 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 56 executed (190.443 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:05:59,564 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 57 +tpv.core.entities DEBUG 2024-12-30 01:05:59,607 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:05:59,607 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (57) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:05:59,612 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (57) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:05:59,631 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (57) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:05:59,652 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (57) Working directory for job is: /galaxy/server/database/jobs_directory/000/57 +galaxy.jobs.runners DEBUG 2024-12-30 01:05:59,661 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [57] queued (48.394 ms) +galaxy.jobs.handler INFO 2024-12-30 01:05:59,667 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (57) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:05:59,670 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 57 +galaxy.jobs DEBUG 2024-12-30 01:05:59,788 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [57] prepared (96.867 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:05:59,813 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/57/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/57/registry.xml' '/galaxy/server/database/jobs_directory/000/57/upload_params.json' '57:/galaxy/server/database/objects/f/7/3/dataset_f731860a-fd80-46b3-8a12-4efe5bf7de87_files:/galaxy/server/database/objects/f/7/3/dataset_f731860a-fd80-46b3-8a12-4efe5bf7de87.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:05:59,826 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (57) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/57/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/57/galaxy_57.ec; sh -c "exit $return_code" +galaxy.jobs.handler DEBUG 2024-12-30 01:06:00,669 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 58, 59 +tpv.core.entities DEBUG 2024-12-30 01:06:00,707 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:06:00,707 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (58) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:06:00,712 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (58) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:06:00,727 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (58) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:06:00,747 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (58) Working directory for job is: /galaxy/server/database/jobs_directory/000/58 +galaxy.jobs.runners DEBUG 2024-12-30 01:06:00,755 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [58] queued (42.876 ms) +galaxy.jobs.handler INFO 2024-12-30 01:06:00,759 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (58) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:06:00,766 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 58 +tpv.core.entities DEBUG 2024-12-30 01:06:00,784 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:06:00,785 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (59) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:06:00,792 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (59) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:06:00,813 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (59) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:06:00,847 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (59) Working directory for job is: /galaxy/server/database/jobs_directory/000/59 +galaxy.jobs.runners DEBUG 2024-12-30 01:06:00,854 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [59] queued (61.549 ms) +galaxy.jobs.handler INFO 2024-12-30 01:06:00,860 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (59) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:06:00,865 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 59 +galaxy.jobs DEBUG 2024-12-30 01:06:00,913 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [58] prepared (115.833 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:06:00,947 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/58/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/58/registry.xml' '/galaxy/server/database/jobs_directory/000/58/upload_params.json' '58:/galaxy/server/database/objects/7/6/5/dataset_765c02a8-6dc0-4307-9417-9468f73def3f_files:/galaxy/server/database/objects/7/6/5/dataset_765c02a8-6dc0-4307-9417-9468f73def3f.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:06:00,982 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (58) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/58/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/58/galaxy_58.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-12-30 01:06:01,007 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [59] prepared (115.934 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:06:01,036 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/59/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/59/registry.xml' '/galaxy/server/database/jobs_directory/000/59/upload_params.json' '59:/galaxy/server/database/objects/0/b/e/dataset_0be8db0d-ed15-4d1b-bbd0-e48481d5ed7e_files:/galaxy/server/database/objects/0/b/e/dataset_0be8db0d-ed15-4d1b-bbd0-e48481d5ed7e.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:06:01,056 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (59) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/59/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/59/galaxy_59.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:06:09,816 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 57: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:06:09,852 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 59: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:06:11,240 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 58: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:06:17,682 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 57 finished +galaxy.jobs.runners DEBUG 2024-12-30 01:06:17,746 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 59 finished +galaxy.model.metadata DEBUG 2024-12-30 01:06:17,782 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 57 +galaxy.model.metadata DEBUG 2024-12-30 01:06:17,820 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 59 +galaxy.jobs INFO 2024-12-30 01:06:17,885 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 59 in /galaxy/server/database/jobs_directory/000/59 +galaxy.jobs INFO 2024-12-30 01:06:17,898 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 57 in /galaxy/server/database/jobs_directory/000/57 +galaxy.jobs DEBUG 2024-12-30 01:06:17,956 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 59 executed (179.417 ms) +galaxy.jobs DEBUG 2024-12-30 01:06:17,978 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 57 executed (265.229 ms) +galaxy.jobs.runners DEBUG 2024-12-30 01:06:18,718 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 58 finished +galaxy.model.metadata DEBUG 2024-12-30 01:06:18,787 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 58 +galaxy.jobs INFO 2024-12-30 01:06:18,827 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 58 in /galaxy/server/database/jobs_directory/000/58 +galaxy.jobs DEBUG 2024-12-30 01:06:18,895 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 58 executed (146.375 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:06:19,430 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 60 +tpv.core.entities DEBUG 2024-12-30 01:06:19,482 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:06:19,483 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (60) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:06:19,489 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (60) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:06:19,508 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (60) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:06:19,531 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (60) Working directory for job is: /galaxy/server/database/jobs_directory/000/60 +galaxy.jobs.runners DEBUG 2024-12-30 01:06:19,542 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [60] queued (52.476 ms) +galaxy.jobs.handler INFO 2024-12-30 01:06:19,546 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (60) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:06:19,551 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 60 +galaxy.jobs DEBUG 2024-12-30 01:06:19,654 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [60] prepared (81.430 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:06:19,655 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:06:19,655 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3: mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:06:19,679 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:06:19,703 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/60/tool_script.sh] for tool command [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/60/outputs/COMMAND_VERSION 2>&1; +addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/0/b/e/dataset_0be8db0d-ed15-4d1b-bbd0-e48481d5ed7e.dat' reference.fa && samtools faidx reference.fa && ln -s '/galaxy/server/database/objects/f/7/3/dataset_f731860a-fd80-46b3-8a12-4efe5bf7de87.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/f/9/a/metadata_f9acfaec-d116-4b6b-b841-76ffece825e9.dat' infile.crai && samtools view -@ $addthreads -b -L '/galaxy/server/database/objects/7/6/5/dataset_765c02a8-6dc0-4307-9417-9468f73def3f.dat' -o outfile -T 'reference.fa' -t 'reference.fa.fai' infile && samtools sort -@ $addthreads -m $addmemory"M" -T "${TMPDIR:-.}" -O bam -o tmpsam outfile && mv tmpsam outfile] +galaxy.jobs.runners DEBUG 2024-12-30 01:06:19,720 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (60) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/60/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/60/galaxy_60.ec; +if [ -f "/galaxy/server/database/jobs_directory/000/60/working/outfile" ] ; then cp "/galaxy/server/database/jobs_directory/000/60/working/outfile" "/galaxy/server/database/objects/c/b/0/dataset_cb012666-9787-44ea-b63d-1c0ec051aab5.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:06:19,732 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:06:19,732 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3: mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:06:19,755 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 01:06:25,193 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 60: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:06:30,374 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 60 finished +galaxy.model.metadata DEBUG 2024-12-30 01:06:30,446 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 60 +galaxy.util WARNING 2024-12-30 01:06:30,506 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/c/b/0/dataset_cb012666-9787-44ea-b63d-1c0ec051aab5.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/c/b/0/dataset_cb012666-9787-44ea-b63d-1c0ec051aab5.dat' +galaxy.jobs INFO 2024-12-30 01:06:30,540 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 60 in /galaxy/server/database/jobs_directory/000/60 +galaxy.jobs DEBUG 2024-12-30 01:06:30,599 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 60 executed (192.995 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:06:31,825 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 61 +tpv.core.entities DEBUG 2024-12-30 01:06:31,863 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:06:31,864 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (61) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:06:31,870 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (61) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:06:31,885 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (61) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:06:31,906 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (61) Working directory for job is: /galaxy/server/database/jobs_directory/000/61 +galaxy.jobs.runners DEBUG 2024-12-30 01:06:31,913 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [61] queued (43.298 ms) +galaxy.jobs.handler INFO 2024-12-30 01:06:31,917 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (61) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:06:31,922 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 61 +galaxy.jobs DEBUG 2024-12-30 01:06:32,051 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [61] prepared (107.357 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:06:32,077 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/61/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/61/registry.xml' '/galaxy/server/database/jobs_directory/000/61/upload_params.json' '61:/galaxy/server/database/objects/d/b/d/dataset_dbdffe9f-c7bc-444e-bbae-300c74415e55_files:/galaxy/server/database/objects/d/b/d/dataset_dbdffe9f-c7bc-444e-bbae-300c74415e55.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:06:32,089 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (61) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/61/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/61/galaxy_61.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:06:41,325 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 61: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:06:46,408 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 61 finished +galaxy.model.metadata DEBUG 2024-12-30 01:06:46,489 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 61 +galaxy.jobs INFO 2024-12-30 01:06:46,543 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 61 in /galaxy/server/database/jobs_directory/000/61 +galaxy.jobs DEBUG 2024-12-30 01:06:46,609 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 61 executed (165.797 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:06:47,265 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 62 +tpv.core.entities DEBUG 2024-12-30 01:06:47,309 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:06:47,309 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (62) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:06:47,315 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (62) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:06:47,334 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (62) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:06:47,353 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (62) Working directory for job is: /galaxy/server/database/jobs_directory/000/62 +galaxy.jobs.runners DEBUG 2024-12-30 01:06:47,361 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [62] queued (46.324 ms) +galaxy.jobs.handler INFO 2024-12-30 01:06:47,366 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (62) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:06:47,370 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 62 +galaxy.jobs DEBUG 2024-12-30 01:06:47,455 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [62] prepared (62.853 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:06:47,456 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:06:47,456 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3: mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:06:47,485 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:06:47,512 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/62/tool_script.sh] for tool command [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/62/outputs/COMMAND_VERSION 2>&1; +addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/d/b/d/dataset_dbdffe9f-c7bc-444e-bbae-300c74415e55.dat' infile && sample_fragment=`samtools view -c infile | awk '{s=$1} END {frac=s/2; print(frac > 1 ? 22814+1/frac : ".0")}'` && samtools view -@ $addthreads -h -s ${sample_fragment} -o outfile infile] +galaxy.jobs.runners DEBUG 2024-12-30 01:06:47,529 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (62) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/62/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/62/galaxy_62.ec; +if [ -f "/galaxy/server/database/jobs_directory/000/62/working/outfile" ] ; then cp "/galaxy/server/database/jobs_directory/000/62/working/outfile" "/galaxy/server/database/objects/1/f/a/dataset_1faf36ab-d895-48a8-8713-be8ddda7cd2f.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:06:47,547 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:06:47,547 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3: mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:06:47,573 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 01:06:52,512 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 62: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:06:57,587 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 62 finished +galaxy.model.metadata DEBUG 2024-12-30 01:06:57,658 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 62 +galaxy.util WARNING 2024-12-30 01:06:57,670 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/1/f/a/dataset_1faf36ab-d895-48a8-8713-be8ddda7cd2f.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/1/f/a/dataset_1faf36ab-d895-48a8-8713-be8ddda7cd2f.dat' +galaxy.jobs INFO 2024-12-30 01:06:57,714 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 62 in /galaxy/server/database/jobs_directory/000/62 +galaxy.jobs DEBUG 2024-12-30 01:06:57,773 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 62 executed (154.622 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:06:58,705 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 63 +tpv.core.entities DEBUG 2024-12-30 01:06:58,743 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:06:58,744 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (63) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:06:58,750 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (63) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:06:58,768 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (63) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:06:58,786 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (63) Working directory for job is: /galaxy/server/database/jobs_directory/000/63 +galaxy.jobs.runners DEBUG 2024-12-30 01:06:58,793 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [63] queued (42.104 ms) +galaxy.jobs.handler INFO 2024-12-30 01:06:58,796 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (63) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:06:58,799 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 63 +galaxy.jobs DEBUG 2024-12-30 01:06:58,916 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [63] prepared (100.805 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:06:58,943 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/63/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/63/registry.xml' '/galaxy/server/database/jobs_directory/000/63/upload_params.json' '63:/galaxy/server/database/objects/7/8/6/dataset_7864d95e-a321-445b-90f0-df71307aacff_files:/galaxy/server/database/objects/7/8/6/dataset_7864d95e-a321-445b-90f0-df71307aacff.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:06:58,959 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (63) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/63/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/63/galaxy_63.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:07:07,736 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 63: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:07:12,766 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 63 finished +galaxy.model.metadata DEBUG 2024-12-30 01:07:12,834 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 63 +galaxy.jobs INFO 2024-12-30 01:07:12,880 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 63 in /galaxy/server/database/jobs_directory/000/63 +galaxy.jobs DEBUG 2024-12-30 01:07:12,949 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 63 executed (153.228 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:07:14,143 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 64 +tpv.core.entities DEBUG 2024-12-30 01:07:14,185 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:07:14,186 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (64) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:07:14,192 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (64) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:07:14,212 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (64) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:07:14,232 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (64) Working directory for job is: /galaxy/server/database/jobs_directory/000/64 +galaxy.jobs.runners DEBUG 2024-12-30 01:07:14,241 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [64] queued (48.596 ms) +galaxy.jobs.handler INFO 2024-12-30 01:07:14,246 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (64) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:07:14,250 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 64 +galaxy.jobs DEBUG 2024-12-30 01:07:14,342 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [64] prepared (69.602 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:07:14,343 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:07:14,343 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3: mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:07:14,367 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:07:14,397 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/64/tool_script.sh] for tool command [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/64/outputs/COMMAND_VERSION 2>&1; +addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/7/8/6/dataset_7864d95e-a321-445b-90f0-df71307aacff.dat' infile && sample_fragment=`samtools view -c infile | awk '{s=$1} END {frac=s/20; print(frac > 1 ? 22282+1/frac : ".0")}'` && samtools view -@ $addthreads -h -s ${sample_fragment} -o outfile infile] +galaxy.jobs.runners DEBUG 2024-12-30 01:07:14,413 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (64) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/64/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/64/galaxy_64.ec; +if [ -f "/galaxy/server/database/jobs_directory/000/64/working/outfile" ] ; then cp "/galaxy/server/database/jobs_directory/000/64/working/outfile" "/galaxy/server/database/objects/2/2/d/dataset_22d05080-35b5-4bb2-a81b-8b122acb85be.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:07:14,427 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:07:14,428 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3: mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:07:14,449 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 01:07:19,873 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 64: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:07:24,925 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 64 finished +galaxy.model.metadata DEBUG 2024-12-30 01:07:24,992 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 64 +galaxy.util WARNING 2024-12-30 01:07:25,003 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/2/2/d/dataset_22d05080-35b5-4bb2-a81b-8b122acb85be.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/2/2/d/dataset_22d05080-35b5-4bb2-a81b-8b122acb85be.dat' +galaxy.jobs INFO 2024-12-30 01:07:25,035 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 64 in /galaxy/server/database/jobs_directory/000/64 +galaxy.jobs DEBUG 2024-12-30 01:07:25,093 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 64 executed (138.223 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:07:26,528 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 65 +tpv.core.entities DEBUG 2024-12-30 01:07:26,561 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:07:26,562 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (65) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:07:26,567 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (65) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:07:26,583 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (65) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:07:26,603 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (65) Working directory for job is: /galaxy/server/database/jobs_directory/000/65 +galaxy.jobs.runners DEBUG 2024-12-30 01:07:26,611 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [65] queued (43.411 ms) +galaxy.jobs.handler INFO 2024-12-30 01:07:26,615 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (65) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:07:26,619 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 65 +galaxy.jobs DEBUG 2024-12-30 01:07:26,733 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [65] prepared (94.729 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:07:26,756 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/65/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/65/registry.xml' '/galaxy/server/database/jobs_directory/000/65/upload_params.json' '65:/galaxy/server/database/objects/0/c/8/dataset_0c830e5f-1034-4803-94bb-5a8039234634_files:/galaxy/server/database/objects/0/c/8/dataset_0c830e5f-1034-4803-94bb-5a8039234634.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:07:26,769 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (65) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/65/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/65/galaxy_65.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:07:36,079 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 65: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:07:41,148 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 65 finished +galaxy.model.metadata DEBUG 2024-12-30 01:07:41,212 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 65 +galaxy.jobs INFO 2024-12-30 01:07:41,264 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 65 in /galaxy/server/database/jobs_directory/000/65 +galaxy.jobs DEBUG 2024-12-30 01:07:41,326 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 65 executed (147.807 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:07:41,969 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 66 +tpv.core.entities DEBUG 2024-12-30 01:07:42,010 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:07:42,011 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (66) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:07:42,017 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (66) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:07:42,036 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (66) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:07:42,055 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (66) Working directory for job is: /galaxy/server/database/jobs_directory/000/66 +galaxy.jobs.runners DEBUG 2024-12-30 01:07:42,064 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [66] queued (47.055 ms) +galaxy.jobs.handler INFO 2024-12-30 01:07:42,068 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (66) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:07:42,072 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 66 +galaxy.jobs DEBUG 2024-12-30 01:07:42,140 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [66] prepared (52.873 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:07:42,140 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:07:42,140 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3: mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:07:42,169 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:07:42,194 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/66/tool_script.sh] for tool command [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/66/outputs/COMMAND_VERSION 2>&1; +addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/0/c/8/dataset_0c830e5f-1034-4803-94bb-5a8039234634.dat' infile && sample_fragment=`samtools view -c infile | awk '{s=$1} END {frac=s/20; print(frac > 1 ? 1296+1/frac : ".0")}'` && samtools view -@ $addthreads -h -s ${sample_fragment} -o outfile infile] +galaxy.jobs.runners DEBUG 2024-12-30 01:07:42,209 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (66) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/66/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/66/galaxy_66.ec; +if [ -f "/galaxy/server/database/jobs_directory/000/66/working/outfile" ] ; then cp "/galaxy/server/database/jobs_directory/000/66/working/outfile" "/galaxy/server/database/objects/4/3/0/dataset_430803ef-01ca-4df5-ba06-88fa7d40363b.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:07:42,224 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:07:42,224 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3: mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:07:42,246 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 01:07:48,209 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 66: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:07:53,101 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 66 finished +galaxy.model.metadata DEBUG 2024-12-30 01:07:53,158 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 66 +galaxy.util WARNING 2024-12-30 01:07:53,172 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/4/3/0/dataset_430803ef-01ca-4df5-ba06-88fa7d40363b.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/4/3/0/dataset_430803ef-01ca-4df5-ba06-88fa7d40363b.dat' +galaxy.jobs INFO 2024-12-30 01:07:53,198 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 66 in /galaxy/server/database/jobs_directory/000/66 +galaxy.jobs DEBUG 2024-12-30 01:07:53,246 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 66 executed (121.088 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:07:54,373 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 67 +tpv.core.entities DEBUG 2024-12-30 01:07:54,412 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:07:54,412 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (67) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:07:54,418 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (67) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:07:54,435 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (67) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:07:54,459 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (67) Working directory for job is: /galaxy/server/database/jobs_directory/000/67 +galaxy.jobs.runners DEBUG 2024-12-30 01:07:54,466 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [67] queued (48.132 ms) +galaxy.jobs.handler INFO 2024-12-30 01:07:54,470 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (67) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:07:54,475 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 67 +galaxy.jobs DEBUG 2024-12-30 01:07:54,583 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [67] prepared (85.578 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:07:54,601 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/67/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/67/registry.xml' '/galaxy/server/database/jobs_directory/000/67/upload_params.json' '67:/galaxy/server/database/objects/7/2/8/dataset_7284bea3-7c90-4bcc-82ae-d861509bd241_files:/galaxy/server/database/objects/7/2/8/dataset_7284bea3-7c90-4bcc-82ae-d861509bd241.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:07:54,612 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (67) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/67/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/67/galaxy_67.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:08:04,434 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 67: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:08:09,676 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 67 finished +galaxy.model.metadata DEBUG 2024-12-30 01:08:09,742 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 67 +galaxy.jobs INFO 2024-12-30 01:08:09,827 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 67 in /galaxy/server/database/jobs_directory/000/67 +galaxy.jobs DEBUG 2024-12-30 01:08:09,903 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 67 executed (196.873 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:08:10,866 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 68 +tpv.core.entities DEBUG 2024-12-30 01:08:10,906 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:08:10,906 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (68) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:08:10,912 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (68) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:08:10,929 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (68) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:08:10,947 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (68) Working directory for job is: /galaxy/server/database/jobs_directory/000/68 +galaxy.jobs.runners DEBUG 2024-12-30 01:08:10,956 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [68] queued (43.285 ms) +galaxy.jobs.handler INFO 2024-12-30 01:08:10,959 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (68) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:08:10,964 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 68 +galaxy.jobs DEBUG 2024-12-30 01:08:11,047 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [68] prepared (63.892 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:08:11,048 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:08:11,048 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3: mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:08:11,072 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:08:11,095 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/68/tool_script.sh] for tool command [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/68/outputs/COMMAND_VERSION 2>&1; +addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/7/2/8/dataset_7284bea3-7c90-4bcc-82ae-d861509bd241.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/8/c/5/metadata_8c58fb01-7778-4431-95af-4bf00b8bb188.dat' infile.bai && sample_fragment=`samtools idxstats infile | awk '{s+=$4+$3} END {frac=s/20; print(frac > 1 ? 25744+1/frac : ".0")}'` && samtools view -@ $addthreads -b -s ${sample_fragment} -o outfile infile] +galaxy.jobs.runners DEBUG 2024-12-30 01:08:11,108 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (68) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/68/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/68/galaxy_68.ec; +if [ -f "/galaxy/server/database/jobs_directory/000/68/working/outfile" ] ; then cp "/galaxy/server/database/jobs_directory/000/68/working/outfile" "/galaxy/server/database/objects/f/b/9/dataset_fb959da4-cc90-42ce-9055-72ea445bf993.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:08:11,120 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:08:11,121 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3: mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:08:11,141 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 01:08:15,743 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 68: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:08:20,893 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 68 finished +galaxy.model.metadata DEBUG 2024-12-30 01:08:20,960 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 68 +galaxy.util WARNING 2024-12-30 01:08:21,013 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/f/b/9/dataset_fb959da4-cc90-42ce-9055-72ea445bf993.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/f/b/9/dataset_fb959da4-cc90-42ce-9055-72ea445bf993.dat' +galaxy.jobs INFO 2024-12-30 01:08:21,043 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 68 in /galaxy/server/database/jobs_directory/000/68 +galaxy.jobs DEBUG 2024-12-30 01:08:21,095 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 68 executed (173.106 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:08:22,219 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 69 +tpv.core.entities DEBUG 2024-12-30 01:08:22,255 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:08:22,256 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (69) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:08:22,260 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (69) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:08:22,280 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (69) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:08:22,301 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (69) Working directory for job is: /galaxy/server/database/jobs_directory/000/69 +galaxy.jobs.runners DEBUG 2024-12-30 01:08:22,308 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [69] queued (47.286 ms) +galaxy.jobs.handler INFO 2024-12-30 01:08:22,311 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (69) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:08:22,315 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 69 +galaxy.jobs DEBUG 2024-12-30 01:08:22,426 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [69] prepared (90.945 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:08:22,449 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/69/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/69/registry.xml' '/galaxy/server/database/jobs_directory/000/69/upload_params.json' '69:/galaxy/server/database/objects/3/6/6/dataset_366a2c7e-195e-47f4-a18e-8be36dbd1e09_files:/galaxy/server/database/objects/3/6/6/dataset_366a2c7e-195e-47f4-a18e-8be36dbd1e09.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:08:22,463 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (69) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/69/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/69/galaxy_69.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:08:30,892 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 69: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:08:35,904 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 69 finished +galaxy.model.metadata DEBUG 2024-12-30 01:08:35,972 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 69 +galaxy.jobs INFO 2024-12-30 01:08:36,018 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 69 in /galaxy/server/database/jobs_directory/000/69 +galaxy.jobs DEBUG 2024-12-30 01:08:36,080 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 69 executed (146.053 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:08:36,667 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 70 +tpv.core.entities DEBUG 2024-12-30 01:08:36,708 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:08:36,709 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (70) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:08:36,714 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (70) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:08:36,730 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (70) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:08:36,749 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (70) Working directory for job is: /galaxy/server/database/jobs_directory/000/70 +galaxy.jobs.runners DEBUG 2024-12-30 01:08:36,758 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [70] queued (43.433 ms) +galaxy.jobs.handler INFO 2024-12-30 01:08:36,763 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (70) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:08:36,768 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 70 +galaxy.jobs DEBUG 2024-12-30 01:08:36,852 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [70] prepared (63.257 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:08:36,853 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:08:36,853 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3: mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:08:36,876 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:08:36,899 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/70/tool_script.sh] for tool command [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/70/outputs/COMMAND_VERSION 2>&1; +addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/3/6/6/dataset_366a2c7e-195e-47f4-a18e-8be36dbd1e09.dat' infile && sample_fragment=`samtools view -c infile | awk '{s=$1} END {frac=s/2; print(frac > 1 ? 7+1/frac : ".0")}'` && samtools view -@ $addthreads -h -s ${sample_fragment} -o outfile infile] +galaxy.jobs.runners DEBUG 2024-12-30 01:08:36,916 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (70) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/70/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/70/galaxy_70.ec; +if [ -f "/galaxy/server/database/jobs_directory/000/70/working/outfile" ] ; then cp "/galaxy/server/database/jobs_directory/000/70/working/outfile" "/galaxy/server/database/objects/6/e/5/dataset_6e5ceffc-3c20-4a21-b185-4321a1330747.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:08:36,930 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:08:36,930 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3: mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:08:36,953 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 01:08:42,048 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 70: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:08:47,018 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 70 finished +galaxy.model.metadata DEBUG 2024-12-30 01:08:47,102 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 70 +galaxy.util WARNING 2024-12-30 01:08:47,111 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/6/e/5/dataset_6e5ceffc-3c20-4a21-b185-4321a1330747.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/6/e/5/dataset_6e5ceffc-3c20-4a21-b185-4321a1330747.dat' +galaxy.jobs INFO 2024-12-30 01:08:47,145 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 70 in /galaxy/server/database/jobs_directory/000/70 +galaxy.jobs DEBUG 2024-12-30 01:08:47,206 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 70 executed (148.190 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:08:48,054 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 71 +tpv.core.entities DEBUG 2024-12-30 01:08:48,098 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:08:48,098 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (71) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:08:48,105 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (71) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:08:48,124 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (71) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:08:48,143 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (71) Working directory for job is: /galaxy/server/database/jobs_directory/000/71 +galaxy.jobs.runners DEBUG 2024-12-30 01:08:48,151 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [71] queued (46.089 ms) +galaxy.jobs.handler INFO 2024-12-30 01:08:48,155 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (71) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:08:48,160 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 71 +galaxy.jobs DEBUG 2024-12-30 01:08:48,277 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [71] prepared (98.399 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:08:48,301 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/71/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/71/registry.xml' '/galaxy/server/database/jobs_directory/000/71/upload_params.json' '71:/galaxy/server/database/objects/3/4/3/dataset_34320bbd-bfb3-461c-825c-5e3b8202e25c_files:/galaxy/server/database/objects/3/4/3/dataset_34320bbd-bfb3-461c-825c-5e3b8202e25c.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:08:48,315 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (71) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/71/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/71/galaxy_71.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:08:58,255 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 71: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:09:03,246 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 71 finished +galaxy.model.metadata DEBUG 2024-12-30 01:09:03,312 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 71 +galaxy.jobs INFO 2024-12-30 01:09:03,388 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 71 in /galaxy/server/database/jobs_directory/000/71 +galaxy.jobs DEBUG 2024-12-30 01:09:03,443 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 71 executed (169.440 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:09:04,544 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 72 +tpv.core.entities DEBUG 2024-12-30 01:09:04,581 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:09:04,581 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (72) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:09:04,586 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (72) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:09:04,601 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (72) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:09:04,618 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (72) Working directory for job is: /galaxy/server/database/jobs_directory/000/72 +galaxy.jobs.runners DEBUG 2024-12-30 01:09:04,626 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [72] queued (39.297 ms) +galaxy.jobs.handler INFO 2024-12-30 01:09:04,631 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (72) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:09:04,635 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 72 +galaxy.jobs DEBUG 2024-12-30 01:09:04,734 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [72] prepared (77.134 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:09:04,735 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:09:04,735 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3: mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:09:04,759 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:09:04,784 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/72/tool_script.sh] for tool command [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/72/outputs/COMMAND_VERSION 2>&1; +addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/3/4/3/dataset_34320bbd-bfb3-461c-825c-5e3b8202e25c.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/1/b/4/metadata_1b4af7a8-cf6f-4516-a099-e5403719b528.dat' infile.bai && sample_fragment=`samtools idxstats infile | awk '{s+=$4+$3} END {frac=s/2; print(frac > 1 ? 7+1/frac : ".0")}'` && samtools view -@ $addthreads -b -s ${sample_fragment} -o outfile infile] +galaxy.jobs.runners DEBUG 2024-12-30 01:09:04,801 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (72) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/72/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/72/galaxy_72.ec; +if [ -f "/galaxy/server/database/jobs_directory/000/72/working/outfile" ] ; then cp "/galaxy/server/database/jobs_directory/000/72/working/outfile" "/galaxy/server/database/objects/3/9/6/dataset_3967188f-52e1-44f1-8b86-e0d6665f48d6.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:09:04,814 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:09:04,814 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3: mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:09:04,836 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 01:09:10,500 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 72: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:09:15,641 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 72 finished +galaxy.model.metadata DEBUG 2024-12-30 01:09:15,706 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 72 +galaxy.util WARNING 2024-12-30 01:09:15,777 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/3/9/6/dataset_3967188f-52e1-44f1-8b86-e0d6665f48d6.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/3/9/6/dataset_3967188f-52e1-44f1-8b86-e0d6665f48d6.dat' +galaxy.jobs INFO 2024-12-30 01:09:15,809 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 72 in /galaxy/server/database/jobs_directory/000/72 +galaxy.jobs DEBUG 2024-12-30 01:09:15,870 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 72 executed (198.703 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:09:16,912 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 73 +tpv.core.entities DEBUG 2024-12-30 01:09:16,950 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:09:16,950 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (73) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:09:16,956 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (73) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:09:16,975 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (73) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:09:17,000 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (73) Working directory for job is: /galaxy/server/database/jobs_directory/000/73 +galaxy.jobs.runners DEBUG 2024-12-30 01:09:17,008 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [73] queued (52.158 ms) +galaxy.jobs.handler INFO 2024-12-30 01:09:17,013 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (73) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:09:17,017 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 73 +galaxy.jobs DEBUG 2024-12-30 01:09:17,138 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [73] prepared (99.275 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:09:17,161 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/73/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/73/registry.xml' '/galaxy/server/database/jobs_directory/000/73/upload_params.json' '73:/galaxy/server/database/objects/f/0/8/dataset_f081eeb7-dc46-42da-825b-3c951e93066d_files:/galaxy/server/database/objects/f/0/8/dataset_f081eeb7-dc46-42da-825b-3c951e93066d.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:09:17,174 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (73) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/73/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/73/galaxy_73.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:09:25,766 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 73: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:09:30,812 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 73 finished +galaxy.model.metadata DEBUG 2024-12-30 01:09:30,880 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 73 +galaxy.jobs INFO 2024-12-30 01:09:30,960 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 73 in /galaxy/server/database/jobs_directory/000/73 +galaxy.jobs DEBUG 2024-12-30 01:09:31,019 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 73 executed (176.515 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:09:31,340 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 74 +tpv.core.entities DEBUG 2024-12-30 01:09:31,381 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:09:31,382 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (74) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:09:31,388 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (74) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:09:31,407 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (74) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:09:31,431 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (74) Working directory for job is: /galaxy/server/database/jobs_directory/000/74 +galaxy.jobs.runners DEBUG 2024-12-30 01:09:31,443 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [74] queued (54.891 ms) +galaxy.jobs.handler INFO 2024-12-30 01:09:31,447 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (74) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:09:31,454 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 74 +galaxy.jobs DEBUG 2024-12-30 01:09:31,566 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [74] prepared (83.578 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:09:31,567 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:09:31,567 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3: mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:09:31,594 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:09:31,622 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/74/tool_script.sh] for tool command [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/74/outputs/COMMAND_VERSION 2>&1; +addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/f/0/8/dataset_f081eeb7-dc46-42da-825b-3c951e93066d.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/6/c/f/metadata_6cf1a4a3-c48d-4415-bf96-49da3a043d08.dat' infile.bai && sample_fragment=`samtools idxstats infile | awk '{s+=$4+$3} END {frac=s/20; print(frac > 1 ? 7+1/frac : ".0")}'` && samtools view -@ $addthreads -b -s ${sample_fragment} -o outfile infile] +galaxy.jobs.runners DEBUG 2024-12-30 01:09:31,641 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (74) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/74/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/74/galaxy_74.ec; +if [ -f "/galaxy/server/database/jobs_directory/000/74/working/outfile" ] ; then cp "/galaxy/server/database/jobs_directory/000/74/working/outfile" "/galaxy/server/database/objects/c/8/9/dataset_c891af48-12bc-4981-b0d6-c01990b56bef.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:09:31,656 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:09:31,657 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3: mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:09:31,677 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 01:09:36,900 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 74: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:09:41,953 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 74 finished +galaxy.model.metadata DEBUG 2024-12-30 01:09:42,022 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 74 +galaxy.util WARNING 2024-12-30 01:09:42,069 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/c/8/9/dataset_c891af48-12bc-4981-b0d6-c01990b56bef.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/c/8/9/dataset_c891af48-12bc-4981-b0d6-c01990b56bef.dat' +galaxy.jobs INFO 2024-12-30 01:09:42,101 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 74 in /galaxy/server/database/jobs_directory/000/74 +galaxy.jobs DEBUG 2024-12-30 01:09:42,156 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 74 executed (173.462 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:09:43,726 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 75 +tpv.core.entities DEBUG 2024-12-30 01:09:43,763 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:09:43,764 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (75) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:09:43,769 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (75) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:09:43,786 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (75) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:09:43,804 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (75) Working directory for job is: /galaxy/server/database/jobs_directory/000/75 +galaxy.jobs.runners DEBUG 2024-12-30 01:09:43,813 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [75] queued (43.269 ms) +galaxy.jobs.handler INFO 2024-12-30 01:09:43,816 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (75) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:09:43,820 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 75 +galaxy.jobs DEBUG 2024-12-30 01:09:43,938 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [75] prepared (97.971 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:09:43,960 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/75/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/75/registry.xml' '/galaxy/server/database/jobs_directory/000/75/upload_params.json' '75:/galaxy/server/database/objects/3/6/3/dataset_36357b41-62d7-4da7-8c70-2c487ecdf0ea_files:/galaxy/server/database/objects/3/6/3/dataset_36357b41-62d7-4da7-8c70-2c487ecdf0ea.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:09:43,972 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (75) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/75/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/75/galaxy_75.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:09:53,090 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 75: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:09:58,135 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 75 finished +galaxy.model.metadata DEBUG 2024-12-30 01:09:58,213 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 75 +galaxy.jobs INFO 2024-12-30 01:09:58,302 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 75 in /galaxy/server/database/jobs_directory/000/75 +galaxy.jobs DEBUG 2024-12-30 01:09:58,363 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 75 executed (194.131 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:09:59,263 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 76 +tpv.core.entities DEBUG 2024-12-30 01:09:59,305 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:09:59,306 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (76) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:09:59,312 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (76) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:09:59,329 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (76) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:09:59,348 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (76) Working directory for job is: /galaxy/server/database/jobs_directory/000/76 +galaxy.jobs.runners DEBUG 2024-12-30 01:09:59,356 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [76] queued (44.259 ms) +galaxy.jobs.handler INFO 2024-12-30 01:09:59,362 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (76) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:09:59,365 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 76 +galaxy.jobs DEBUG 2024-12-30 01:09:59,462 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [76] prepared (74.133 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:09:59,463 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:09:59,463 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3: mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:09:59,643 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:09:59,671 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/76/tool_script.sh] for tool command [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/76/outputs/COMMAND_VERSION 2>&1; +addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/3/6/3/dataset_36357b41-62d7-4da7-8c70-2c487ecdf0ea.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/c/7/a/metadata_c7a4e5c8-fe59-48f0-860f-ff69d7a43b36.dat' infile.bai && samtools view -@ $addthreads -b -s 7.2 -o outfile infile] +galaxy.jobs.runners DEBUG 2024-12-30 01:09:59,688 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (76) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/76/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/76/galaxy_76.ec; +if [ -f "/galaxy/server/database/jobs_directory/000/76/working/outfile" ] ; then cp "/galaxy/server/database/jobs_directory/000/76/working/outfile" "/galaxy/server/database/objects/e/1/d/dataset_e1df2083-2462-4a96-9964-343af95751cb.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:09:59,703 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:09:59,703 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3: mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:09:59,726 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 01:10:05,245 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 76: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:10:10,461 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 76 finished +galaxy.model.metadata DEBUG 2024-12-30 01:10:10,528 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 76 +galaxy.util WARNING 2024-12-30 01:10:10,576 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/e/1/d/dataset_e1df2083-2462-4a96-9964-343af95751cb.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/e/1/d/dataset_e1df2083-2462-4a96-9964-343af95751cb.dat' +galaxy.jobs INFO 2024-12-30 01:10:10,607 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 76 in /galaxy/server/database/jobs_directory/000/76 +galaxy.jobs DEBUG 2024-12-30 01:10:10,675 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 76 executed (182.616 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:10:11,646 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 77 +tpv.core.entities DEBUG 2024-12-30 01:10:11,683 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:10:11,683 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (77) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:10:11,688 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (77) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:10:11,704 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (77) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:10:11,724 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (77) Working directory for job is: /galaxy/server/database/jobs_directory/000/77 +galaxy.jobs.runners DEBUG 2024-12-30 01:10:11,732 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [77] queued (43.427 ms) +galaxy.jobs.handler INFO 2024-12-30 01:10:11,737 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (77) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:10:11,741 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 77 +galaxy.jobs DEBUG 2024-12-30 01:10:11,868 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [77] prepared (107.154 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:10:11,892 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/77/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/77/registry.xml' '/galaxy/server/database/jobs_directory/000/77/upload_params.json' '77:/galaxy/server/database/objects/4/4/0/dataset_440ad6f8-dc03-403b-92bc-d3948fd1f884_files:/galaxy/server/database/objects/4/4/0/dataset_440ad6f8-dc03-403b-92bc-d3948fd1f884.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:10:11,908 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (77) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/77/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/77/galaxy_77.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:10:20,458 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 77: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:10:25,444 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 77 finished +galaxy.model.metadata DEBUG 2024-12-30 01:10:25,509 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 77 +galaxy.jobs INFO 2024-12-30 01:10:25,585 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 77 in /galaxy/server/database/jobs_directory/000/77 +galaxy.jobs DEBUG 2024-12-30 01:10:25,662 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 77 executed (188.921 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:10:26,058 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 78 +tpv.core.entities DEBUG 2024-12-30 01:10:26,095 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:10:26,096 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (78) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:10:26,101 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (78) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:10:26,117 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (78) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:10:26,134 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (78) Working directory for job is: /galaxy/server/database/jobs_directory/000/78 +galaxy.jobs.runners DEBUG 2024-12-30 01:10:26,141 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [78] queued (39.975 ms) +galaxy.jobs.handler INFO 2024-12-30 01:10:26,145 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (78) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:10:26,150 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 78 +galaxy.jobs DEBUG 2024-12-30 01:10:26,236 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [78] prepared (64.906 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:10:26,236 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:10:26,236 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3: mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:10:26,259 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:10:26,284 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/78/tool_script.sh] for tool command [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/78/outputs/COMMAND_VERSION 2>&1; +addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/4/4/0/dataset_440ad6f8-dc03-403b-92bc-d3948fd1f884.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/5/7/3/metadata_573cfc1b-413f-49a2-b21f-dbdbd92c7e16.dat' infile.bai && samtools view -@ $addthreads -b -s 7.8 -U outfile -o /dev/null infile] +galaxy.jobs.runners DEBUG 2024-12-30 01:10:26,298 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (78) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/78/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/78/galaxy_78.ec; +if [ -f "/galaxy/server/database/jobs_directory/000/78/working/outfile" ] ; then cp "/galaxy/server/database/jobs_directory/000/78/working/outfile" "/galaxy/server/database/objects/9/8/c/dataset_98c860a0-9501-4576-90aa-7bc5a2ecb386.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:10:26,311 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:10:26,311 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3: mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:10:26,330 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:e3f57919aec2b96cba49c23b81609837e1db9c33-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 01:10:31,666 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 78: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:10:36,619 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 78 finished +galaxy.model.metadata DEBUG 2024-12-30 01:10:36,681 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 78 +galaxy.util WARNING 2024-12-30 01:10:36,728 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/9/8/c/dataset_98c860a0-9501-4576-90aa-7bc5a2ecb386.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/9/8/c/dataset_98c860a0-9501-4576-90aa-7bc5a2ecb386.dat' +galaxy.jobs INFO 2024-12-30 01:10:36,755 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 78 in /galaxy/server/database/jobs_directory/000/78 +galaxy.jobs DEBUG 2024-12-30 01:10:36,813 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 78 executed (166.162 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:10:39,447 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 79 +tpv.core.entities DEBUG 2024-12-30 01:10:39,485 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:10:39,486 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (79) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:10:39,491 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (79) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:10:39,509 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (79) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:10:39,526 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (79) Working directory for job is: /galaxy/server/database/jobs_directory/000/79 +galaxy.jobs.runners DEBUG 2024-12-30 01:10:39,533 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [79] queued (41.046 ms) +galaxy.jobs.handler INFO 2024-12-30 01:10:39,536 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (79) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:10:39,541 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 79 +galaxy.jobs DEBUG 2024-12-30 01:10:39,654 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [79] prepared (91.926 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:10:39,678 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/79/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/79/registry.xml' '/galaxy/server/database/jobs_directory/000/79/upload_params.json' '79:/galaxy/server/database/objects/1/6/c/dataset_16c65af2-71c6-444d-b73a-9dbe010b8b63_files:/galaxy/server/database/objects/1/6/c/dataset_16c65af2-71c6-444d-b73a-9dbe010b8b63.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:10:39,693 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (79) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/79/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/79/galaxy_79.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:10:49,877 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 79: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:10:54,820 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 79 finished +galaxy.model.metadata DEBUG 2024-12-30 01:10:54,887 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 79 +galaxy.jobs INFO 2024-12-30 01:10:54,966 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 79 in /galaxy/server/database/jobs_directory/000/79 +galaxy.jobs DEBUG 2024-12-30 01:10:55,026 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 79 executed (174.877 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:10:56,069 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 80 +tpv.core.entities DEBUG 2024-12-30 01:10:56,115 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:10:56,116 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (80) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:10:56,122 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (80) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:10:56,143 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (80) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:10:56,166 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (80) Working directory for job is: /galaxy/server/database/jobs_directory/000/80 +galaxy.jobs.runners DEBUG 2024-12-30 01:10:56,175 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [80] queued (52.261 ms) +galaxy.jobs.handler INFO 2024-12-30 01:10:56,180 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (80) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:10:56,184 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 80 +galaxy.jobs DEBUG 2024-12-30 01:10:56,280 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [80] prepared (72.773 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:10:56,280 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:10:56,281 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.9: samtools:1.9 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:10:56,528 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.9--h10a08f8_12,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:10:56,551 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/80/tool_script.sh] for tool command [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/80/outputs/COMMAND_VERSION 2>&1; +addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && samtools split -f 'Read_Group_%!.bam' -u '/galaxy/server/database/objects/1/4/c/dataset_14cae4b9-035c-43dd-b791-7a371b5cb643.dat' -@ $addthreads '/galaxy/server/database/objects/1/6/c/dataset_16c65af2-71c6-444d-b73a-9dbe010b8b63.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:10:56,565 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (80) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/80/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/80/galaxy_80.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:10:56,579 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:10:56,580 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.9: samtools:1.9 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:10:56,603 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.9--h10a08f8_12,type=docker]] +galaxy.jobs.runners.kubernetes ERROR 2024-12-30 01:11:04,007 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Could not clean up k8s batch job. Ignoring... +Traceback (most recent call last): + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/http.py", line 437, in raise_for_status + resp.raise_for_status() + File "/galaxy/server/.venv/lib/python3.10/site-packages/requests/models.py", line 1021, in raise_for_status + raise HTTPError(http_error_msg, response=self) +requests.exceptions.HTTPError: 409 Client Error: Conflict for url: https://10.107.32.1:443/apis/batch/v1/namespaces/prod-24-12-30-00-37-1/jobs/gxy-6hvzc + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 817, in _handle_job_failure + self.__cleanup_k8s_job(job) + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 824, in __cleanup_k8s_job + delete_job(job, k8s_cleanup_job) + File "/galaxy/server/lib/galaxy/jobs/runners/util/pykube_util.py", line 107, in delete_job + job.scale(replicas=0) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/mixins.py", line 30, in scale + self.update() + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 165, in update + self.patch(self.obj, subresource=subresource) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 157, in patch + self.api.raise_for_status(r) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/http.py", line 444, in raise_for_status + raise HTTPError(resp.status_code, payload["message"]) +pykube.exceptions.HTTPError: Operation cannot be fulfilled on jobs.batch "gxy-6hvzc": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:11:04,064 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (80/gxy-6hvzc) Terminated at user's request +galaxy.jobs.handler DEBUG 2024-12-30 01:11:07,424 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 82, 81 +tpv.core.entities DEBUG 2024-12-30 01:11:07,470 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:11:07,470 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (81) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:11:07,478 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (81) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:11:07,500 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (81) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:11:07,523 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (81) Working directory for job is: /galaxy/server/database/jobs_directory/000/81 +galaxy.jobs.runners DEBUG 2024-12-30 01:11:07,531 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [81] queued (52.205 ms) +galaxy.jobs.handler INFO 2024-12-30 01:11:07,535 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (81) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:11:07,542 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 81 +tpv.core.entities DEBUG 2024-12-30 01:11:07,558 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:11:07,559 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (82) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:11:07,567 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (82) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:11:07,587 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (82) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:11:07,621 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (82) Working directory for job is: /galaxy/server/database/jobs_directory/000/82 +galaxy.jobs.runners DEBUG 2024-12-30 01:11:07,628 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [82] queued (61.563 ms) +galaxy.jobs.handler INFO 2024-12-30 01:11:07,633 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (82) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:11:07,638 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 82 +galaxy.jobs DEBUG 2024-12-30 01:11:07,687 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [81] prepared (117.666 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:11:07,718 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/81/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/81/registry.xml' '/galaxy/server/database/jobs_directory/000/81/upload_params.json' '81:/galaxy/server/database/objects/4/1/a/dataset_41a0c711-dcba-4b9d-8dbf-1aee90e79a98_files:/galaxy/server/database/objects/4/1/a/dataset_41a0c711-dcba-4b9d-8dbf-1aee90e79a98.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:11:07,735 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (81) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/81/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/81/galaxy_81.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-12-30 01:11:07,769 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [82] prepared (106.133 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:11:07,788 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/82/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/82/registry.xml' '/galaxy/server/database/jobs_directory/000/82/upload_params.json' '82:/galaxy/server/database/objects/d/a/2/dataset_da253d4a-6bff-4c68-80c3-bb94a23a44f2_files:/galaxy/server/database/objects/d/a/2/dataset_da253d4a-6bff-4c68-80c3-bb94a23a44f2.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:11:07,803 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (82) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/82/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/82/galaxy_82.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:11:16,634 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 81: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:11:16,663 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 82: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:11:21,755 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 82 finished +galaxy.jobs.runners DEBUG 2024-12-30 01:11:21,817 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 81 finished +galaxy.model.metadata DEBUG 2024-12-30 01:11:21,831 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 82 +galaxy.jobs INFO 2024-12-30 01:11:21,880 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 82 in /galaxy/server/database/jobs_directory/000/82 +galaxy.model.metadata DEBUG 2024-12-30 01:11:21,899 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 81 +galaxy.jobs INFO 2024-12-30 01:11:21,939 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 81 in /galaxy/server/database/jobs_directory/000/81 +galaxy.jobs DEBUG 2024-12-30 01:11:21,961 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 82 executed (174.155 ms) +galaxy.jobs DEBUG 2024-12-30 01:11:22,014 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 81 executed (158.120 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:11:22,977 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 83 +tpv.core.entities DEBUG 2024-12-30 01:11:23,019 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:11:23,019 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (83) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:11:23,025 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (83) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:11:23,043 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (83) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:11:23,060 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (83) Working directory for job is: /galaxy/server/database/jobs_directory/000/83 +galaxy.jobs.runners DEBUG 2024-12-30 01:11:23,071 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [83] queued (45.303 ms) +galaxy.jobs.handler INFO 2024-12-30 01:11:23,075 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (83) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:11:23,081 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 83 +galaxy.jobs DEBUG 2024-12-30 01:11:23,186 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [83] prepared (84.145 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:11:23,186 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:11:23,186 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.15.1+galaxy4: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a +galaxy.tool_util.deps.containers INFO 2024-12-30 01:11:23,396 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:11:23,418 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/83/tool_script.sh] for tool command [bcftools 2>&1 | grep 'Version:' > /galaxy/server/database/jobs_directory/000/83/outputs/COMMAND_VERSION 2>&1; +export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/4/1/a/dataset_41a0c711-dcba-4b9d-8dbf-1aee90e79a98.dat' > input0.vcf.gz && bcftools index input0.vcf.gz && echo 'input0.vcf.gz' >> vcfs_list && bgzip -c '/galaxy/server/database/objects/d/a/2/dataset_da253d4a-6bff-4c68-80c3-bb94a23a44f2.dat' > input1.vcf.gz && bcftools index input1.vcf.gz && echo 'input1.vcf.gz' >> vcfs_list && bcftools concat --allow-overlaps --min-PQ 30 --output-type 'v' --threads ${GALAXY_SLOTS:-4} input0.vcf.gz input1.vcf.gz > '/galaxy/server/database/objects/c/d/4/dataset_cd4b4459-4ca0-4198-b112-0a626a3cac1b.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:11:23,433 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (83) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/83/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/83/galaxy_83.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:11:23,447 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:11:23,447 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.15.1+galaxy4: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a +galaxy.tool_util.deps.containers INFO 2024-12-30 01:11:23,469 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 01:11:33,881 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 83: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:11:38,928 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 83 finished +galaxy.model.metadata DEBUG 2024-12-30 01:11:38,989 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 83 +galaxy.jobs INFO 2024-12-30 01:11:39,032 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 83 in /galaxy/server/database/jobs_directory/000/83 +galaxy.jobs DEBUG 2024-12-30 01:11:39,088 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 83 executed (132.286 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:11:40,466 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 84, 85 +tpv.core.entities DEBUG 2024-12-30 01:11:40,505 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:11:40,505 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (84) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:11:40,512 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (84) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:11:40,531 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (84) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:11:40,553 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (84) Working directory for job is: /galaxy/server/database/jobs_directory/000/84 +galaxy.jobs.runners DEBUG 2024-12-30 01:11:40,560 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [84] queued (47.585 ms) +galaxy.jobs.handler INFO 2024-12-30 01:11:40,564 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (84) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:11:40,569 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 84 +tpv.core.entities DEBUG 2024-12-30 01:11:40,584 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:11:40,584 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (85) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:11:40,592 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (85) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:11:40,615 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (85) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:11:40,645 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (85) Working directory for job is: /galaxy/server/database/jobs_directory/000/85 +galaxy.jobs.runners DEBUG 2024-12-30 01:11:40,654 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [85] queued (62.750 ms) +galaxy.jobs.handler INFO 2024-12-30 01:11:40,660 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (85) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:11:40,666 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 85 +galaxy.jobs DEBUG 2024-12-30 01:11:40,705 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [84] prepared (111.296 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:11:40,736 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/84/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/84/registry.xml' '/galaxy/server/database/jobs_directory/000/84/upload_params.json' '84:/galaxy/server/database/objects/e/9/0/dataset_e90d19ab-bf2a-447d-b514-61dd6ca213c2_files:/galaxy/server/database/objects/e/9/0/dataset_e90d19ab-bf2a-447d-b514-61dd6ca213c2.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:11:40,772 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (84) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/84/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/84/galaxy_84.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-12-30 01:11:40,809 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [85] prepared (119.655 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:11:40,836 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/85/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/85/registry.xml' '/galaxy/server/database/jobs_directory/000/85/upload_params.json' '85:/galaxy/server/database/objects/9/1/4/dataset_9145dd52-76ae-445c-8be4-983a4d5d4559_files:/galaxy/server/database/objects/9/1/4/dataset_9145dd52-76ae-445c-8be4-983a4d5d4559.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:11:40,854 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (85) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/85/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/85/galaxy_85.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:11:50,261 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 84: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:11:50,287 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 85: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:11:55,457 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 84 finished +galaxy.jobs.runners DEBUG 2024-12-30 01:11:55,550 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 85 finished +galaxy.model.metadata DEBUG 2024-12-30 01:11:55,556 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 84 +galaxy.jobs INFO 2024-12-30 01:11:55,607 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 84 in /galaxy/server/database/jobs_directory/000/84 +galaxy.model.metadata DEBUG 2024-12-30 01:11:55,661 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 85 +galaxy.jobs INFO 2024-12-30 01:11:55,697 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 85 in /galaxy/server/database/jobs_directory/000/85 +galaxy.jobs DEBUG 2024-12-30 01:11:55,710 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 84 executed (222.997 ms) +galaxy.jobs DEBUG 2024-12-30 01:11:55,794 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 85 executed (207.299 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:11:57,025 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 86 +tpv.core.entities DEBUG 2024-12-30 01:11:57,071 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:11:57,071 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (86) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:11:57,079 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (86) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:11:57,099 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (86) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:11:57,128 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (86) Working directory for job is: /galaxy/server/database/jobs_directory/000/86 +galaxy.jobs.runners DEBUG 2024-12-30 01:11:57,139 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [86] queued (59.740 ms) +galaxy.jobs.handler INFO 2024-12-30 01:11:57,143 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (86) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:11:57,148 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 86 +galaxy.jobs DEBUG 2024-12-30 01:11:57,234 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [86] prepared (63.382 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:11:57,235 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:11:57,235 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.15.1+galaxy4: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a +galaxy.tool_util.deps.containers INFO 2024-12-30 01:11:57,259 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:11:57,280 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/86/tool_script.sh] for tool command [bcftools 2>&1 | grep 'Version:' > /galaxy/server/database/jobs_directory/000/86/outputs/COMMAND_VERSION 2>&1; +export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/e/9/0/dataset_e90d19ab-bf2a-447d-b514-61dd6ca213c2.dat' > input0.vcf.gz && bcftools index input0.vcf.gz && echo 'input0.vcf.gz' >> vcfs_list && bgzip -c '/galaxy/server/database/objects/9/1/4/dataset_9145dd52-76ae-445c-8be4-983a4d5d4559.dat' > input1.vcf.gz && bcftools index input1.vcf.gz && echo 'input1.vcf.gz' >> vcfs_list && bcftools concat --allow-overlaps --min-PQ 30 --output-type 'v' --threads ${GALAXY_SLOTS:-4} input0.vcf.gz input1.vcf.gz > '/galaxy/server/database/objects/f/6/0/dataset_f60ca435-7e08-4b25-a5ab-2544c6f5e1f0.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:11:57,294 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (86) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/86/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/86/galaxy_86.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:11:57,308 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:11:57,308 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.15.1+galaxy4: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a +galaxy.tool_util.deps.containers INFO 2024-12-30 01:11:57,329 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 01:12:02,421 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 86: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:12:07,415 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 86 finished +galaxy.model.metadata DEBUG 2024-12-30 01:12:07,486 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 86 +galaxy.jobs INFO 2024-12-30 01:12:07,542 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 86 in /galaxy/server/database/jobs_directory/000/86 +galaxy.jobs DEBUG 2024-12-30 01:12:07,605 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 86 executed (161.368 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:12:08,539 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 88, 87 +tpv.core.entities DEBUG 2024-12-30 01:12:08,575 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:12:08,576 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (87) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:12:08,582 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (87) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:12:08,601 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (87) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:12:08,621 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (87) Working directory for job is: /galaxy/server/database/jobs_directory/000/87 +galaxy.jobs.runners DEBUG 2024-12-30 01:12:08,629 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [87] queued (46.572 ms) +galaxy.jobs.handler INFO 2024-12-30 01:12:08,633 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (87) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:12:08,637 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 87 +tpv.core.entities DEBUG 2024-12-30 01:12:08,656 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:12:08,656 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (88) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:12:08,662 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (88) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:12:08,680 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (88) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:12:08,711 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (88) Working directory for job is: /galaxy/server/database/jobs_directory/000/88 +galaxy.jobs.runners DEBUG 2024-12-30 01:12:08,720 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [88] queued (57.906 ms) +galaxy.jobs.handler INFO 2024-12-30 01:12:08,724 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (88) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:12:08,731 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 88 +galaxy.jobs DEBUG 2024-12-30 01:12:08,773 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [87] prepared (111.727 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:12:08,807 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/87/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/87/registry.xml' '/galaxy/server/database/jobs_directory/000/87/upload_params.json' '87:/galaxy/server/database/objects/8/2/3/dataset_8236698a-f809-4b23-b6ef-a17385bdfaa5_files:/galaxy/server/database/objects/8/2/3/dataset_8236698a-f809-4b23-b6ef-a17385bdfaa5.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:12:08,824 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (87) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/87/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/87/galaxy_87.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-12-30 01:12:08,857 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [88] prepared (99.360 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:12:08,880 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/88/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/88/registry.xml' '/galaxy/server/database/jobs_directory/000/88/upload_params.json' '88:/galaxy/server/database/objects/2/2/0/dataset_2207c916-be53-48de-98d1-447e01386689_files:/galaxy/server/database/objects/2/2/0/dataset_2207c916-be53-48de-98d1-447e01386689.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:12:08,893 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (88) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/88/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/88/galaxy_88.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:12:16,794 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 88: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:12:21,706 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 88 finished +galaxy.model.metadata DEBUG 2024-12-30 01:12:21,773 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 88 +galaxy.jobs INFO 2024-12-30 01:12:21,812 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 88 in /galaxy/server/database/jobs_directory/000/88 +galaxy.jobs DEBUG 2024-12-30 01:12:21,866 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 88 executed (130.105 ms) +galaxy.jobs.runners DEBUG 2024-12-30 01:12:22,925 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 87: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:12:28,065 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 87 finished +galaxy.model.metadata DEBUG 2024-12-30 01:12:28,139 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 87 +galaxy.jobs INFO 2024-12-30 01:12:28,197 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 87 in /galaxy/server/database/jobs_directory/000/87 +galaxy.jobs DEBUG 2024-12-30 01:12:28,270 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 87 executed (173.314 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:12:29,198 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 89 +tpv.core.entities DEBUG 2024-12-30 01:12:29,238 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:12:29,239 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (89) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:12:29,245 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (89) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:12:29,261 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (89) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:12:29,278 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (89) Working directory for job is: /galaxy/server/database/jobs_directory/000/89 +galaxy.jobs.runners DEBUG 2024-12-30 01:12:29,286 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [89] queued (41.162 ms) +galaxy.jobs.handler INFO 2024-12-30 01:12:29,289 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (89) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:12:29,294 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 89 +galaxy.jobs DEBUG 2024-12-30 01:12:29,395 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [89] prepared (75.964 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:12:29,395 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:12:29,395 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.15.1+galaxy4: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a +galaxy.tool_util.deps.containers INFO 2024-12-30 01:12:29,419 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:12:29,441 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/89/tool_script.sh] for tool command [bcftools 2>&1 | grep 'Version:' > /galaxy/server/database/jobs_directory/000/89/outputs/COMMAND_VERSION 2>&1; +export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/8/2/3/dataset_8236698a-f809-4b23-b6ef-a17385bdfaa5.dat' > input0.vcf.gz && bcftools index input0.vcf.gz && echo 'input0.vcf.gz' >> vcfs_list && bgzip -c '/galaxy/server/database/objects/2/2/0/dataset_2207c916-be53-48de-98d1-447e01386689.dat' > input1.vcf.gz && bcftools index input1.vcf.gz && echo 'input1.vcf.gz' >> vcfs_list && bcftools concat --allow-overlaps --min-PQ 30 --output-type 'v' --threads ${GALAXY_SLOTS:-4} input0.vcf.gz input1.vcf.gz > '/galaxy/server/database/objects/2/3/0/dataset_2300e8a2-e345-4666-b964-46d2622571d7.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:12:29,457 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (89) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/89/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/89/galaxy_89.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:12:29,471 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:12:29,471 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.15.1+galaxy4: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a +galaxy.tool_util.deps.containers INFO 2024-12-30 01:12:29,491 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 01:12:36,086 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 89: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:12:41,053 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 89 finished +galaxy.model.metadata DEBUG 2024-12-30 01:12:41,113 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 89 +galaxy.jobs INFO 2024-12-30 01:12:41,147 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 89 in /galaxy/server/database/jobs_directory/000/89 +galaxy.jobs DEBUG 2024-12-30 01:12:41,208 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 89 executed (125.753 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:12:42,572 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 90, 91 +tpv.core.entities DEBUG 2024-12-30 01:12:42,606 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:12:42,606 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (90) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:12:42,611 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (90) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:12:42,627 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (90) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:12:42,647 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (90) Working directory for job is: /galaxy/server/database/jobs_directory/000/90 +galaxy.jobs.runners DEBUG 2024-12-30 01:12:42,654 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [90] queued (42.932 ms) +galaxy.jobs.handler INFO 2024-12-30 01:12:42,657 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (90) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:12:42,663 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 90 +tpv.core.entities DEBUG 2024-12-30 01:12:42,675 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:12:42,676 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (91) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:12:42,681 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (91) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:12:42,704 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (91) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:12:42,739 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (91) Working directory for job is: /galaxy/server/database/jobs_directory/000/91 +galaxy.jobs.runners DEBUG 2024-12-30 01:12:42,748 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [91] queued (66.471 ms) +galaxy.jobs.handler INFO 2024-12-30 01:12:42,753 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (91) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:12:42,759 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 91 +galaxy.jobs DEBUG 2024-12-30 01:12:42,805 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [90] prepared (117.546 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:12:42,840 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/90/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/90/registry.xml' '/galaxy/server/database/jobs_directory/000/90/upload_params.json' '90:/galaxy/server/database/objects/c/1/1/dataset_c117bbb6-a4ec-4dc3-be7b-2cdf8c77d746_files:/galaxy/server/database/objects/c/1/1/dataset_c117bbb6-a4ec-4dc3-be7b-2cdf8c77d746.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:12:42,874 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (90) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/90/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/90/galaxy_90.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-12-30 01:12:42,895 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [91] prepared (110.467 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:12:42,919 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/91/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/91/registry.xml' '/galaxy/server/database/jobs_directory/000/91/upload_params.json' '91:/galaxy/server/database/objects/b/9/0/dataset_b9071fe7-8b47-469d-bcf2-d2f28cf53649_files:/galaxy/server/database/objects/b/9/0/dataset_b9071fe7-8b47-469d-bcf2-d2f28cf53649.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:12:42,934 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (91) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/91/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/91/galaxy_91.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes ERROR 2024-12-30 01:12:51,532 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Could not clean up k8s batch job. Ignoring... +Traceback (most recent call last): + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/http.py", line 437, in raise_for_status + resp.raise_for_status() + File "/galaxy/server/.venv/lib/python3.10/site-packages/requests/models.py", line 1021, in raise_for_status + raise HTTPError(http_error_msg, response=self) +requests.exceptions.HTTPError: 409 Client Error: Conflict for url: https://10.107.32.1:443/apis/batch/v1/namespaces/prod-24-12-30-00-37-1/jobs/gxy-7lk46 + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 817, in _handle_job_failure + self.__cleanup_k8s_job(job) + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 824, in __cleanup_k8s_job + delete_job(job, k8s_cleanup_job) + File "/galaxy/server/lib/galaxy/jobs/runners/util/pykube_util.py", line 107, in delete_job + job.scale(replicas=0) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/mixins.py", line 30, in scale + self.update() + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 165, in update + self.patch(self.obj, subresource=subresource) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 157, in patch + self.api.raise_for_status(r) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/http.py", line 444, in raise_for_status + raise HTTPError(resp.status_code, payload["message"]) +pykube.exceptions.HTTPError: Operation cannot be fulfilled on jobs.batch "gxy-7lk46": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:12:51,577 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (90/gxy-7lk46) Terminated at user's request +galaxy.jobs.runners DEBUG 2024-12-30 01:12:51,731 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 91: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.handler DEBUG 2024-12-30 01:12:52,980 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 92, 93 +tpv.core.entities DEBUG 2024-12-30 01:12:53,022 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:12:53,023 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (92) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:12:53,029 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (92) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:12:53,043 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (92) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:12:53,060 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (92) Working directory for job is: /galaxy/server/database/jobs_directory/000/92 +galaxy.jobs.runners DEBUG 2024-12-30 01:12:53,068 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [92] queued (39.212 ms) +galaxy.jobs.handler INFO 2024-12-30 01:12:53,073 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (92) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:12:53,076 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 92 +tpv.core.entities DEBUG 2024-12-30 01:12:53,095 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:12:53,095 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (93) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:12:53,102 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (93) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:12:53,118 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (93) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:12:53,151 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (93) Working directory for job is: /galaxy/server/database/jobs_directory/000/93 +galaxy.jobs.runners DEBUG 2024-12-30 01:12:53,158 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [93] queued (56.317 ms) +galaxy.jobs.handler INFO 2024-12-30 01:12:53,164 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (93) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:12:53,169 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 93 +galaxy.jobs DEBUG 2024-12-30 01:12:53,212 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [92] prepared (111.536 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:12:53,245 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/92/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/92/registry.xml' '/galaxy/server/database/jobs_directory/000/92/upload_params.json' '92:/galaxy/server/database/objects/5/a/d/dataset_5ad67651-0695-4121-9aec-b46dd9734f02_files:/galaxy/server/database/objects/5/a/d/dataset_5ad67651-0695-4121-9aec-b46dd9734f02.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:12:53,262 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (92) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/92/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/92/galaxy_92.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-12-30 01:12:53,296 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [93] prepared (103.393 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:12:53,318 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/93/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/93/registry.xml' '/galaxy/server/database/jobs_directory/000/93/upload_params.json' '93:/galaxy/server/database/objects/b/7/0/dataset_b7097205-1559-4f3f-a1d9-53de22150368_files:/galaxy/server/database/objects/b/7/0/dataset_b7097205-1559-4f3f-a1d9-53de22150368.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:12:53,331 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (93) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/93/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/93/galaxy_93.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:12:56,799 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 91 finished +galaxy.model.metadata DEBUG 2024-12-30 01:12:56,865 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 91 +galaxy.jobs INFO 2024-12-30 01:12:56,909 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 91 in /galaxy/server/database/jobs_directory/000/91 +galaxy.jobs DEBUG 2024-12-30 01:12:56,967 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 91 executed (139.327 ms) +galaxy.jobs.runners DEBUG 2024-12-30 01:13:03,155 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 92: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:13:03,172 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 93: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:13:08,619 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 92 finished +galaxy.jobs.runners DEBUG 2024-12-30 01:13:08,659 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 93 finished +galaxy.model.metadata DEBUG 2024-12-30 01:13:08,678 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 92 +galaxy.jobs INFO 2024-12-30 01:13:08,732 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 92 in /galaxy/server/database/jobs_directory/000/92 +galaxy.model.metadata DEBUG 2024-12-30 01:13:08,739 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 93 +galaxy.jobs INFO 2024-12-30 01:13:08,788 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 93 in /galaxy/server/database/jobs_directory/000/93 +galaxy.jobs DEBUG 2024-12-30 01:13:08,812 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 92 executed (165.566 ms) +galaxy.jobs DEBUG 2024-12-30 01:13:08,855 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 93 executed (167.222 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:13:09,574 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 94 +tpv.core.entities DEBUG 2024-12-30 01:13:09,612 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:13:09,613 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (94) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:13:09,618 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (94) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:13:09,634 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (94) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:13:09,652 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (94) Working directory for job is: /galaxy/server/database/jobs_directory/000/94 +galaxy.jobs.runners DEBUG 2024-12-30 01:13:09,663 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [94] queued (44.876 ms) +galaxy.jobs.handler INFO 2024-12-30 01:13:09,667 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (94) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:13:09,674 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 94 +galaxy.jobs DEBUG 2024-12-30 01:13:09,770 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [94] prepared (72.665 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:13:09,770 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:13:09,771 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.15.1+galaxy4: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a +galaxy.tool_util.deps.containers INFO 2024-12-30 01:13:09,798 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:13:09,823 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/94/tool_script.sh] for tool command [bcftools 2>&1 | grep 'Version:' > /galaxy/server/database/jobs_directory/000/94/outputs/COMMAND_VERSION 2>&1; +export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/5/a/d/dataset_5ad67651-0695-4121-9aec-b46dd9734f02.dat' > input0.vcf.gz && bcftools index input0.vcf.gz && echo 'input0.vcf.gz' >> vcfs_list && bgzip -c '/galaxy/server/database/objects/b/7/0/dataset_b7097205-1559-4f3f-a1d9-53de22150368.dat' > input1.vcf.gz && bcftools index input1.vcf.gz && echo 'input1.vcf.gz' >> vcfs_list && bcftools concat --allow-overlaps --min-PQ 30 --regions-overlap 1 --output-type 'v' --threads ${GALAXY_SLOTS:-4} input0.vcf.gz input1.vcf.gz > '/galaxy/server/database/objects/f/f/e/dataset_ffebfbd5-46f3-44c8-a54c-98b60c9ec0e3.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:13:09,837 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (94) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/94/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/94/galaxy_94.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:13:09,854 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:13:09,854 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.15.1+galaxy4: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a +galaxy.tool_util.deps.containers INFO 2024-12-30 01:13:09,877 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 01:13:15,314 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 94: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:13:20,451 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 94 finished +galaxy.model.metadata DEBUG 2024-12-30 01:13:20,513 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 94 +galaxy.jobs INFO 2024-12-30 01:13:20,555 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 94 in /galaxy/server/database/jobs_directory/000/94 +galaxy.jobs DEBUG 2024-12-30 01:13:20,613 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 94 executed (133.224 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:13:21,938 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 95, 96 +tpv.core.entities DEBUG 2024-12-30 01:13:21,976 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:13:21,976 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (95) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:13:21,981 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (95) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:13:21,995 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (95) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:13:22,012 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (95) Working directory for job is: /galaxy/server/database/jobs_directory/000/95 +galaxy.jobs.runners DEBUG 2024-12-30 01:13:22,020 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [95] queued (38.228 ms) +galaxy.jobs.handler INFO 2024-12-30 01:13:22,024 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (95) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:13:22,030 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 95 +tpv.core.entities DEBUG 2024-12-30 01:13:22,042 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:13:22,043 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (96) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:13:22,049 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (96) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:13:22,067 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (96) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:13:22,093 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (96) Working directory for job is: /galaxy/server/database/jobs_directory/000/96 +galaxy.jobs.runners DEBUG 2024-12-30 01:13:22,102 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [96] queued (53.360 ms) +galaxy.jobs.handler INFO 2024-12-30 01:13:22,106 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (96) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:13:22,111 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 96 +galaxy.jobs DEBUG 2024-12-30 01:13:22,177 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [95] prepared (120.349 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:13:22,205 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/95/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/95/registry.xml' '/galaxy/server/database/jobs_directory/000/95/upload_params.json' '95:/galaxy/server/database/objects/3/c/5/dataset_3c5bd436-9e00-47ff-bacf-16ba83503a0a_files:/galaxy/server/database/objects/3/c/5/dataset_3c5bd436-9e00-47ff-bacf-16ba83503a0a.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:13:22,222 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (95) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/95/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/95/galaxy_95.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-12-30 01:13:22,237 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [96] prepared (103.788 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:13:22,263 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/96/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/96/registry.xml' '/galaxy/server/database/jobs_directory/000/96/upload_params.json' '96:/galaxy/server/database/objects/4/3/6/dataset_4362608b-2033-46e3-9f03-9ae4ab2a427f_files:/galaxy/server/database/objects/4/3/6/dataset_4362608b-2033-46e3-9f03-9ae4ab2a427f.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:13:22,278 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (96) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/96/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/96/galaxy_96.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes ERROR 2024-12-30 01:13:29,643 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Could not clean up k8s batch job. Ignoring... +Traceback (most recent call last): + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/http.py", line 437, in raise_for_status + resp.raise_for_status() + File "/galaxy/server/.venv/lib/python3.10/site-packages/requests/models.py", line 1021, in raise_for_status + raise HTTPError(http_error_msg, response=self) +requests.exceptions.HTTPError: 409 Client Error: Conflict for url: https://10.107.32.1:443/apis/batch/v1/namespaces/prod-24-12-30-00-37-1/jobs/gxy-r69wd + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 817, in _handle_job_failure + self.__cleanup_k8s_job(job) + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 824, in __cleanup_k8s_job + delete_job(job, k8s_cleanup_job) + File "/galaxy/server/lib/galaxy/jobs/runners/util/pykube_util.py", line 107, in delete_job + job.scale(replicas=0) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/mixins.py", line 30, in scale + self.update() + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 165, in update + self.patch(self.obj, subresource=subresource) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 157, in patch + self.api.raise_for_status(r) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/http.py", line 444, in raise_for_status + raise HTTPError(resp.status_code, payload["message"]) +pykube.exceptions.HTTPError: Operation cannot be fulfilled on jobs.batch "gxy-r69wd": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:13:29,685 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (96/gxy-r69wd) Terminated at user's request +galaxy.jobs.runners DEBUG 2024-12-30 01:13:30,840 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 95: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:13:35,861 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 95 finished +galaxy.model.metadata DEBUG 2024-12-30 01:13:35,926 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 95 +galaxy.jobs INFO 2024-12-30 01:13:35,966 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 95 in /galaxy/server/database/jobs_directory/000/95 +galaxy.jobs DEBUG 2024-12-30 01:13:36,020 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 95 executed (130.275 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:13:38,508 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 98, 99, 97 +tpv.core.entities DEBUG 2024-12-30 01:13:38,547 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:13:38,548 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (97) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:13:38,554 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (97) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:13:38,573 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (97) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:13:38,595 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (97) Working directory for job is: /galaxy/server/database/jobs_directory/000/97 +galaxy.jobs.runners DEBUG 2024-12-30 01:13:38,602 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [97] queued (48.005 ms) +galaxy.jobs.handler INFO 2024-12-30 01:13:38,606 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (97) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:13:38,612 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 97 +tpv.core.entities DEBUG 2024-12-30 01:13:38,629 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:13:38,630 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (98) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:13:38,637 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (98) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:13:38,659 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (98) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:13:38,692 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (98) Working directory for job is: /galaxy/server/database/jobs_directory/000/98 +galaxy.jobs.runners DEBUG 2024-12-30 01:13:38,701 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [98] queued (63.468 ms) +galaxy.jobs.handler INFO 2024-12-30 01:13:38,705 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (98) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:13:38,715 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 98 +tpv.core.entities DEBUG 2024-12-30 01:13:38,730 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:13:38,731 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (99) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:13:38,747 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (99) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:13:38,767 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [97] prepared (129.562 ms) +galaxy.jobs DEBUG 2024-12-30 01:13:38,777 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (99) Persisting job destination (destination id: k8s) +galaxy.jobs.command_factory INFO 2024-12-30 01:13:38,807 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/97/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/97/registry.xml' '/galaxy/server/database/jobs_directory/000/97/upload_params.json' '97:/galaxy/server/database/objects/8/7/e/dataset_87e83e9b-e659-4ed7-b098-a7cf77a18af8_files:/galaxy/server/database/objects/8/7/e/dataset_87e83e9b-e659-4ed7-b098-a7cf77a18af8.dat'] +galaxy.jobs DEBUG 2024-12-30 01:13:38,818 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (99) Working directory for job is: /galaxy/server/database/jobs_directory/000/99 +galaxy.jobs.runners DEBUG 2024-12-30 01:13:38,829 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [99] queued (80.043 ms) +galaxy.jobs.runners DEBUG 2024-12-30 01:13:38,830 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (97) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/97/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/97/galaxy_97.ec; sh -c "exit $return_code" +galaxy.jobs.handler INFO 2024-12-30 01:13:38,834 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (99) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:13:38,842 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 99 +galaxy.jobs DEBUG 2024-12-30 01:13:38,893 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [98] prepared (146.510 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:13:38,928 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/98/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/98/registry.xml' '/galaxy/server/database/jobs_directory/000/98/upload_params.json' '98:/galaxy/server/database/objects/7/8/0/dataset_78060287-94ab-411f-b691-b171e383ab24_files:/galaxy/server/database/objects/7/8/0/dataset_78060287-94ab-411f-b691-b171e383ab24.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:13:38,947 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (98) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/98/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/98/galaxy_98.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-12-30 01:13:38,987 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [99] prepared (118.934 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:13:39,012 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/99/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/99/registry.xml' '/galaxy/server/database/jobs_directory/000/99/upload_params.json' '99:/galaxy/server/database/objects/3/e/1/dataset_3e145f34-9981-4c90-a2fe-113fb30a839d_files:/galaxy/server/database/objects/3/e/1/dataset_3e145f34-9981-4c90-a2fe-113fb30a839d.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:13:39,026 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (99) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/99/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/99/galaxy_99.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:13:47,310 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 97: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:13:47,347 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 98: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:13:49,464 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 99: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:13:54,196 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 97 finished +galaxy.model.metadata DEBUG 2024-12-30 01:13:54,308 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 97 +galaxy.jobs INFO 2024-12-30 01:13:54,378 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 97 in /galaxy/server/database/jobs_directory/000/97 +galaxy.jobs.runners DEBUG 2024-12-30 01:13:54,384 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 98 finished +galaxy.model.metadata DEBUG 2024-12-30 01:13:54,458 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 98 +galaxy.jobs DEBUG 2024-12-30 01:13:54,459 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 97 executed (196.812 ms) +galaxy.jobs INFO 2024-12-30 01:13:54,515 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 98 in /galaxy/server/database/jobs_directory/000/98 +galaxy.jobs DEBUG 2024-12-30 01:13:54,574 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 98 executed (160.753 ms) +galaxy.jobs.runners DEBUG 2024-12-30 01:13:56,069 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 99 finished +galaxy.model.metadata DEBUG 2024-12-30 01:13:56,127 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 99 +galaxy.jobs INFO 2024-12-30 01:13:56,165 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 99 in /galaxy/server/database/jobs_directory/000/99 +galaxy.jobs DEBUG 2024-12-30 01:13:56,225 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 99 executed (129.263 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:13:57,353 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 100 +tpv.core.entities DEBUG 2024-12-30 01:13:57,404 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:13:57,405 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (100) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:13:57,410 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (100) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:13:57,427 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (100) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:13:57,446 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (100) Working directory for job is: /galaxy/server/database/jobs_directory/000/100 +galaxy.jobs.runners DEBUG 2024-12-30 01:13:57,457 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [100] queued (46.949 ms) +galaxy.jobs.handler INFO 2024-12-30 01:13:57,461 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (100) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:13:57,466 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 100 +galaxy.jobs DEBUG 2024-12-30 01:13:57,596 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [100] prepared (108.329 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:13:57,596 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:13:57,596 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a +galaxy.tool_util.deps.containers INFO 2024-12-30 01:13:57,619 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:13:57,641 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/100/tool_script.sh] for tool command [bcftools 2>&1 | grep 'Version:' > /galaxy/server/database/jobs_directory/000/100/outputs/COMMAND_VERSION 2>&1; +export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/8/7/e/dataset_87e83e9b-e659-4ed7-b098-a7cf77a18af8.dat' > input.vcf.gz && bcftools index input.vcf.gz && bgzip -c '/galaxy/server/database/objects/7/8/0/dataset_78060287-94ab-411f-b691-b171e383ab24.dat' > annotations.tab.gz && tabix -s 1 -b 2 -e 2 annotations.tab.gz && bcftools annotate --columns 'CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL' --annotations 'annotations.tab.gz' --header-lines '/galaxy/server/database/objects/3/e/1/dataset_3e145f34-9981-4c90-a2fe-113fb30a839d.dat' --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/8/6/f/dataset_86f508c9-6efd-4be4-87a8-bc2649422f61.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:13:57,654 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (100) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/100/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/100/galaxy_100.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:13:57,668 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:13:57,668 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a +galaxy.tool_util.deps.containers INFO 2024-12-30 01:13:57,689 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 01:14:04,021 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 100: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:14:09,037 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 100 finished +galaxy.model.metadata DEBUG 2024-12-30 01:14:09,098 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 100 +galaxy.jobs INFO 2024-12-30 01:14:09,138 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 100 in /galaxy/server/database/jobs_directory/000/100 +galaxy.objectstore CRITICAL 2024-12-30 01:14:09,184 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] None delete error [Errno 13] Permission denied: 'tmppigbqpe_' +galaxy.jobs DEBUG 2024-12-30 01:14:09,184 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 100 executed (119.103 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:14:10,769 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 103, 102, 101 +tpv.core.entities DEBUG 2024-12-30 01:14:10,810 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:14:10,810 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (101) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:14:10,815 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (101) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:14:10,832 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (101) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:14:10,852 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (101) Working directory for job is: /galaxy/server/database/jobs_directory/000/101 +galaxy.jobs.runners DEBUG 2024-12-30 01:14:10,860 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [101] queued (44.312 ms) +galaxy.jobs.handler INFO 2024-12-30 01:14:10,864 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (101) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:14:10,870 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 101 +tpv.core.entities DEBUG 2024-12-30 01:14:10,882 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:14:10,882 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (102) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:14:10,889 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (102) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:14:10,907 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (102) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:14:10,940 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (102) Working directory for job is: /galaxy/server/database/jobs_directory/000/102 +galaxy.jobs.runners DEBUG 2024-12-30 01:14:10,947 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [102] queued (57.868 ms) +galaxy.jobs.handler INFO 2024-12-30 01:14:10,952 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (102) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:14:10,957 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 102 +tpv.core.entities DEBUG 2024-12-30 01:14:10,977 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:14:10,977 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (103) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:14:10,984 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (103) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:14:11,009 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (103) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:14:11,011 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [101] prepared (119.498 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:14:11,049 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/101/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/101/registry.xml' '/galaxy/server/database/jobs_directory/000/101/upload_params.json' '101:/galaxy/server/database/objects/7/6/e/dataset_76e03c9a-ada9-488b-a8f7-0dc3e745b284_files:/galaxy/server/database/objects/7/6/e/dataset_76e03c9a-ada9-488b-a8f7-0dc3e745b284.dat'] +galaxy.jobs DEBUG 2024-12-30 01:14:11,050 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (103) Working directory for job is: /galaxy/server/database/jobs_directory/000/103 +galaxy.jobs.runners DEBUG 2024-12-30 01:14:11,060 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [103] queued (75.340 ms) +galaxy.jobs.handler INFO 2024-12-30 01:14:11,065 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (103) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:14:11,079 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 103 +galaxy.jobs.runners DEBUG 2024-12-30 01:14:11,088 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (101) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/101/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/101/galaxy_101.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-12-30 01:14:11,108 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [102] prepared (124.325 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:14:11,140 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/102/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/102/registry.xml' '/galaxy/server/database/jobs_directory/000/102/upload_params.json' '102:/galaxy/server/database/objects/1/1/9/dataset_11957baa-fd8d-4e9e-992b-50cc5182b2b3_files:/galaxy/server/database/objects/1/1/9/dataset_11957baa-fd8d-4e9e-992b-50cc5182b2b3.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:14:11,161 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (102) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/102/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/102/galaxy_102.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-12-30 01:14:11,229 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [103] prepared (120.804 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:14:11,251 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/103/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/103/registry.xml' '/galaxy/server/database/jobs_directory/000/103/upload_params.json' '103:/galaxy/server/database/objects/8/c/7/dataset_8c7883fa-b4ef-4e56-8831-21952c8b7155_files:/galaxy/server/database/objects/8/c/7/dataset_8c7883fa-b4ef-4e56-8831-21952c8b7155.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:14:11,265 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (103) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/103/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/103/galaxy_103.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:14:20,547 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 101: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:14:21,827 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 103: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:14:21,841 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 102: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:14:27,981 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 101 finished +galaxy.model.metadata DEBUG 2024-12-30 01:14:28,079 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 101 +galaxy.jobs INFO 2024-12-30 01:14:28,123 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 101 in /galaxy/server/database/jobs_directory/000/101 +galaxy.jobs DEBUG 2024-12-30 01:14:28,192 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 101 executed (178.969 ms) +galaxy.jobs.runners DEBUG 2024-12-30 01:14:29,118 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 103 finished +galaxy.jobs.runners DEBUG 2024-12-30 01:14:29,143 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 102 finished +galaxy.model.metadata DEBUG 2024-12-30 01:14:29,183 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 103 +galaxy.model.metadata DEBUG 2024-12-30 01:14:29,216 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 102 +galaxy.jobs INFO 2024-12-30 01:14:29,242 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 103 in /galaxy/server/database/jobs_directory/000/103 +galaxy.jobs INFO 2024-12-30 01:14:29,262 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 102 in /galaxy/server/database/jobs_directory/000/102 +galaxy.jobs DEBUG 2024-12-30 01:14:29,311 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 103 executed (165.166 ms) +galaxy.jobs DEBUG 2024-12-30 01:14:29,329 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 102 executed (152.608 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:14:29,676 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 104 +tpv.core.entities DEBUG 2024-12-30 01:14:29,723 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:14:29,723 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (104) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:14:29,732 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (104) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:14:29,754 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (104) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:14:29,776 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (104) Working directory for job is: /galaxy/server/database/jobs_directory/000/104 +galaxy.jobs.runners DEBUG 2024-12-30 01:14:29,786 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [104] queued (53.282 ms) +galaxy.jobs.handler INFO 2024-12-30 01:14:29,790 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (104) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:14:29,794 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 104 +galaxy.jobs DEBUG 2024-12-30 01:14:29,904 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [104] prepared (89.543 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:14:29,905 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:14:29,905 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a +galaxy.tool_util.deps.containers INFO 2024-12-30 01:14:29,932 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:14:29,956 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/104/tool_script.sh] for tool command [bcftools 2>&1 | grep 'Version:' > /galaxy/server/database/jobs_directory/000/104/outputs/COMMAND_VERSION 2>&1; +export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/7/6/e/dataset_76e03c9a-ada9-488b-a8f7-0dc3e745b284.dat' > input.vcf.gz && bcftools index input.vcf.gz && bgzip -c '/galaxy/server/database/objects/1/1/9/dataset_11957baa-fd8d-4e9e-992b-50cc5182b2b3.dat' > annotations.bed.gz && tabix -s 1 -b 2 -e 3 annotations.bed.gz && bcftools annotate --columns 'CHROM,FROM,TO,T_STR' --annotations 'annotations.bed.gz' --header-lines '/galaxy/server/database/objects/8/c/7/dataset_8c7883fa-b4ef-4e56-8831-21952c8b7155.dat' --set-id '%CHROM\_%POS\_%REF\_%FIRST_ALT' --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/4/2/a/dataset_42ae429f-2974-4975-a633-248bf9c8ebe0.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:14:29,973 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (104) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/104/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/104/galaxy_104.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:14:29,988 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:14:29,988 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a +galaxy.tool_util.deps.containers INFO 2024-12-30 01:14:30,009 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 01:14:34,995 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 104: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:14:40,082 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 104 finished +galaxy.model.metadata DEBUG 2024-12-30 01:14:40,150 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 104 +galaxy.jobs INFO 2024-12-30 01:14:40,194 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 104 in /galaxy/server/database/jobs_directory/000/104 +galaxy.objectstore CRITICAL 2024-12-30 01:14:40,242 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] None delete error [Errno 13] Permission denied: 'tmpnsyl1qs2' +galaxy.jobs DEBUG 2024-12-30 01:14:40,242 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 104 executed (130.590 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:14:42,064 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 106, 105 +tpv.core.entities DEBUG 2024-12-30 01:14:42,100 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:14:42,101 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (105) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:14:42,105 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (105) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:14:42,120 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (105) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:14:42,138 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (105) Working directory for job is: /galaxy/server/database/jobs_directory/000/105 +galaxy.jobs.runners DEBUG 2024-12-30 01:14:42,145 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [105] queued (40.193 ms) +galaxy.jobs.handler INFO 2024-12-30 01:14:42,149 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (105) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:14:42,154 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 105 +tpv.core.entities DEBUG 2024-12-30 01:14:42,169 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:14:42,169 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (106) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:14:42,177 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (106) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:14:42,197 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (106) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:14:42,231 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (106) Working directory for job is: /galaxy/server/database/jobs_directory/000/106 +galaxy.jobs.runners DEBUG 2024-12-30 01:14:42,241 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [106] queued (64.451 ms) +galaxy.jobs.handler INFO 2024-12-30 01:14:42,246 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (106) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:14:42,252 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 106 +galaxy.jobs DEBUG 2024-12-30 01:14:42,306 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [105] prepared (122.904 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:14:42,338 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/105/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/105/registry.xml' '/galaxy/server/database/jobs_directory/000/105/upload_params.json' '105:/galaxy/server/database/objects/5/2/1/dataset_52180263-b245-42fd-8312-7c1b6ca814b3_files:/galaxy/server/database/objects/5/2/1/dataset_52180263-b245-42fd-8312-7c1b6ca814b3.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:14:42,354 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (105) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/105/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/105/galaxy_105.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-12-30 01:14:42,392 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [106] prepared (116.920 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:14:42,416 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/106/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/106/registry.xml' '/galaxy/server/database/jobs_directory/000/106/upload_params.json' '106:/galaxy/server/database/objects/6/9/2/dataset_6928abe5-e71e-495d-a879-80e778c654de_files:/galaxy/server/database/objects/6/9/2/dataset_6928abe5-e71e-495d-a879-80e778c654de.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:14:42,428 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (106) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/106/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/106/galaxy_106.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:14:51,412 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 105: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:14:51,455 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 106: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:14:56,745 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 105 finished +galaxy.jobs.runners DEBUG 2024-12-30 01:14:56,763 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 106 finished +galaxy.model.metadata DEBUG 2024-12-30 01:14:56,826 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 105 +galaxy.model.metadata DEBUG 2024-12-30 01:14:56,834 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 106 +galaxy.jobs INFO 2024-12-30 01:14:56,878 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 105 in /galaxy/server/database/jobs_directory/000/105 +galaxy.jobs INFO 2024-12-30 01:14:56,888 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 106 in /galaxy/server/database/jobs_directory/000/106 +galaxy.jobs DEBUG 2024-12-30 01:14:56,942 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 105 executed (156.950 ms) +galaxy.jobs DEBUG 2024-12-30 01:14:56,955 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 106 executed (152.816 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:14:57,791 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 107 +tpv.core.entities DEBUG 2024-12-30 01:14:57,838 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:14:57,839 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (107) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:14:57,845 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (107) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:14:57,864 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (107) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:14:57,886 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (107) Working directory for job is: /galaxy/server/database/jobs_directory/000/107 +galaxy.jobs.runners DEBUG 2024-12-30 01:14:57,896 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [107] queued (50.863 ms) +galaxy.jobs.handler INFO 2024-12-30 01:14:57,900 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (107) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:14:57,905 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 107 +galaxy.jobs DEBUG 2024-12-30 01:14:58,004 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [107] prepared (78.460 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:14:58,005 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:14:58,005 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a +galaxy.tool_util.deps.containers INFO 2024-12-30 01:14:58,028 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:14:58,052 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/107/tool_script.sh] for tool command [bcftools 2>&1 | grep 'Version:' > /galaxy/server/database/jobs_directory/000/107/outputs/COMMAND_VERSION 2>&1; +export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/5/2/1/dataset_52180263-b245-42fd-8312-7c1b6ca814b3.dat' > input.vcf.gz && bcftools index input.vcf.gz && bgzip -c '/galaxy/server/database/objects/6/9/2/dataset_6928abe5-e71e-495d-a879-80e778c654de.dat' > annotations.vcf.gz && bcftools index annotations.vcf.gz && bcftools annotate --columns 'STR,ID,QUAL,FILTER' --annotations 'annotations.vcf.gz' --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/2/1/8/dataset_218c8d36-0b8c-49d5-aca2-a09d4e3b004e.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:14:58,067 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (107) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/107/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/107/galaxy_107.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:14:58,080 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:14:58,081 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a +galaxy.tool_util.deps.containers INFO 2024-12-30 01:14:58,099 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 01:15:03,886 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 107: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:15:08,877 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 107 finished +galaxy.model.metadata DEBUG 2024-12-30 01:15:08,938 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 107 +galaxy.jobs INFO 2024-12-30 01:15:08,979 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 107 in /galaxy/server/database/jobs_directory/000/107 +galaxy.objectstore CRITICAL 2024-12-30 01:15:09,021 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] None delete error [Errno 13] Permission denied: 'tmp3q61b6db' +galaxy.jobs DEBUG 2024-12-30 01:15:09,021 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 107 executed (115.775 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:15:10,156 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 108 +tpv.core.entities DEBUG 2024-12-30 01:15:10,199 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:15:10,200 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (108) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:15:10,205 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (108) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:15:10,223 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (108) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:15:10,245 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (108) Working directory for job is: /galaxy/server/database/jobs_directory/000/108 +galaxy.jobs.runners DEBUG 2024-12-30 01:15:10,253 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [108] queued (48.352 ms) +galaxy.jobs.handler INFO 2024-12-30 01:15:10,258 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (108) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:15:10,263 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 108 +galaxy.jobs DEBUG 2024-12-30 01:15:10,381 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [108] prepared (95.239 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:15:10,403 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/108/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/108/registry.xml' '/galaxy/server/database/jobs_directory/000/108/upload_params.json' '108:/galaxy/server/database/objects/d/e/5/dataset_de571565-2b7f-4c97-bfe0-49f4e17c0a46_files:/galaxy/server/database/objects/d/e/5/dataset_de571565-2b7f-4c97-bfe0-49f4e17c0a46.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:15:10,415 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (108) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/108/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/108/galaxy_108.ec; sh -c "exit $return_code" +galaxy.jobs.handler DEBUG 2024-12-30 01:15:11,260 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 109 +tpv.core.entities DEBUG 2024-12-30 01:15:11,298 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:15:11,299 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (109) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:15:11,303 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (109) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:15:11,321 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (109) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:15:11,340 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (109) Working directory for job is: /galaxy/server/database/jobs_directory/000/109 +galaxy.jobs.runners DEBUG 2024-12-30 01:15:11,348 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [109] queued (44.094 ms) +galaxy.jobs.handler INFO 2024-12-30 01:15:11,354 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (109) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:15:11,356 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 109 +galaxy.jobs DEBUG 2024-12-30 01:15:11,477 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [109] prepared (99.364 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:15:11,500 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/109/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/109/registry.xml' '/galaxy/server/database/jobs_directory/000/109/upload_params.json' '109:/galaxy/server/database/objects/c/b/7/dataset_cb718df6-aa41-462f-8504-9662e3b8ec3f_files:/galaxy/server/database/objects/c/b/7/dataset_cb718df6-aa41-462f-8504-9662e3b8ec3f.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:15:11,513 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (109) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/109/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/109/galaxy_109.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:15:19,265 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 108: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:15:19,300 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 109: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:15:24,397 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 108 finished +galaxy.model.metadata DEBUG 2024-12-30 01:15:24,464 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 108 +galaxy.jobs INFO 2024-12-30 01:15:24,510 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 108 in /galaxy/server/database/jobs_directory/000/108 +galaxy.jobs DEBUG 2024-12-30 01:15:24,566 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 108 executed (138.828 ms) +galaxy.jobs.runners DEBUG 2024-12-30 01:15:24,678 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 109 finished +galaxy.model.metadata DEBUG 2024-12-30 01:15:24,730 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 109 +galaxy.jobs INFO 2024-12-30 01:15:24,796 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 109 in /galaxy/server/database/jobs_directory/000/109 +galaxy.jobs DEBUG 2024-12-30 01:15:24,843 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 109 executed (140.864 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:15:25,697 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 110 +tpv.core.entities DEBUG 2024-12-30 01:15:25,738 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:15:25,738 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (110) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:15:25,743 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (110) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:15:25,760 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (110) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:15:25,780 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (110) Working directory for job is: /galaxy/server/database/jobs_directory/000/110 +galaxy.jobs.runners DEBUG 2024-12-30 01:15:25,788 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [110] queued (44.839 ms) +galaxy.jobs.handler INFO 2024-12-30 01:15:25,792 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (110) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:15:25,797 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 110 +galaxy.jobs DEBUG 2024-12-30 01:15:25,884 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [110] prepared (69.085 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:15:25,884 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:15:25,885 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a +galaxy.tool_util.deps.containers INFO 2024-12-30 01:15:26,086 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:15:26,106 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/110/tool_script.sh] for tool command [bcftools 2>&1 | grep 'Version:' > /galaxy/server/database/jobs_directory/000/110/outputs/COMMAND_VERSION 2>&1; +export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/d/e/5/dataset_de571565-2b7f-4c97-bfe0-49f4e17c0a46.dat' > input.vcf.gz && bcftools index input.vcf.gz && ln -s '/galaxy/server/database/objects/c/b/7/dataset_cb718df6-aa41-462f-8504-9662e3b8ec3f.dat' annotations.bcf && ln -s '/galaxy/server/database/objects/_metadata_files/f/4/7/metadata_f47e915f-0797-4080-b325-d3337d0ee746.dat' annotations.bcf.csi && bcftools annotate --columns 'STR,ID,QUAL,FILTER' --annotations 'annotations.bcf' --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/f/d/1/dataset_fd1002d7-f588-432e-8b88-b83b4a4ce0c2.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:15:26,118 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (110) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/110/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/110/galaxy_110.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:15:26,129 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:15:26,129 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a +galaxy.tool_util.deps.containers INFO 2024-12-30 01:15:26,147 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 01:15:31,395 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 110: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:15:36,356 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 110 finished +galaxy.model.metadata DEBUG 2024-12-30 01:15:36,418 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 110 +galaxy.jobs INFO 2024-12-30 01:15:36,453 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 110 in /galaxy/server/database/jobs_directory/000/110 +galaxy.objectstore CRITICAL 2024-12-30 01:15:36,495 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] None delete error [Errno 13] Permission denied: 'tmpjlt930o_' +galaxy.jobs DEBUG 2024-12-30 01:15:36,496 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 110 executed (111.518 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:15:38,062 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 112, 111 +tpv.core.entities DEBUG 2024-12-30 01:15:38,104 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:15:38,104 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (111) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:15:38,110 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (111) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:15:38,127 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (111) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:15:38,150 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (111) Working directory for job is: /galaxy/server/database/jobs_directory/000/111 +galaxy.jobs.runners DEBUG 2024-12-30 01:15:38,156 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [111] queued (46.432 ms) +galaxy.jobs.handler INFO 2024-12-30 01:15:38,160 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (111) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:15:38,167 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 111 +tpv.core.entities DEBUG 2024-12-30 01:15:38,182 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:15:38,182 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (112) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:15:38,189 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (112) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:15:38,207 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (112) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:15:38,247 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (112) Working directory for job is: /galaxy/server/database/jobs_directory/000/112 +galaxy.jobs.runners DEBUG 2024-12-30 01:15:38,256 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [112] queued (67.123 ms) +galaxy.jobs.handler INFO 2024-12-30 01:15:38,261 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (112) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:15:38,266 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 112 +galaxy.jobs DEBUG 2024-12-30 01:15:38,313 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [111] prepared (122.212 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:15:38,348 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/111/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/111/registry.xml' '/galaxy/server/database/jobs_directory/000/111/upload_params.json' '111:/galaxy/server/database/objects/0/0/e/dataset_00ef2145-8a3e-461d-8ecd-faba5ac99ac5_files:/galaxy/server/database/objects/0/0/e/dataset_00ef2145-8a3e-461d-8ecd-faba5ac99ac5.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:15:38,367 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (111) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/111/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/111/galaxy_111.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-12-30 01:15:38,404 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [112] prepared (111.565 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:15:38,427 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/112/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/112/registry.xml' '/galaxy/server/database/jobs_directory/000/112/upload_params.json' '112:/galaxy/server/database/objects/6/3/c/dataset_63cb5c9c-eaab-477e-b663-1312cf53b120_files:/galaxy/server/database/objects/6/3/c/dataset_63cb5c9c-eaab-477e-b663-1312cf53b120.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:15:38,442 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (112) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/112/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/112/galaxy_112.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:15:47,746 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 111: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:15:47,778 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 112: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:15:52,789 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 112 finished +galaxy.jobs.runners DEBUG 2024-12-30 01:15:52,794 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 111 finished +galaxy.model.metadata DEBUG 2024-12-30 01:15:52,849 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 112 +galaxy.model.metadata DEBUG 2024-12-30 01:15:52,853 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 111 +galaxy.jobs INFO 2024-12-30 01:15:52,896 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 112 in /galaxy/server/database/jobs_directory/000/112 +galaxy.jobs INFO 2024-12-30 01:15:52,906 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 111 in /galaxy/server/database/jobs_directory/000/111 +galaxy.jobs DEBUG 2024-12-30 01:15:52,954 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 112 executed (137.739 ms) +galaxy.jobs DEBUG 2024-12-30 01:15:52,967 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 111 executed (146.907 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:15:53,601 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 113 +tpv.core.entities DEBUG 2024-12-30 01:15:53,637 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:15:53,637 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (113) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:15:53,641 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (113) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:15:53,655 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (113) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:15:53,675 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (113) Working directory for job is: /galaxy/server/database/jobs_directory/000/113 +galaxy.jobs.runners DEBUG 2024-12-30 01:15:53,685 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [113] queued (43.776 ms) +galaxy.jobs.handler INFO 2024-12-30 01:15:53,690 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (113) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:15:53,694 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 113 +galaxy.jobs DEBUG 2024-12-30 01:15:53,778 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [113] prepared (64.227 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:15:53,779 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:15:53,779 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a +galaxy.tool_util.deps.containers INFO 2024-12-30 01:15:53,800 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:15:53,821 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/113/tool_script.sh] for tool command [bcftools 2>&1 | grep 'Version:' > /galaxy/server/database/jobs_directory/000/113/outputs/COMMAND_VERSION 2>&1; +export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/0/0/e/dataset_00ef2145-8a3e-461d-8ecd-faba5ac99ac5.dat' > input.vcf.gz && bcftools index input.vcf.gz && bgzip -c '/galaxy/server/database/objects/6/3/c/dataset_63cb5c9c-eaab-477e-b663-1312cf53b120.dat' > annotations.vcf.gz && bcftools index annotations.vcf.gz && bcftools annotate --columns 'ID,QUAL,FILTER,INFO,FMT' --annotations 'annotations.vcf.gz' --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/e/1/6/dataset_e163629d-5e1b-4dc1-a76a-082e01ec5e3b.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:15:53,833 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (113) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/113/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/113/galaxy_113.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:15:53,844 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:15:53,845 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a +galaxy.tool_util.deps.containers INFO 2024-12-30 01:15:53,862 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 01:15:59,894 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 113: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:16:04,819 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 113 finished +galaxy.model.metadata DEBUG 2024-12-30 01:16:04,885 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 113 +galaxy.jobs INFO 2024-12-30 01:16:04,928 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 113 in /galaxy/server/database/jobs_directory/000/113 +galaxy.objectstore CRITICAL 2024-12-30 01:16:04,977 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] None delete error [Errno 13] Permission denied: 'tmp__8vpg07' +galaxy.jobs DEBUG 2024-12-30 01:16:04,977 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 113 executed (129.364 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:16:06,059 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 115, 114 +tpv.core.entities DEBUG 2024-12-30 01:16:06,097 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:16:06,098 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (114) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:16:06,103 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (114) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:16:06,121 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (114) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:16:06,140 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (114) Working directory for job is: /galaxy/server/database/jobs_directory/000/114 +galaxy.jobs.runners DEBUG 2024-12-30 01:16:06,149 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [114] queued (45.725 ms) +galaxy.jobs.handler INFO 2024-12-30 01:16:06,153 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (114) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:16:06,158 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 114 +tpv.core.entities DEBUG 2024-12-30 01:16:06,172 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:16:06,172 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (115) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:16:06,180 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (115) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:16:06,200 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (115) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:16:06,236 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (115) Working directory for job is: /galaxy/server/database/jobs_directory/000/115 +galaxy.jobs.runners DEBUG 2024-12-30 01:16:06,244 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [115] queued (62.990 ms) +galaxy.jobs.handler INFO 2024-12-30 01:16:06,248 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (115) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:16:06,253 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 115 +galaxy.jobs DEBUG 2024-12-30 01:16:06,295 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [114] prepared (112.455 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:16:06,330 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/114/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/114/registry.xml' '/galaxy/server/database/jobs_directory/000/114/upload_params.json' '114:/galaxy/server/database/objects/f/e/f/dataset_fef346b3-faf2-4ddb-9a09-add15474021c_files:/galaxy/server/database/objects/f/e/f/dataset_fef346b3-faf2-4ddb-9a09-add15474021c.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:16:06,364 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (114) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/114/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/114/galaxy_114.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-12-30 01:16:06,393 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [115] prepared (114.279 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:16:06,417 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/115/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/115/registry.xml' '/galaxy/server/database/jobs_directory/000/115/upload_params.json' '115:/galaxy/server/database/objects/a/d/5/dataset_ad5fca75-0707-4434-8629-004dde032b7c_files:/galaxy/server/database/objects/a/d/5/dataset_ad5fca75-0707-4434-8629-004dde032b7c.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:16:06,435 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (115) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/115/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/115/galaxy_115.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:16:16,256 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 114: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:16:16,284 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 115: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:16:21,429 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 114 finished +galaxy.model.metadata DEBUG 2024-12-30 01:16:21,492 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 114 +galaxy.jobs.runners DEBUG 2024-12-30 01:16:21,506 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 115 finished +galaxy.jobs INFO 2024-12-30 01:16:21,537 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 114 in /galaxy/server/database/jobs_directory/000/114 +galaxy.model.metadata DEBUG 2024-12-30 01:16:21,574 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 115 +galaxy.jobs DEBUG 2024-12-30 01:16:21,608 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 114 executed (150.321 ms) +galaxy.jobs INFO 2024-12-30 01:16:21,618 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 115 in /galaxy/server/database/jobs_directory/000/115 +galaxy.jobs DEBUG 2024-12-30 01:16:21,687 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 115 executed (148.788 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:16:22,668 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 116 +tpv.core.entities DEBUG 2024-12-30 01:16:22,707 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:16:22,707 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (116) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:16:22,713 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (116) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:16:22,730 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (116) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:16:22,751 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (116) Working directory for job is: /galaxy/server/database/jobs_directory/000/116 +galaxy.jobs.runners DEBUG 2024-12-30 01:16:22,760 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [116] queued (46.660 ms) +galaxy.jobs.handler INFO 2024-12-30 01:16:22,763 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (116) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:16:22,768 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 116 +galaxy.jobs DEBUG 2024-12-30 01:16:22,858 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [116] prepared (70.381 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:16:22,858 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:16:22,859 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a +galaxy.tool_util.deps.containers INFO 2024-12-30 01:16:22,878 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:16:22,900 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/116/tool_script.sh] for tool command [bcftools 2>&1 | grep 'Version:' > /galaxy/server/database/jobs_directory/000/116/outputs/COMMAND_VERSION 2>&1; +export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/f/e/f/dataset_fef346b3-faf2-4ddb-9a09-add15474021c.dat' > input.vcf.gz && bcftools index input.vcf.gz && bgzip -c '/galaxy/server/database/objects/a/d/5/dataset_ad5fca75-0707-4434-8629-004dde032b7c.dat' > annotations.vcf.gz && bcftools index annotations.vcf.gz && bcftools annotate --columns 'ID,QUAL,FILTER,INFO,FMT' --annotations 'annotations.vcf.gz' --samples 'A' --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/a/b/6/dataset_ab6fa7f4-3214-46f3-a764-7ff952535b5e.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:16:22,913 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (116) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/116/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/116/galaxy_116.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:16:22,927 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:16:22,927 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a +galaxy.tool_util.deps.containers INFO 2024-12-30 01:16:22,946 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 01:16:27,439 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 116: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:16:32,339 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 116 finished +galaxy.model.metadata DEBUG 2024-12-30 01:16:32,397 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 116 +galaxy.jobs INFO 2024-12-30 01:16:32,434 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 116 in /galaxy/server/database/jobs_directory/000/116 +galaxy.objectstore CRITICAL 2024-12-30 01:16:32,474 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] None delete error [Errno 13] Permission denied: 'tmpdazxjwc6' +galaxy.jobs DEBUG 2024-12-30 01:16:32,474 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 116 executed (109.228 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:16:34,002 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 117 +tpv.core.entities DEBUG 2024-12-30 01:16:34,036 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:16:34,036 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (117) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:16:34,042 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (117) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:16:34,056 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (117) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:16:34,073 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (117) Working directory for job is: /galaxy/server/database/jobs_directory/000/117 +galaxy.jobs.runners DEBUG 2024-12-30 01:16:34,080 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [117] queued (37.882 ms) +galaxy.jobs.handler INFO 2024-12-30 01:16:34,084 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (117) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:16:34,087 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 117 +galaxy.jobs DEBUG 2024-12-30 01:16:34,195 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [117] prepared (88.018 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:16:34,216 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/117/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/117/registry.xml' '/galaxy/server/database/jobs_directory/000/117/upload_params.json' '117:/galaxy/server/database/objects/1/f/6/dataset_1f68ac62-bc3b-4e01-bcee-dda9316a409b_files:/galaxy/server/database/objects/1/f/6/dataset_1f68ac62-bc3b-4e01-bcee-dda9316a409b.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:16:34,228 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (117) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/117/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/117/galaxy_117.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:16:41,606 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 117: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:16:46,628 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 117 finished +galaxy.model.metadata DEBUG 2024-12-30 01:16:46,680 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 117 +galaxy.jobs INFO 2024-12-30 01:16:46,719 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 117 in /galaxy/server/database/jobs_directory/000/117 +galaxy.jobs DEBUG 2024-12-30 01:16:46,776 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 117 executed (122.693 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:16:47,370 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 118 +tpv.core.entities DEBUG 2024-12-30 01:16:47,411 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:16:47,412 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (118) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:16:47,418 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (118) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:16:47,435 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (118) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:16:47,455 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (118) Working directory for job is: /galaxy/server/database/jobs_directory/000/118 +galaxy.jobs.runners DEBUG 2024-12-30 01:16:47,464 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [118] queued (46.295 ms) +galaxy.jobs.handler INFO 2024-12-30 01:16:47,469 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (118) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:16:47,474 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 118 +galaxy.jobs DEBUG 2024-12-30 01:16:47,568 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [118] prepared (72.375 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:16:47,568 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:16:47,568 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a +galaxy.tool_util.deps.containers INFO 2024-12-30 01:16:47,593 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:16:47,614 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/118/tool_script.sh] for tool command [bcftools 2>&1 | grep 'Version:' > /galaxy/server/database/jobs_directory/000/118/outputs/COMMAND_VERSION 2>&1; +export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/1/f/6/dataset_1f68ac62-bc3b-4e01-bcee-dda9316a409b.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools annotate --remove 'ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL' --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/9/4/f/dataset_94ff8681-6038-4a0a-950f-c9da043d66ad.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:16:47,629 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (118) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/118/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/118/galaxy_118.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:16:47,641 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:16:47,641 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a +galaxy.tool_util.deps.containers INFO 2024-12-30 01:16:47,660 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 01:16:52,755 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 118: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:16:57,810 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 118 finished +galaxy.model.metadata DEBUG 2024-12-30 01:16:57,882 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 118 +galaxy.jobs INFO 2024-12-30 01:16:57,930 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 118 in /galaxy/server/database/jobs_directory/000/118 +galaxy.objectstore CRITICAL 2024-12-30 01:16:57,978 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] None delete error [Errno 13] Permission denied: 'tmpe_4ebzfr' +galaxy.jobs DEBUG 2024-12-30 01:16:57,979 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 118 executed (134.512 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:16:59,754 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 119 +tpv.core.entities DEBUG 2024-12-30 01:16:59,792 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:16:59,793 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (119) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:16:59,799 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (119) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:16:59,819 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (119) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:16:59,838 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (119) Working directory for job is: /galaxy/server/database/jobs_directory/000/119 +galaxy.jobs.runners DEBUG 2024-12-30 01:16:59,845 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [119] queued (45.986 ms) +galaxy.jobs.handler INFO 2024-12-30 01:16:59,849 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (119) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:16:59,854 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 119 +galaxy.jobs DEBUG 2024-12-30 01:16:59,977 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [119] prepared (104.443 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:17:00,002 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/119/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/119/registry.xml' '/galaxy/server/database/jobs_directory/000/119/upload_params.json' '119:/galaxy/server/database/objects/3/f/8/dataset_3f8dc32a-c3d3-43f6-a19a-f44ca1f2544e_files:/galaxy/server/database/objects/3/f/8/dataset_3f8dc32a-c3d3-43f6-a19a-f44ca1f2544e.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:17:00,016 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (119) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/119/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/119/galaxy_119.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:17:07,947 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 119: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:17:12,960 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 119 finished +galaxy.model.metadata DEBUG 2024-12-30 01:17:13,027 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 119 +galaxy.jobs INFO 2024-12-30 01:17:13,074 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 119 in /galaxy/server/database/jobs_directory/000/119 +galaxy.jobs DEBUG 2024-12-30 01:17:13,135 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 119 executed (145.353 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:17:14,173 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 120 +tpv.core.entities DEBUG 2024-12-30 01:17:14,216 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:17:14,216 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (120) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:17:14,222 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (120) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:17:14,242 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (120) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:17:14,265 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (120) Working directory for job is: /galaxy/server/database/jobs_directory/000/120 +galaxy.jobs.runners DEBUG 2024-12-30 01:17:14,274 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [120] queued (52.032 ms) +galaxy.jobs.handler INFO 2024-12-30 01:17:14,279 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (120) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:17:14,283 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 120 +galaxy.jobs DEBUG 2024-12-30 01:17:14,381 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [120] prepared (74.817 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:17:14,382 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:17:14,382 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a +galaxy.tool_util.deps.containers INFO 2024-12-30 01:17:14,403 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:17:14,425 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/120/tool_script.sh] for tool command [bcftools 2>&1 | grep 'Version:' > /galaxy/server/database/jobs_directory/000/120/outputs/COMMAND_VERSION 2>&1; +export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/3/f/8/dataset_3f8dc32a-c3d3-43f6-a19a-f44ca1f2544e.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools annotate --remove 'FORMAT' --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/8/0/2/dataset_8022584c-4e18-4a38-b23e-be1f18c0ca0f.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:17:14,440 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (120) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/120/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/120/galaxy_120.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:17:14,452 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:17:14,452 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a +galaxy.tool_util.deps.containers INFO 2024-12-30 01:17:14,471 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 01:17:20,099 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 120: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:17:25,079 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 120 finished +galaxy.model.metadata DEBUG 2024-12-30 01:17:25,139 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 120 +galaxy.jobs INFO 2024-12-30 01:17:25,177 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 120 in /galaxy/server/database/jobs_directory/000/120 +galaxy.objectstore CRITICAL 2024-12-30 01:17:25,222 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] None delete error [Errno 13] Permission denied: 'tmpq2wcp17q' +galaxy.jobs DEBUG 2024-12-30 01:17:25,222 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 120 executed (114.077 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:17:26,557 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 121 +tpv.core.entities DEBUG 2024-12-30 01:17:26,597 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:17:26,597 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (121) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:17:26,602 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (121) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:17:26,620 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (121) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:17:26,638 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (121) Working directory for job is: /galaxy/server/database/jobs_directory/000/121 +galaxy.jobs.runners DEBUG 2024-12-30 01:17:26,645 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [121] queued (43.073 ms) +galaxy.jobs.handler INFO 2024-12-30 01:17:26,650 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (121) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:17:26,654 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 121 +galaxy.jobs DEBUG 2024-12-30 01:17:26,773 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [121] prepared (96.535 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:17:26,797 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/121/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/121/registry.xml' '/galaxy/server/database/jobs_directory/000/121/upload_params.json' '121:/galaxy/server/database/objects/5/b/0/dataset_5b022d4d-94e5-4fc1-b553-69708d6757e5_files:/galaxy/server/database/objects/5/b/0/dataset_5b022d4d-94e5-4fc1-b553-69708d6757e5.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:17:26,809 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (121) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/121/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/121/galaxy_121.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:17:36,303 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 121: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:17:41,264 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 121 finished +galaxy.model.metadata DEBUG 2024-12-30 01:17:41,328 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 121 +galaxy.jobs INFO 2024-12-30 01:17:41,371 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 121 in /galaxy/server/database/jobs_directory/000/121 +galaxy.jobs DEBUG 2024-12-30 01:17:41,423 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 121 executed (131.331 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:17:42,011 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 122 +tpv.core.entities DEBUG 2024-12-30 01:17:42,050 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:17:42,051 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (122) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:17:42,057 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (122) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:17:42,072 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (122) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:17:42,092 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (122) Working directory for job is: /galaxy/server/database/jobs_directory/000/122 +galaxy.jobs.runners DEBUG 2024-12-30 01:17:42,101 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [122] queued (44.433 ms) +galaxy.jobs.handler INFO 2024-12-30 01:17:42,105 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (122) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:17:42,109 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 122 +galaxy.jobs DEBUG 2024-12-30 01:17:42,188 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [122] prepared (64.040 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:17:42,189 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:17:42,189 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a +galaxy.tool_util.deps.containers INFO 2024-12-30 01:17:42,211 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:17:42,232 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/122/tool_script.sh] for tool command [bcftools 2>&1 | grep 'Version:' > /galaxy/server/database/jobs_directory/000/122/outputs/COMMAND_VERSION 2>&1; +export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/5/b/0/dataset_5b022d4d-94e5-4fc1-b553-69708d6757e5.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools annotate --remove 'FORMAT' --regions-overlap 1 --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/5/9/7/dataset_597eaa6c-1db4-44f8-af96-6ae2bad7639f.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:17:42,249 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (122) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/122/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/122/galaxy_122.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:17:42,263 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:17:42,263 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a +galaxy.tool_util.deps.containers INFO 2024-12-30 01:17:42,282 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 01:17:48,441 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 122: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:17:53,394 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 122 finished +galaxy.model.metadata DEBUG 2024-12-30 01:17:53,461 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 122 +galaxy.jobs INFO 2024-12-30 01:17:53,503 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 122 in /galaxy/server/database/jobs_directory/000/122 +galaxy.objectstore CRITICAL 2024-12-30 01:17:53,546 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] None delete error [Errno 13] Permission denied: 'tmp06oddxvv' +galaxy.jobs DEBUG 2024-12-30 01:17:53,547 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 122 executed (123.646 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:17:54,391 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 123 +tpv.core.entities DEBUG 2024-12-30 01:17:54,435 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:17:54,435 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (123) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:17:54,441 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (123) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:17:54,460 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (123) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:17:54,484 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (123) Working directory for job is: /galaxy/server/database/jobs_directory/000/123 +galaxy.jobs.runners DEBUG 2024-12-30 01:17:54,491 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [123] queued (49.734 ms) +galaxy.jobs.handler INFO 2024-12-30 01:17:54,495 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (123) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:17:54,500 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 123 +galaxy.jobs DEBUG 2024-12-30 01:17:54,617 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [123] prepared (93.997 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:17:54,641 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/123/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/123/registry.xml' '/galaxy/server/database/jobs_directory/000/123/upload_params.json' '123:/galaxy/server/database/objects/c/a/4/dataset_ca478d32-1a6d-408d-a1b7-f0190ae03182_files:/galaxy/server/database/objects/c/a/4/dataset_ca478d32-1a6d-408d-a1b7-f0190ae03182.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:17:54,656 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (123) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/123/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/123/galaxy_123.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes ERROR 2024-12-30 01:18:02,567 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Could not clean up k8s batch job. Ignoring... +Traceback (most recent call last): + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/http.py", line 437, in raise_for_status + resp.raise_for_status() + File "/galaxy/server/.venv/lib/python3.10/site-packages/requests/models.py", line 1021, in raise_for_status + raise HTTPError(http_error_msg, response=self) +requests.exceptions.HTTPError: 409 Client Error: Conflict for url: https://10.107.32.1:443/apis/batch/v1/namespaces/prod-24-12-30-00-37-1/jobs/gxy-4npg9 + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 817, in _handle_job_failure + self.__cleanup_k8s_job(job) + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 824, in __cleanup_k8s_job + delete_job(job, k8s_cleanup_job) + File "/galaxy/server/lib/galaxy/jobs/runners/util/pykube_util.py", line 107, in delete_job + job.scale(replicas=0) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/mixins.py", line 30, in scale + self.update() + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 165, in update + self.patch(self.obj, subresource=subresource) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 157, in patch + self.api.raise_for_status(r) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/http.py", line 444, in raise_for_status + raise HTTPError(resp.status_code, payload["message"]) +pykube.exceptions.HTTPError: Operation cannot be fulfilled on jobs.batch "gxy-4npg9": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:18:02,620 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (123/gxy-4npg9) Terminated at user's request +galaxy.jobs.handler DEBUG 2024-12-30 01:18:04,727 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 124 +tpv.core.entities DEBUG 2024-12-30 01:18:04,767 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:18:04,767 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (124) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:18:04,773 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (124) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:18:04,791 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (124) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:18:04,813 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (124) Working directory for job is: /galaxy/server/database/jobs_directory/000/124 +galaxy.jobs.runners DEBUG 2024-12-30 01:18:04,820 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [124] queued (47.505 ms) +galaxy.jobs.handler INFO 2024-12-30 01:18:04,825 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (124) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:18:04,829 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 124 +galaxy.jobs DEBUG 2024-12-30 01:18:04,952 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [124] prepared (102.164 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:18:04,976 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/124/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/124/registry.xml' '/galaxy/server/database/jobs_directory/000/124/upload_params.json' '124:/galaxy/server/database/objects/a/4/5/dataset_a45fba20-919d-4a06-a036-a1097b9ed7fe_files:/galaxy/server/database/objects/a/4/5/dataset_a45fba20-919d-4a06-a036-a1097b9ed7fe.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:18:04,989 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (124) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/124/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/124/galaxy_124.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:18:12,889 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 124: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:18:17,922 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 124 finished +galaxy.model.metadata DEBUG 2024-12-30 01:18:17,991 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 124 +galaxy.jobs INFO 2024-12-30 01:18:18,030 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 124 in /galaxy/server/database/jobs_directory/000/124 +galaxy.jobs DEBUG 2024-12-30 01:18:18,089 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 124 executed (136.405 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:18:19,151 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 125 +tpv.core.entities DEBUG 2024-12-30 01:18:19,193 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:18:19,193 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (125) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:18:19,199 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (125) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:18:19,218 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (125) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:18:19,239 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (125) Working directory for job is: /galaxy/server/database/jobs_directory/000/125 +galaxy.jobs.runners DEBUG 2024-12-30 01:18:19,246 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [125] queued (47.038 ms) +galaxy.jobs.handler INFO 2024-12-30 01:18:19,251 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (125) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:18:19,255 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 125 +galaxy.jobs DEBUG 2024-12-30 01:18:19,329 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [125] prepared (55.726 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:18:19,330 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:18:19,330 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/vcffixup/vcffixup/1.0.0_rc3+galaxy0: vcflib:1.0.0_rc3 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:18:19,504 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/vcflib:1.0.0_rc3--py37hc088bd4_0,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:18:19,530 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/125/tool_script.sh] for tool command [vcffixup '/galaxy/server/database/objects/a/4/5/dataset_a45fba20-919d-4a06-a036-a1097b9ed7fe.dat' > '/galaxy/server/database/objects/f/7/9/dataset_f799635b-3404-4f7d-bd84-1b767736ec4f.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:18:19,543 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (125) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/125/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/125/galaxy_125.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:18:19,556 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:18:19,556 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/vcffixup/vcffixup/1.0.0_rc3+galaxy0: vcflib:1.0.0_rc3 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:18:19,576 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/vcflib:1.0.0_rc3--py37hc088bd4_0,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 01:18:31,117 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 125: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:18:36,062 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 125 finished +galaxy.model.metadata DEBUG 2024-12-30 01:18:36,127 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 125 +galaxy.jobs INFO 2024-12-30 01:18:36,173 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 125 in /galaxy/server/database/jobs_directory/000/125 +galaxy.jobs DEBUG 2024-12-30 01:18:36,231 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 125 executed (139.240 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:18:38,715 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 126 +tpv.core.entities DEBUG 2024-12-30 01:18:38,754 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:18:38,754 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (126) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:18:38,760 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (126) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:18:38,774 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (126) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:18:38,794 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (126) Working directory for job is: /galaxy/server/database/jobs_directory/000/126 +galaxy.jobs.runners DEBUG 2024-12-30 01:18:38,802 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [126] queued (42.144 ms) +galaxy.jobs.handler INFO 2024-12-30 01:18:38,806 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (126) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:18:38,811 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 126 +galaxy.jobs DEBUG 2024-12-30 01:18:38,922 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [126] prepared (92.368 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:18:38,946 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/126/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/126/registry.xml' '/galaxy/server/database/jobs_directory/000/126/upload_params.json' '126:/galaxy/server/database/objects/1/d/9/dataset_1d9f2eb0-c28b-4a7c-9e2e-2c663729747f_files:/galaxy/server/database/objects/1/d/9/dataset_1d9f2eb0-c28b-4a7c-9e2e-2c663729747f.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:18:38,960 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (126) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/126/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/126/galaxy_126.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:18:47,337 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 126: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:18:52,221 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 126 finished +galaxy.model.metadata DEBUG 2024-12-30 01:18:52,284 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 126 +galaxy.jobs INFO 2024-12-30 01:18:52,323 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 126 in /galaxy/server/database/jobs_directory/000/126 +galaxy.jobs DEBUG 2024-12-30 01:18:52,374 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 126 executed (121.016 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:18:53,133 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 127 +tpv.core.entities DEBUG 2024-12-30 01:18:53,174 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:18:53,175 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (127) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:18:53,180 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (127) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:18:53,198 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (127) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:18:53,218 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (127) Working directory for job is: /galaxy/server/database/jobs_directory/000/127 +galaxy.jobs.runners DEBUG 2024-12-30 01:18:53,227 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [127] queued (46.751 ms) +galaxy.jobs.handler INFO 2024-12-30 01:18:53,234 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (127) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:18:53,236 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 127 +galaxy.jobs DEBUG 2024-12-30 01:18:53,305 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [127] prepared (49.210 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:18:53,305 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:18:53,305 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/vcftools_annotate/vcftools_annotate/0.1: vcftools:0.1.11 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:18:53,644 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/vcftools:0.1.11--2,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:18:53,668 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/127/tool_script.sh] for tool command [echo "{ tag => 'FORMAT/FREQ', name => 'MinAF', desc => 'MinAF [7]', test => sub { my @t = split('%', @\$MATCH[0]); return @t[0] >= 7 ? \$PASS : \$FAIL }, }," > f.txt ; vcf-annotate -f f.txt /galaxy/server/database/objects/1/d/9/dataset_1d9f2eb0-c28b-4a7c-9e2e-2c663729747f.dat > /galaxy/server/database/objects/4/4/2/dataset_44201c8e-7902-4b0d-b11f-21cad2194d61.dat] +galaxy.jobs.runners DEBUG 2024-12-30 01:18:53,681 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (127) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/127/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/127/galaxy_127.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:18:53,695 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:18:53,695 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/vcftools_annotate/vcftools_annotate/0.1: vcftools:0.1.11 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:18:53,714 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/vcftools:0.1.11--2,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 01:19:03,728 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 127: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:19:08,615 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 127 finished +galaxy.model.metadata DEBUG 2024-12-30 01:19:08,696 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 127 +galaxy.jobs INFO 2024-12-30 01:19:08,755 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 127 in /galaxy/server/database/jobs_directory/000/127 +galaxy.jobs DEBUG 2024-12-30 01:19:08,808 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 127 executed (165.657 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:19:10,603 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 128 +tpv.core.entities DEBUG 2024-12-30 01:19:10,637 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:19:10,638 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (128) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:19:10,643 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (128) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:19:10,658 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (128) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:19:10,679 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (128) Working directory for job is: /galaxy/server/database/jobs_directory/000/128 +galaxy.jobs.runners DEBUG 2024-12-30 01:19:10,686 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [128] queued (43.134 ms) +galaxy.jobs.handler INFO 2024-12-30 01:19:10,690 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (128) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:19:10,695 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 128 +galaxy.jobs DEBUG 2024-12-30 01:19:10,812 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [128] prepared (96.229 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:19:10,836 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/128/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/128/registry.xml' '/galaxy/server/database/jobs_directory/000/128/upload_params.json' '128:/galaxy/server/database/objects/8/e/d/dataset_8eded40f-a858-4405-966f-216e8dfed63d_files:/galaxy/server/database/objects/8/e/d/dataset_8eded40f-a858-4405-966f-216e8dfed63d.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:19:10,849 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (128) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/128/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/128/galaxy_128.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:19:18,973 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 128: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:19:23,868 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 128 finished +galaxy.model.metadata DEBUG 2024-12-30 01:19:23,930 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 128 +galaxy.jobs INFO 2024-12-30 01:19:23,973 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 128 in /galaxy/server/database/jobs_directory/000/128 +galaxy.jobs DEBUG 2024-12-30 01:19:24,037 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 128 executed (140.481 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:19:25,154 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 129 +tpv.core.entities DEBUG 2024-12-30 01:19:25,190 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/.*, abstract=False, cores=1, mem=40, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:19:25,191 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (129) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:19:25,196 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (129) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:19:25,214 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (129) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:19:25,234 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (129) Working directory for job is: /galaxy/server/database/jobs_directory/000/129 +galaxy.jobs.runners DEBUG 2024-12-30 01:19:25,241 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [129] queued (45.216 ms) +galaxy.jobs.handler INFO 2024-12-30 01:19:25,245 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (129) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:19:25,250 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 129 +galaxy.jobs DEBUG 2024-12-30 01:19:25,340 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [129] prepared (67.121 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:19:25,341 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:19:25,341 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0: porechop:0.2.4 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:19:25,540 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/porechop:0.2.4--py312hf731ba3_9,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:19:25,562 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/129/tool_script.sh] for tool command [porechop --version > /galaxy/server/database/jobs_directory/000/129/outputs/COMMAND_VERSION 2>&1; +porechop -i '/galaxy/server/database/objects/8/e/d/dataset_8eded40f-a858-4405-966f-216e8dfed63d.dat' --format 'fasta' --barcode_threshold '75.0' --barcode_diff '5.0' --adapter_threshold '90.0' --check_reads '10000' --scoring_scheme '3,-6,-5,-2' --end_size '150' --min_trim_size '4' --extra_end_trim '2' --end_threshold '75.0' --middle_threshold '85.0' --extra_middle_trim_good_side '10' --extra_middle_trim_bad_side '100' --min_split_read_size '1000' -o 'out.fasta'] +galaxy.jobs.runners DEBUG 2024-12-30 01:19:25,578 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (129) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/129/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/129/galaxy_129.ec; +if [ -f "/galaxy/server/database/jobs_directory/000/129/working/out."*"" ] ; then cp "/galaxy/server/database/jobs_directory/000/129/working/out."*"" "/galaxy/server/database/objects/8/4/0/dataset_840b2760-7376-4b6e-8295-8795d4d3abb6.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:19:25,590 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:19:25,591 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0: porechop:0.2.4 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:19:25,613 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/porechop:0.2.4--py312hf731ba3_9,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 01:19:37,238 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 129: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:19:42,242 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 129 finished +galaxy.model.metadata DEBUG 2024-12-30 01:19:42,307 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 129 +galaxy.util WARNING 2024-12-30 01:19:42,318 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/8/4/0/dataset_840b2760-7376-4b6e-8295-8795d4d3abb6.dat, group remains grp.struct_group(gr_name='nogroup', gr_passwd='x', gr_gid=65534, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/8/4/0/dataset_840b2760-7376-4b6e-8295-8795d4d3abb6.dat' +galaxy.jobs INFO 2024-12-30 01:19:42,353 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 129 in /galaxy/server/database/jobs_directory/000/129 +galaxy.jobs DEBUG 2024-12-30 01:19:42,414 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 129 executed (142.901 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:19:43,652 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 130 +tpv.core.entities DEBUG 2024-12-30 01:19:43,691 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:19:43,691 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (130) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:19:43,696 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (130) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:19:43,714 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (130) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:19:43,734 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (130) Working directory for job is: /galaxy/server/database/jobs_directory/000/130 +galaxy.jobs.runners DEBUG 2024-12-30 01:19:43,741 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [130] queued (44.950 ms) +galaxy.jobs.handler INFO 2024-12-30 01:19:43,745 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (130) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:19:43,750 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 130 +galaxy.jobs DEBUG 2024-12-30 01:19:43,863 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [130] prepared (95.137 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:19:43,887 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/130/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/130/registry.xml' '/galaxy/server/database/jobs_directory/000/130/upload_params.json' '130:/galaxy/server/database/objects/a/6/0/dataset_a60e903a-1dc8-4c7b-ad77-2427e659d5d2_files:/galaxy/server/database/objects/a/6/0/dataset_a60e903a-1dc8-4c7b-ad77-2427e659d5d2.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:19:43,903 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (130) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/130/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/130/galaxy_130.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:19:52,489 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 130: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:19:57,676 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 130 finished +galaxy.model.metadata DEBUG 2024-12-30 01:19:57,749 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 130 +galaxy.jobs INFO 2024-12-30 01:19:57,798 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 130 in /galaxy/server/database/jobs_directory/000/130 +galaxy.jobs DEBUG 2024-12-30 01:19:57,877 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 130 executed (170.223 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:19:59,104 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 131 +tpv.core.entities DEBUG 2024-12-30 01:19:59,146 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/.*, abstract=False, cores=1, mem=40, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:19:59,147 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (131) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:19:59,153 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (131) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:19:59,169 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (131) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:19:59,190 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (131) Working directory for job is: /galaxy/server/database/jobs_directory/000/131 +galaxy.jobs.runners DEBUG 2024-12-30 01:19:59,200 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [131] queued (46.918 ms) +galaxy.jobs.handler INFO 2024-12-30 01:19:59,203 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (131) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:19:59,208 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 131 +galaxy.jobs DEBUG 2024-12-30 01:19:59,295 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [131] prepared (65.723 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:19:59,295 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:19:59,295 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0: porechop:0.2.4 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:19:59,318 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/porechop:0.2.4--py312hf731ba3_9,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:19:59,344 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/131/tool_script.sh] for tool command [porechop --version > /galaxy/server/database/jobs_directory/000/131/outputs/COMMAND_VERSION 2>&1; +porechop -i '/galaxy/server/database/objects/a/6/0/dataset_a60e903a-1dc8-4c7b-ad77-2427e659d5d2.dat' --format 'fastq' --barcode_threshold '75.0' --barcode_diff '5.0' --adapter_threshold '90.0' --check_reads '10000' --scoring_scheme '3,-6,-5,-2' --end_size '150' --min_trim_size '4' --extra_end_trim '2' --end_threshold '75.0' --middle_threshold '85.0' --extra_middle_trim_good_side '10' --extra_middle_trim_bad_side '100' --min_split_read_size '1000' -o 'out.fastq'] +galaxy.jobs.runners DEBUG 2024-12-30 01:19:59,362 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (131) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/131/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/131/galaxy_131.ec; +if [ -f "/galaxy/server/database/jobs_directory/000/131/working/out."*"" ] ; then cp "/galaxy/server/database/jobs_directory/000/131/working/out."*"" "/galaxy/server/database/objects/6/1/8/dataset_61814dd4-91ee-43de-9163-0fdcb42e5007.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:19:59,377 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:19:59,377 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0: porechop:0.2.4 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:19:59,397 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/porechop:0.2.4--py312hf731ba3_9,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 01:20:04,675 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 131: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:20:09,827 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 131 finished +galaxy.model.metadata DEBUG 2024-12-30 01:20:09,896 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 131 +galaxy.util WARNING 2024-12-30 01:20:09,907 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/6/1/8/dataset_61814dd4-91ee-43de-9163-0fdcb42e5007.dat, group remains grp.struct_group(gr_name='nogroup', gr_passwd='x', gr_gid=65534, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/6/1/8/dataset_61814dd4-91ee-43de-9163-0fdcb42e5007.dat' +galaxy.jobs INFO 2024-12-30 01:20:09,942 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 131 in /galaxy/server/database/jobs_directory/000/131 +galaxy.jobs DEBUG 2024-12-30 01:20:09,999 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 131 executed (139.033 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:20:11,490 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 132 +tpv.core.entities DEBUG 2024-12-30 01:20:11,529 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:20:11,529 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (132) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:20:11,534 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (132) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:20:11,550 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (132) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:20:11,572 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (132) Working directory for job is: /galaxy/server/database/jobs_directory/000/132 +galaxy.jobs.runners DEBUG 2024-12-30 01:20:11,579 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [132] queued (44.894 ms) +galaxy.jobs.handler INFO 2024-12-30 01:20:11,583 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (132) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:20:11,588 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 132 +galaxy.jobs DEBUG 2024-12-30 01:20:11,700 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [132] prepared (91.245 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:20:11,722 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/132/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/132/registry.xml' '/galaxy/server/database/jobs_directory/000/132/upload_params.json' '132:/galaxy/server/database/objects/2/6/0/dataset_26086907-339b-4ad4-9f75-5e65d05ab0cc_files:/galaxy/server/database/objects/2/6/0/dataset_26086907-339b-4ad4-9f75-5e65d05ab0cc.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:20:11,736 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (132) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/132/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/132/galaxy_132.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:20:19,831 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 132: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:20:24,624 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 132 finished +galaxy.model.metadata DEBUG 2024-12-30 01:20:24,696 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 132 +galaxy.jobs INFO 2024-12-30 01:20:24,734 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 132 in /galaxy/server/database/jobs_directory/000/132 +galaxy.jobs DEBUG 2024-12-30 01:20:24,788 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 132 executed (130.798 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:20:25,959 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 133 +tpv.core.entities DEBUG 2024-12-30 01:20:25,998 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/.*, abstract=False, cores=1, mem=40, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:20:25,999 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (133) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:20:26,005 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (133) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:20:26,023 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (133) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:20:26,045 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (133) Working directory for job is: /galaxy/server/database/jobs_directory/000/133 +galaxy.jobs.runners DEBUG 2024-12-30 01:20:26,055 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [133] queued (49.576 ms) +galaxy.jobs.handler INFO 2024-12-30 01:20:26,060 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (133) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:20:26,065 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 133 +galaxy.jobs DEBUG 2024-12-30 01:20:26,138 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [133] prepared (54.154 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:20:26,139 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:20:26,139 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0: porechop:0.2.4 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:20:26,318 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/porechop:0.2.4--py312hf731ba3_9,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:20:26,342 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/133/tool_script.sh] for tool command [porechop --version > /galaxy/server/database/jobs_directory/000/133/outputs/COMMAND_VERSION 2>&1; +porechop -i '/galaxy/server/database/objects/2/6/0/dataset_26086907-339b-4ad4-9f75-5e65d05ab0cc.dat' --format 'fastq' --barcode_threshold '75.0' --barcode_diff '5.0' --adapter_threshold '90.0' --check_reads '10000' --scoring_scheme '3,-6,-5,-2' --end_size '150' --min_trim_size '4' --extra_end_trim '2' --end_threshold '75.0' --middle_threshold '85.0' --extra_middle_trim_good_side '10' --extra_middle_trim_bad_side '100' --min_split_read_size '1000' -o 'out.fastq'] +galaxy.jobs.runners DEBUG 2024-12-30 01:20:26,358 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (133) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/133/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/133/galaxy_133.ec; +if [ -f "/galaxy/server/database/jobs_directory/000/133/working/out."*"" ] ; then cp "/galaxy/server/database/jobs_directory/000/133/working/out."*"" "/galaxy/server/database/objects/a/e/2/dataset_ae2ce737-6b1b-4296-aac5-b2f0e08f277b.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:20:26,371 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:20:26,371 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0: porechop:0.2.4 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:20:26,393 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/porechop:0.2.4--py312hf731ba3_9,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 01:20:31,973 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 133: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:20:36,978 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 133 finished +galaxy.model.metadata DEBUG 2024-12-30 01:20:37,044 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 133 +galaxy.util WARNING 2024-12-30 01:20:37,053 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/a/e/2/dataset_ae2ce737-6b1b-4296-aac5-b2f0e08f277b.dat, group remains grp.struct_group(gr_name='nogroup', gr_passwd='x', gr_gid=65534, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/a/e/2/dataset_ae2ce737-6b1b-4296-aac5-b2f0e08f277b.dat' +galaxy.jobs INFO 2024-12-30 01:20:37,086 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 133 in /galaxy/server/database/jobs_directory/000/133 +galaxy.jobs DEBUG 2024-12-30 01:20:37,142 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 133 executed (133.733 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:20:38,336 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 134 +tpv.core.entities DEBUG 2024-12-30 01:20:38,369 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:20:38,369 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (134) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:20:38,375 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (134) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:20:38,392 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (134) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:20:38,410 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (134) Working directory for job is: /galaxy/server/database/jobs_directory/000/134 +galaxy.jobs.runners DEBUG 2024-12-30 01:20:38,418 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [134] queued (42.340 ms) +galaxy.jobs.handler INFO 2024-12-30 01:20:38,424 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (134) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:20:38,427 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 134 +galaxy.jobs DEBUG 2024-12-30 01:20:38,548 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [134] prepared (99.195 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:20:38,571 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/134/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/134/registry.xml' '/galaxy/server/database/jobs_directory/000/134/upload_params.json' '134:/galaxy/server/database/objects/2/6/1/dataset_261587ba-6f35-4919-99ac-dd8495488eab_files:/galaxy/server/database/objects/2/6/1/dataset_261587ba-6f35-4919-99ac-dd8495488eab.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:20:38,586 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (134) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/134/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/134/galaxy_134.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:20:47,184 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 134: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:20:52,115 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 134 finished +galaxy.model.metadata DEBUG 2024-12-30 01:20:52,182 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 134 +galaxy.jobs INFO 2024-12-30 01:20:52,227 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 134 in /galaxy/server/database/jobs_directory/000/134 +galaxy.jobs DEBUG 2024-12-30 01:20:52,283 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 134 executed (135.325 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:20:52,756 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 135 +tpv.core.entities DEBUG 2024-12-30 01:20:52,797 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/.*, abstract=False, cores=1, mem=40, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:20:52,798 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (135) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:20:52,803 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (135) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:20:52,820 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (135) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:20:52,842 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (135) Working directory for job is: /galaxy/server/database/jobs_directory/000/135 +galaxy.jobs.runners DEBUG 2024-12-30 01:20:52,850 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [135] queued (46.851 ms) +galaxy.jobs.handler INFO 2024-12-30 01:20:52,853 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (135) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:20:52,859 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 135 +galaxy.jobs DEBUG 2024-12-30 01:20:52,936 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [135] prepared (59.234 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:20:52,937 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:20:52,937 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0: porechop:0.2.4 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:20:52,959 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/porechop:0.2.4--py312hf731ba3_9,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:20:52,982 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/135/tool_script.sh] for tool command [porechop --version > /galaxy/server/database/jobs_directory/000/135/outputs/COMMAND_VERSION 2>&1; +porechop -i '/galaxy/server/database/objects/2/6/1/dataset_261587ba-6f35-4919-99ac-dd8495488eab.dat' --format 'fasta.gz' --barcode_threshold '75.0' --barcode_diff '5.0' --adapter_threshold '90.0' --check_reads '10000' --scoring_scheme '3,-6,-5,-2' --end_size '150' --min_trim_size '4' --extra_end_trim '2' --end_threshold '75.0' --middle_threshold '85.0' --extra_middle_trim_good_side '10' --extra_middle_trim_bad_side '100' --min_split_read_size '1000' -o 'out.fasta.gz'] +galaxy.jobs.runners DEBUG 2024-12-30 01:20:52,998 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (135) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/135/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/135/galaxy_135.ec; +if [ -f "/galaxy/server/database/jobs_directory/000/135/working/out."*"" ] ; then cp "/galaxy/server/database/jobs_directory/000/135/working/out."*"" "/galaxy/server/database/objects/6/2/a/dataset_62a0d775-cab4-4fce-b293-c8a81f22373f.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:20:53,012 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:20:53,012 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0: porechop:0.2.4 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:20:53,033 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/porechop:0.2.4--py312hf731ba3_9,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 01:20:59,343 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 135: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:21:04,161 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 135 finished +galaxy.model.metadata DEBUG 2024-12-30 01:21:04,227 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 135 +galaxy.util WARNING 2024-12-30 01:21:04,238 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/6/2/a/dataset_62a0d775-cab4-4fce-b293-c8a81f22373f.dat, group remains grp.struct_group(gr_name='nogroup', gr_passwd='x', gr_gid=65534, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/6/2/a/dataset_62a0d775-cab4-4fce-b293-c8a81f22373f.dat' +galaxy.jobs INFO 2024-12-30 01:21:04,269 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 135 in /galaxy/server/database/jobs_directory/000/135 +galaxy.jobs DEBUG 2024-12-30 01:21:04,323 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 135 executed (129.585 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:21:06,133 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 136 +tpv.core.entities DEBUG 2024-12-30 01:21:06,168 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:21:06,169 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (136) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:21:06,174 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (136) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:21:06,190 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (136) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:21:06,209 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (136) Working directory for job is: /galaxy/server/database/jobs_directory/000/136 +galaxy.jobs.runners DEBUG 2024-12-30 01:21:06,216 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [136] queued (41.796 ms) +galaxy.jobs.handler INFO 2024-12-30 01:21:06,220 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (136) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:21:06,225 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 136 +galaxy.jobs DEBUG 2024-12-30 01:21:06,340 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [136] prepared (93.891 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:21:06,365 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/136/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/136/registry.xml' '/galaxy/server/database/jobs_directory/000/136/upload_params.json' '136:/galaxy/server/database/objects/6/4/b/dataset_64b22bcd-c800-4207-9736-15d61ef12e06_files:/galaxy/server/database/objects/6/4/b/dataset_64b22bcd-c800-4207-9736-15d61ef12e06.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:21:06,379 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (136) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/136/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/136/galaxy_136.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:21:15,687 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 136: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:21:20,622 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 136 finished +galaxy.model.metadata DEBUG 2024-12-30 01:21:20,683 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 136 +galaxy.jobs INFO 2024-12-30 01:21:20,727 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 136 in /galaxy/server/database/jobs_directory/000/136 +galaxy.jobs DEBUG 2024-12-30 01:21:20,792 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 136 executed (140.401 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:21:21,554 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 137 +tpv.core.entities DEBUG 2024-12-30 01:21:21,595 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/.*, abstract=False, cores=1, mem=40, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:21:21,596 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (137) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:21:21,601 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (137) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:21:21,621 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (137) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:21:21,642 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (137) Working directory for job is: /galaxy/server/database/jobs_directory/000/137 +galaxy.jobs.runners DEBUG 2024-12-30 01:21:21,651 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [137] queued (49.323 ms) +galaxy.jobs.handler INFO 2024-12-30 01:21:21,655 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (137) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:21:21,660 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 137 +galaxy.jobs DEBUG 2024-12-30 01:21:21,744 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [137] prepared (61.617 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:21:21,745 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:21:21,745 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0: porechop:0.2.4 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:21:21,767 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/porechop:0.2.4--py312hf731ba3_9,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:21:21,794 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/137/tool_script.sh] for tool command [porechop --version > /galaxy/server/database/jobs_directory/000/137/outputs/COMMAND_VERSION 2>&1; +porechop -i '/galaxy/server/database/objects/6/4/b/dataset_64b22bcd-c800-4207-9736-15d61ef12e06.dat' --format 'fastq.gz' --barcode_threshold '75.0' --barcode_diff '5.0' --adapter_threshold '90.0' --check_reads '10000' --scoring_scheme '3,-6,-5,-2' --end_size '150' --min_trim_size '4' --extra_end_trim '2' --end_threshold '75.0' --middle_threshold '85.0' --extra_middle_trim_good_side '10' --extra_middle_trim_bad_side '100' --min_split_read_size '1000' -o 'out.fastq.gz'] +galaxy.jobs.runners DEBUG 2024-12-30 01:21:21,811 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (137) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/137/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/137/galaxy_137.ec; +if [ -f "/galaxy/server/database/jobs_directory/000/137/working/out."*"" ] ; then cp "/galaxy/server/database/jobs_directory/000/137/working/out."*"" "/galaxy/server/database/objects/a/1/4/dataset_a146f0b5-37ca-48b5-8f8d-3ea59cf047e9.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:21:21,824 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:21:21,824 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0: porechop:0.2.4 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:21:21,845 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/porechop:0.2.4--py312hf731ba3_9,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 01:21:27,803 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 137: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:21:32,754 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 137 finished +galaxy.model.metadata DEBUG 2024-12-30 01:21:32,810 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 137 +galaxy.util WARNING 2024-12-30 01:21:32,818 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/a/1/4/dataset_a146f0b5-37ca-48b5-8f8d-3ea59cf047e9.dat, group remains grp.struct_group(gr_name='nogroup', gr_passwd='x', gr_gid=65534, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/a/1/4/dataset_a146f0b5-37ca-48b5-8f8d-3ea59cf047e9.dat' +galaxy.jobs INFO 2024-12-30 01:21:32,846 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 137 in /galaxy/server/database/jobs_directory/000/137 +galaxy.jobs DEBUG 2024-12-30 01:21:32,894 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 137 executed (113.789 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:21:34,983 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 138 +tpv.core.entities DEBUG 2024-12-30 01:21:35,019 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:21:35,019 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (138) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:21:35,024 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (138) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:21:35,041 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (138) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:21:35,060 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (138) Working directory for job is: /galaxy/server/database/jobs_directory/000/138 +galaxy.jobs.runners DEBUG 2024-12-30 01:21:35,068 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [138] queued (44.093 ms) +galaxy.jobs.handler INFO 2024-12-30 01:21:35,072 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (138) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:21:35,077 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 138 +galaxy.jobs DEBUG 2024-12-30 01:21:35,181 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [138] prepared (86.946 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:21:35,203 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/138/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/138/registry.xml' '/galaxy/server/database/jobs_directory/000/138/upload_params.json' '138:/galaxy/server/database/objects/7/7/8/dataset_778ce91e-3e64-4bc8-9084-c99006669b2d_files:/galaxy/server/database/objects/7/7/8/dataset_778ce91e-3e64-4bc8-9084-c99006669b2d.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:21:35,216 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (138) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/138/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/138/galaxy_138.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:21:44,035 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 138: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:21:48,979 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 138 finished +galaxy.model.metadata DEBUG 2024-12-30 01:21:49,041 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 138 +galaxy.jobs INFO 2024-12-30 01:21:49,081 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 138 in /galaxy/server/database/jobs_directory/000/138 +galaxy.jobs DEBUG 2024-12-30 01:21:49,145 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 138 executed (137.100 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:21:50,407 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 139 +tpv.core.entities DEBUG 2024-12-30 01:21:50,445 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/.*, abstract=False, cores=1, mem=40, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:21:50,446 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (139) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:21:50,451 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (139) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:21:50,467 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (139) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:21:50,486 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (139) Working directory for job is: /galaxy/server/database/jobs_directory/000/139 +galaxy.jobs.runners DEBUG 2024-12-30 01:21:50,493 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [139] queued (41.625 ms) +galaxy.jobs.handler INFO 2024-12-30 01:21:50,496 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (139) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:21:50,501 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 139 +galaxy.jobs DEBUG 2024-12-30 01:21:50,582 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [139] prepared (61.580 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:21:50,583 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:21:50,583 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0: porechop:0.2.4 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:21:50,605 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/porechop:0.2.4--py312hf731ba3_9,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:21:50,627 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/139/tool_script.sh] for tool command [porechop --version > /galaxy/server/database/jobs_directory/000/139/outputs/COMMAND_VERSION 2>&1; +porechop -i '/galaxy/server/database/objects/7/7/8/dataset_778ce91e-3e64-4bc8-9084-c99006669b2d.dat' --format 'fasta' --barcode_threshold '70.0' --barcode_diff '4.0' --require_two_barcodes --discard_unassigned --adapter_threshold '90.0' --check_reads '10000' --scoring_scheme '3,-6,-5,-2' --end_size '100' --min_trim_size '2' --extra_end_trim '1' --end_threshold '80.0' --discard_middle --middle_threshold '90.0' --extra_middle_trim_good_side '10' --extra_middle_trim_bad_side '100' --min_split_read_size '1500' -o 'out.fasta'] +galaxy.jobs.runners DEBUG 2024-12-30 01:21:50,646 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (139) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/139/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/139/galaxy_139.ec; +if [ -f "/galaxy/server/database/jobs_directory/000/139/working/out."*"" ] ; then cp "/galaxy/server/database/jobs_directory/000/139/working/out."*"" "/galaxy/server/database/objects/9/8/a/dataset_98af874d-a463-43f2-8a49-1bd38b8fb0aa.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:21:50,660 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:21:50,660 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0: porechop:0.2.4 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:21:50,680 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/porechop:0.2.4--py312hf731ba3_9,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 01:21:57,192 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 139: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:22:02,113 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 139 finished +galaxy.model.metadata DEBUG 2024-12-30 01:22:02,176 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 139 +galaxy.util WARNING 2024-12-30 01:22:02,186 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/9/8/a/dataset_98af874d-a463-43f2-8a49-1bd38b8fb0aa.dat, group remains grp.struct_group(gr_name='nogroup', gr_passwd='x', gr_gid=65534, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/9/8/a/dataset_98af874d-a463-43f2-8a49-1bd38b8fb0aa.dat' +galaxy.jobs INFO 2024-12-30 01:22:02,218 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 139 in /galaxy/server/database/jobs_directory/000/139 +galaxy.jobs DEBUG 2024-12-30 01:22:02,281 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 139 executed (138.523 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:22:04,825 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 141, 140 +tpv.core.entities DEBUG 2024-12-30 01:22:04,864 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:22:04,865 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (140) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:22:04,871 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (140) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:22:04,890 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (140) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:22:04,912 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (140) Working directory for job is: /galaxy/server/database/jobs_directory/000/140 +galaxy.jobs.runners DEBUG 2024-12-30 01:22:04,919 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [140] queued (48.042 ms) +galaxy.jobs.handler INFO 2024-12-30 01:22:04,924 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (140) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:22:04,930 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 140 +tpv.core.entities DEBUG 2024-12-30 01:22:04,946 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:22:04,947 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (141) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:22:04,954 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (141) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:22:04,975 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (141) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:22:05,012 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (141) Working directory for job is: /galaxy/server/database/jobs_directory/000/141 +galaxy.jobs.runners DEBUG 2024-12-30 01:22:05,020 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [141] queued (65.582 ms) +galaxy.jobs.handler INFO 2024-12-30 01:22:05,025 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (141) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:22:05,031 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 141 +galaxy.jobs DEBUG 2024-12-30 01:22:05,073 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [140] prepared (114.934 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:22:05,107 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/140/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/140/registry.xml' '/galaxy/server/database/jobs_directory/000/140/upload_params.json' '140:/galaxy/server/database/objects/3/7/3/dataset_3734d46b-308d-4777-9bb3-b8d6b5e76153_files:/galaxy/server/database/objects/3/7/3/dataset_3734d46b-308d-4777-9bb3-b8d6b5e76153.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:22:05,123 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (140) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/140/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/140/galaxy_140.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-12-30 01:22:05,170 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [141] prepared (112.516 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:22:05,194 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/141/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/141/registry.xml' '/galaxy/server/database/jobs_directory/000/141/upload_params.json' '141:/galaxy/server/database/objects/5/8/d/dataset_58d1c012-f6f0-4dc5-ac52-6a247ec0862f_files:/galaxy/server/database/objects/5/8/d/dataset_58d1c012-f6f0-4dc5-ac52-6a247ec0862f.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:22:05,208 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (141) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/141/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/141/galaxy_141.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:22:15,748 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 140: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:22:15,782 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 141: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:22:20,919 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 141 finished +galaxy.jobs.runners DEBUG 2024-12-30 01:22:20,948 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 140 finished +galaxy.model.metadata DEBUG 2024-12-30 01:22:20,985 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 141 +galaxy.model.metadata DEBUG 2024-12-30 01:22:21,023 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 140 +galaxy.jobs INFO 2024-12-30 01:22:21,029 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 141 in /galaxy/server/database/jobs_directory/000/141 +galaxy.jobs INFO 2024-12-30 01:22:21,098 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 140 in /galaxy/server/database/jobs_directory/000/140 +galaxy.jobs DEBUG 2024-12-30 01:22:21,101 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 141 executed (154.519 ms) +galaxy.jobs DEBUG 2024-12-30 01:22:21,157 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 140 executed (177.535 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:22:22,423 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 142 +tpv.core.entities DEBUG 2024-12-30 01:22:22,462 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/.*, abstract=False, cores=10, mem=24, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:22:22,463 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (142) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:22:22,469 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (142) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:22:22,483 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (142) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:22:22,502 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (142) Working directory for job is: /galaxy/server/database/jobs_directory/000/142 +galaxy.jobs.runners DEBUG 2024-12-30 01:22:22,510 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [142] queued (40.648 ms) +galaxy.jobs.handler INFO 2024-12-30 01:22:22,514 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (142) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:22:22,518 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 142 +galaxy.jobs DEBUG 2024-12-30 01:22:22,597 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [142] prepared (63.519 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:22:22,598 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:22:22,598 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/3.5.4+galaxy0: mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:bcea566aaf2a8cd09765df369b45c50e0b7e9f18 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:22:22,790 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:bcea566aaf2a8cd09765df369b45c50e0b7e9f18-1,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:22:22,812 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/142/tool_script.sh] for tool command [computeGCBias --version > /galaxy/server/database/jobs_directory/000/142/outputs/COMMAND_VERSION 2>&1; +ln -s '/galaxy/server/database/objects/3/7/3/dataset_3734d46b-308d-4777-9bb3-b8d6b5e76153.dat' local_bamInput.bam && ln -s '/galaxy/server/database/objects/_metadata_files/5/e/3/metadata_5e37ba68-658e-4309-84aa-125bffdbb7ab.dat' local_bamInput.bam.bai && computeGCBias --numberOfProcessors "${GALAXY_SLOTS:-4}" --bamfile local_bamInput.bam --GCbiasFrequenciesFile /galaxy/server/database/objects/d/8/4/dataset_d84da292-0cee-4866-8d65-82ce35ed2a96.dat --fragmentLength 300 --genome /galaxy/server/database/objects/5/8/d/dataset_58d1c012-f6f0-4dc5-ac52-6a247ec0862f.dat --effectiveGenomeSize 10050 --region 'chr2L' --sampleSize '10' --regionSize '1'] +galaxy.jobs.runners DEBUG 2024-12-30 01:22:22,824 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (142) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/142/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/142/galaxy_142.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:22:22,837 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:22:22,837 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/3.5.4+galaxy0: mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:bcea566aaf2a8cd09765df369b45c50e0b7e9f18 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:22:22,854 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:bcea566aaf2a8cd09765df369b45c50e0b7e9f18-1,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 01:22:45,160 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 142: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:22:50,049 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 142 finished +galaxy.model.metadata DEBUG 2024-12-30 01:22:50,110 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 142 +galaxy.jobs INFO 2024-12-30 01:22:50,155 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 142 in /galaxy/server/database/jobs_directory/000/142 +galaxy.objectstore CRITICAL 2024-12-30 01:22:50,191 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] None delete error [Errno 13] Permission denied: 'matplotlib' +galaxy.jobs DEBUG 2024-12-30 01:22:50,191 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 142 executed (112.797 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:22:52,184 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 143 +tpv.core.entities DEBUG 2024-12-30 01:22:52,221 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:22:52,222 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (143) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:22:52,228 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (143) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:22:52,244 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (143) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:22:52,265 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (143) Working directory for job is: /galaxy/server/database/jobs_directory/000/143 +galaxy.jobs.runners DEBUG 2024-12-30 01:22:52,272 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [143] queued (44.187 ms) +galaxy.jobs.handler INFO 2024-12-30 01:22:52,277 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (143) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:22:52,282 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 143 +galaxy.jobs DEBUG 2024-12-30 01:22:52,384 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [143] prepared (83.277 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:22:52,403 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/143/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/143/registry.xml' '/galaxy/server/database/jobs_directory/000/143/upload_params.json' '143:/galaxy/server/database/objects/d/6/2/dataset_d62b40cf-3712-410b-af8d-e5caf23bfdf0_files:/galaxy/server/database/objects/d/6/2/dataset_d62b40cf-3712-410b-af8d-e5caf23bfdf0.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:22:52,414 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (143) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/143/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/143/galaxy_143.ec; sh -c "exit $return_code" +galaxy.jobs.handler DEBUG 2024-12-30 01:22:53,280 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 144 +tpv.core.entities DEBUG 2024-12-30 01:22:53,310 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:22:53,310 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (144) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:22:53,315 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (144) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:22:53,329 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (144) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:22:53,348 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (144) Working directory for job is: /galaxy/server/database/jobs_directory/000/144 +galaxy.jobs.runners DEBUG 2024-12-30 01:22:53,356 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [144] queued (40.781 ms) +galaxy.jobs.handler INFO 2024-12-30 01:22:53,360 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (144) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:22:53,364 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 144 +galaxy.jobs DEBUG 2024-12-30 01:22:53,465 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [144] prepared (80.726 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:22:53,484 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/144/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/144/registry.xml' '/galaxy/server/database/jobs_directory/000/144/upload_params.json' '144:/galaxy/server/database/objects/b/9/b/dataset_b9b211ff-d0df-4c46-b9be-0aa461ad4daf_files:/galaxy/server/database/objects/b/9/b/dataset_b9b211ff-d0df-4c46-b9be-0aa461ad4daf.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:22:53,499 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (144) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/144/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/144/galaxy_144.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:23:01,484 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 143: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:23:01,512 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 144: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:23:06,861 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 143 finished +galaxy.jobs.runners DEBUG 2024-12-30 01:23:06,905 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 144 finished +galaxy.model.metadata DEBUG 2024-12-30 01:23:06,938 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 143 +galaxy.model.metadata DEBUG 2024-12-30 01:23:06,990 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 144 +galaxy.jobs INFO 2024-12-30 01:23:06,994 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 143 in /galaxy/server/database/jobs_directory/000/143 +galaxy.jobs INFO 2024-12-30 01:23:07,034 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 144 in /galaxy/server/database/jobs_directory/000/144 +galaxy.jobs DEBUG 2024-12-30 01:23:07,072 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 143 executed (174.231 ms) +galaxy.jobs DEBUG 2024-12-30 01:23:07,105 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 144 executed (160.555 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:23:07,891 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 145 +tpv.core.entities DEBUG 2024-12-30 01:23:07,934 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/.*, abstract=False, cores=8, mem=20, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:23:07,935 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (145) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:23:07,941 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (145) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:23:07,958 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (145) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:23:07,976 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (145) Working directory for job is: /galaxy/server/database/jobs_directory/000/145 +galaxy.jobs.runners DEBUG 2024-12-30 01:23:07,986 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [145] queued (45.375 ms) +galaxy.jobs.handler INFO 2024-12-30 01:23:07,990 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (145) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:23:07,995 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 145 +galaxy.jobs DEBUG 2024-12-30 01:23:08,157 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [145] prepared (138.413 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:23:08,157 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:23:08,158 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.18: mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:1bd8542a8a0b42e0981337910954371d0230828e +galaxy.tool_util.deps.containers INFO 2024-12-30 01:23:08,385 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:1bd8542a8a0b42e0981337910954371d0230828e-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:23:08,409 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/145/tool_script.sh] for tool command [set -o | grep -q pipefail && set -o pipefail; ln -s '/galaxy/server/database/objects/d/6/2/dataset_d62b40cf-3712-410b-af8d-e5caf23bfdf0.dat' 'localref.fa' && bwa index 'localref.fa' && bwa aln -t "${GALAXY_SLOTS:-1}" 'localref.fa' '/galaxy/server/database/objects/b/9/b/dataset_b9b211ff-d0df-4c46-b9be-0aa461ad4daf.dat' > first.sai && bwa samse 'localref.fa' first.sai '/galaxy/server/database/objects/b/9/b/dataset_b9b211ff-d0df-4c46-b9be-0aa461ad4daf.dat' | samtools sort -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O bam -o '/galaxy/server/database/objects/d/1/6/dataset_d16a2d20-8081-493c-94f4-3d02bc894176.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:23:08,421 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (145) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/145/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/145/galaxy_145.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:23:08,434 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:23:08,434 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.18: mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:1bd8542a8a0b42e0981337910954371d0230828e +galaxy.tool_util.deps.containers INFO 2024-12-30 01:23:08,452 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:1bd8542a8a0b42e0981337910954371d0230828e-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 01:23:20,768 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 145: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:23:25,804 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 145 finished +galaxy.model.metadata DEBUG 2024-12-30 01:23:25,857 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 145 +galaxy.jobs INFO 2024-12-30 01:23:25,934 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 145 in /galaxy/server/database/jobs_directory/000/145 +galaxy.jobs DEBUG 2024-12-30 01:23:25,991 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 145 executed (159.418 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:23:27,419 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 146, 147 +tpv.core.entities DEBUG 2024-12-30 01:23:27,458 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:23:27,459 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (146) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:23:27,466 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (146) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:23:27,485 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (146) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:23:27,505 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (146) Working directory for job is: /galaxy/server/database/jobs_directory/000/146 +galaxy.jobs.runners DEBUG 2024-12-30 01:23:27,512 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [146] queued (45.943 ms) +galaxy.jobs.handler INFO 2024-12-30 01:23:27,516 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (146) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:23:27,521 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 146 +tpv.core.entities DEBUG 2024-12-30 01:23:27,534 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:23:27,534 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (147) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:23:27,542 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (147) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:23:27,562 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (147) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:23:27,593 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (147) Working directory for job is: /galaxy/server/database/jobs_directory/000/147 +galaxy.jobs.runners DEBUG 2024-12-30 01:23:27,600 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [147] queued (57.940 ms) +galaxy.jobs.handler INFO 2024-12-30 01:23:27,606 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (147) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:23:27,609 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 147 +galaxy.jobs DEBUG 2024-12-30 01:23:27,660 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [146] prepared (115.518 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:23:27,685 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/146/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/146/registry.xml' '/galaxy/server/database/jobs_directory/000/146/upload_params.json' '146:/galaxy/server/database/objects/b/8/b/dataset_b8b99bf5-7071-4c84-b5f4-3fa44463e901_files:/galaxy/server/database/objects/b/8/b/dataset_b8b99bf5-7071-4c84-b5f4-3fa44463e901.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:23:27,697 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (146) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/146/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/146/galaxy_146.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-12-30 01:23:27,723 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [147] prepared (92.381 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:23:27,749 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/147/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/147/registry.xml' '/galaxy/server/database/jobs_directory/000/147/upload_params.json' '147:/galaxy/server/database/objects/e/2/9/dataset_e29437f7-8a81-4bac-a8fa-dbd9d6a70c43_files:/galaxy/server/database/objects/e/2/9/dataset_e29437f7-8a81-4bac-a8fa-dbd9d6a70c43.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:23:27,764 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (147) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/147/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/147/galaxy_147.ec; sh -c "exit $return_code" +galaxy.jobs.handler DEBUG 2024-12-30 01:23:28,609 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 148 +tpv.core.entities DEBUG 2024-12-30 01:23:28,642 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:23:28,642 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (148) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:23:28,647 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (148) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:23:28,662 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (148) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:23:28,687 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (148) Working directory for job is: /galaxy/server/database/jobs_directory/000/148 +galaxy.jobs.runners DEBUG 2024-12-30 01:23:28,695 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [148] queued (48.184 ms) +galaxy.jobs.handler INFO 2024-12-30 01:23:28,700 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (148) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:23:28,706 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 148 +galaxy.jobs DEBUG 2024-12-30 01:23:28,816 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [148] prepared (90.409 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:23:28,837 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/148/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/148/registry.xml' '/galaxy/server/database/jobs_directory/000/148/upload_params.json' '148:/galaxy/server/database/objects/e/7/a/dataset_e7aa1d48-72f5-469b-987a-cee73ae4ed9e_files:/galaxy/server/database/objects/e/7/a/dataset_e7aa1d48-72f5-469b-987a-cee73ae4ed9e.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:23:28,852 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (148) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/148/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/148/galaxy_148.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:23:37,300 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 146: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:23:37,331 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 147: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:23:37,358 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 148: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:23:44,873 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 146 finished +galaxy.model.metadata DEBUG 2024-12-30 01:23:44,971 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 146 +galaxy.jobs INFO 2024-12-30 01:23:45,013 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 146 in /galaxy/server/database/jobs_directory/000/146 +galaxy.jobs.runners DEBUG 2024-12-30 01:23:45,040 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 147 finished +galaxy.jobs.runners DEBUG 2024-12-30 01:23:45,092 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 148 finished +galaxy.model.metadata DEBUG 2024-12-30 01:23:45,111 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 147 +galaxy.jobs DEBUG 2024-12-30 01:23:45,122 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 146 executed (218.830 ms) +galaxy.jobs INFO 2024-12-30 01:23:45,174 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 147 in /galaxy/server/database/jobs_directory/000/147 +galaxy.model.metadata DEBUG 2024-12-30 01:23:45,179 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 148 +galaxy.jobs INFO 2024-12-30 01:23:45,221 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 148 in /galaxy/server/database/jobs_directory/000/148 +galaxy.jobs DEBUG 2024-12-30 01:23:45,241 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 147 executed (170.568 ms) +galaxy.jobs DEBUG 2024-12-30 01:23:45,279 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 148 executed (151.944 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:23:46,471 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 149 +tpv.core.entities DEBUG 2024-12-30 01:23:46,519 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/.*, abstract=False, cores=8, mem=20, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:23:46,520 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (149) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:23:46,525 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (149) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:23:46,543 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (149) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:23:46,561 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (149) Working directory for job is: /galaxy/server/database/jobs_directory/000/149 +galaxy.jobs.runners DEBUG 2024-12-30 01:23:46,571 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [149] queued (46.256 ms) +galaxy.jobs.handler INFO 2024-12-30 01:23:46,575 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (149) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:23:46,579 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 149 +galaxy.jobs DEBUG 2024-12-30 01:23:46,663 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [149] prepared (64.053 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:23:46,664 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:23:46,664 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.18: mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:1bd8542a8a0b42e0981337910954371d0230828e +galaxy.tool_util.deps.containers INFO 2024-12-30 01:23:46,684 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:1bd8542a8a0b42e0981337910954371d0230828e-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:23:46,706 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/149/tool_script.sh] for tool command [set -o | grep -q pipefail && set -o pipefail; ln -s '/galaxy/server/database/objects/b/8/b/dataset_b8b99bf5-7071-4c84-b5f4-3fa44463e901.dat' 'localref.fa' && bwa index 'localref.fa' && bwa aln -t "${GALAXY_SLOTS:-1}" 'localref.fa' '/galaxy/server/database/objects/e/2/9/dataset_e29437f7-8a81-4bac-a8fa-dbd9d6a70c43.dat' > first.sai && bwa aln -t "${GALAXY_SLOTS:-1}" 'localref.fa' '/galaxy/server/database/objects/e/7/a/dataset_e7aa1d48-72f5-469b-987a-cee73ae4ed9e.dat' > second.sai && bwa sampe 'localref.fa' first.sai second.sai '/galaxy/server/database/objects/e/2/9/dataset_e29437f7-8a81-4bac-a8fa-dbd9d6a70c43.dat' '/galaxy/server/database/objects/e/7/a/dataset_e7aa1d48-72f5-469b-987a-cee73ae4ed9e.dat' | samtools sort -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O bam -o '/galaxy/server/database/objects/2/6/9/dataset_2690073e-63ff-4898-b73f-fa0f96430ca6.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:23:46,716 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (149) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/149/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/149/galaxy_149.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:23:46,728 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:23:46,728 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.18: mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:1bd8542a8a0b42e0981337910954371d0230828e +galaxy.tool_util.deps.containers INFO 2024-12-30 01:23:46,749 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:1bd8542a8a0b42e0981337910954371d0230828e-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 01:23:52,542 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 149: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:23:57,462 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 149 finished +galaxy.model.metadata DEBUG 2024-12-30 01:23:57,532 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 149 +galaxy.jobs INFO 2024-12-30 01:23:57,611 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 149 in /galaxy/server/database/jobs_directory/000/149 +galaxy.jobs DEBUG 2024-12-30 01:23:57,670 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 149 executed (173.967 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:23:58,846 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 150 +tpv.core.entities DEBUG 2024-12-30 01:23:58,882 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:23:58,882 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (150) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:23:58,887 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (150) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:23:58,902 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (150) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:23:58,921 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (150) Working directory for job is: /galaxy/server/database/jobs_directory/000/150 +galaxy.jobs.runners DEBUG 2024-12-30 01:23:58,929 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [150] queued (42.312 ms) +galaxy.jobs.handler INFO 2024-12-30 01:23:58,933 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (150) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:23:58,939 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 150 +galaxy.jobs DEBUG 2024-12-30 01:23:59,043 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [150] prepared (84.323 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:23:59,064 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/150/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/150/registry.xml' '/galaxy/server/database/jobs_directory/000/150/upload_params.json' '150:/galaxy/server/database/objects/9/2/e/dataset_92e7072c-bd26-4720-9dd9-24b19f4d0fd5_files:/galaxy/server/database/objects/9/2/e/dataset_92e7072c-bd26-4720-9dd9-24b19f4d0fd5.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:23:59,078 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (150) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/150/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/150/galaxy_150.ec; sh -c "exit $return_code" +galaxy.jobs.handler DEBUG 2024-12-30 01:23:59,936 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 152, 151 +tpv.core.entities DEBUG 2024-12-30 01:23:59,971 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:23:59,972 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (151) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:23:59,977 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (151) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:23:59,996 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (151) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:24:00,015 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (151) Working directory for job is: /galaxy/server/database/jobs_directory/000/151 +galaxy.jobs.runners DEBUG 2024-12-30 01:24:00,022 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [151] queued (44.620 ms) +galaxy.jobs.handler INFO 2024-12-30 01:24:00,025 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (151) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:24:00,030 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 151 +tpv.core.entities DEBUG 2024-12-30 01:24:00,040 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:24:00,041 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (152) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:24:00,047 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (152) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:24:00,065 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (152) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:24:00,095 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (152) Working directory for job is: /galaxy/server/database/jobs_directory/000/152 +galaxy.jobs.runners DEBUG 2024-12-30 01:24:00,105 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [152] queued (57.720 ms) +galaxy.jobs.handler INFO 2024-12-30 01:24:00,109 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (152) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:24:00,116 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 152 +galaxy.jobs DEBUG 2024-12-30 01:24:00,178 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [151] prepared (122.720 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:24:00,211 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/151/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/151/registry.xml' '/galaxy/server/database/jobs_directory/000/151/upload_params.json' '151:/galaxy/server/database/objects/2/6/4/dataset_264c0006-1915-42c6-b660-7092a32ed281_files:/galaxy/server/database/objects/2/6/4/dataset_264c0006-1915-42c6-b660-7092a32ed281.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:24:00,228 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (151) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/151/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/151/galaxy_151.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-12-30 01:24:00,262 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [152] prepared (118.993 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:24:00,287 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/152/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/152/registry.xml' '/galaxy/server/database/jobs_directory/000/152/upload_params.json' '152:/galaxy/server/database/objects/1/5/9/dataset_1596e2c3-89b8-4066-9f36-474713b9d5e5_files:/galaxy/server/database/objects/1/5/9/dataset_1596e2c3-89b8-4066-9f36-474713b9d5e5.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:24:00,303 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (152) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/152/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/152/galaxy_152.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes ERROR 2024-12-30 01:24:06,934 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Could not clean up k8s batch job. Ignoring... +Traceback (most recent call last): + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/http.py", line 437, in raise_for_status + resp.raise_for_status() + File "/galaxy/server/.venv/lib/python3.10/site-packages/requests/models.py", line 1021, in raise_for_status + raise HTTPError(http_error_msg, response=self) +requests.exceptions.HTTPError: 409 Client Error: Conflict for url: https://10.107.32.1:443/apis/batch/v1/namespaces/prod-24-12-30-00-37-1/jobs/gxy-bw9r7 + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 817, in _handle_job_failure + self.__cleanup_k8s_job(job) + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 824, in __cleanup_k8s_job + delete_job(job, k8s_cleanup_job) + File "/galaxy/server/lib/galaxy/jobs/runners/util/pykube_util.py", line 107, in delete_job + job.scale(replicas=0) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/mixins.py", line 30, in scale + self.update() + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 165, in update + self.patch(self.obj, subresource=subresource) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 157, in patch + self.api.raise_for_status(r) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/http.py", line 444, in raise_for_status + raise HTTPError(resp.status_code, payload["message"]) +pykube.exceptions.HTTPError: Operation cannot be fulfilled on jobs.batch "gxy-bw9r7": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:24:06,982 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (150/gxy-bw9r7) Terminated at user's request +galaxy.jobs.runners DEBUG 2024-12-30 01:24:08,132 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 151: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.handler DEBUG 2024-12-30 01:24:08,281 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 153, 154 +tpv.core.entities DEBUG 2024-12-30 01:24:08,323 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:24:08,323 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (153) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:24:08,329 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (153) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:24:08,345 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (153) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:24:08,367 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (153) Working directory for job is: /galaxy/server/database/jobs_directory/000/153 +galaxy.jobs.runners DEBUG 2024-12-30 01:24:08,375 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [153] queued (45.927 ms) +galaxy.jobs.handler INFO 2024-12-30 01:24:08,380 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (153) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:24:08,387 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 153 +tpv.core.entities DEBUG 2024-12-30 01:24:08,400 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:24:08,400 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (154) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:24:08,406 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (154) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:24:08,423 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (154) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:24:08,451 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (154) Working directory for job is: /galaxy/server/database/jobs_directory/000/154 +galaxy.jobs.runners DEBUG 2024-12-30 01:24:08,458 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [154] queued (51.461 ms) +galaxy.jobs.handler INFO 2024-12-30 01:24:08,462 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (154) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:24:08,469 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 154 +galaxy.jobs DEBUG 2024-12-30 01:24:08,513 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [153] prepared (101.111 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:24:08,543 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/153/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/153/registry.xml' '/galaxy/server/database/jobs_directory/000/153/upload_params.json' '153:/galaxy/server/database/objects/8/6/a/dataset_86a852c0-322b-4204-ad4e-e305ea2cc15f_files:/galaxy/server/database/objects/8/6/a/dataset_86a852c0-322b-4204-ad4e-e305ea2cc15f.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:24:08,570 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (153) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/153/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/153/galaxy_153.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-12-30 01:24:08,593 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [154] prepared (98.111 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:24:08,617 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/154/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/154/registry.xml' '/galaxy/server/database/jobs_directory/000/154/upload_params.json' '154:/galaxy/server/database/objects/f/5/4/dataset_f544c714-2316-4665-af54-671b2dc53035_files:/galaxy/server/database/objects/f/5/4/dataset_f544c714-2316-4665-af54-671b2dc53035.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:24:08,631 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (154) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/154/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/154/galaxy_154.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:24:09,320 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 152: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:24:13,391 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 151 finished +galaxy.model.metadata DEBUG 2024-12-30 01:24:13,444 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 151 +galaxy.jobs INFO 2024-12-30 01:24:13,482 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 151 in /galaxy/server/database/jobs_directory/000/151 +galaxy.jobs DEBUG 2024-12-30 01:24:13,546 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 151 executed (128.970 ms) +galaxy.jobs.runners DEBUG 2024-12-30 01:24:14,487 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 152 finished +galaxy.model.metadata DEBUG 2024-12-30 01:24:14,543 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 152 +galaxy.jobs INFO 2024-12-30 01:24:14,575 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 152 in /galaxy/server/database/jobs_directory/000/152 +galaxy.jobs DEBUG 2024-12-30 01:24:14,642 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 152 executed (128.928 ms) +galaxy.jobs.runners DEBUG 2024-12-30 01:24:17,850 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 154: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:24:17,864 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 153: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:24:22,957 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 154 finished +galaxy.jobs.runners DEBUG 2024-12-30 01:24:22,995 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 153 finished +galaxy.model.metadata DEBUG 2024-12-30 01:24:23,029 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 154 +galaxy.model.metadata DEBUG 2024-12-30 01:24:23,066 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 153 +galaxy.jobs INFO 2024-12-30 01:24:23,123 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 153 in /galaxy/server/database/jobs_directory/000/153 +galaxy.jobs INFO 2024-12-30 01:24:23,126 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 154 in /galaxy/server/database/jobs_directory/000/154 +galaxy.jobs DEBUG 2024-12-30 01:24:23,185 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 153 executed (158.387 ms) +galaxy.jobs DEBUG 2024-12-30 01:24:23,192 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 154 executed (204.237 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:24:23,948 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 155 +tpv.core.entities DEBUG 2024-12-30 01:24:23,992 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/.*, abstract=False, cores=8, mem=20, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:24:23,993 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (155) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:24:23,998 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (155) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:24:24,014 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (155) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:24:24,033 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (155) Working directory for job is: /galaxy/server/database/jobs_directory/000/155 +galaxy.jobs.runners DEBUG 2024-12-30 01:24:24,042 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [155] queued (44.187 ms) +galaxy.jobs.handler INFO 2024-12-30 01:24:24,046 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (155) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:24:24,051 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 155 +galaxy.jobs DEBUG 2024-12-30 01:24:24,138 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [155] prepared (66.031 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:24:24,139 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:24:24,139 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.18: mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:1bd8542a8a0b42e0981337910954371d0230828e +galaxy.tool_util.deps.containers INFO 2024-12-30 01:24:24,162 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:1bd8542a8a0b42e0981337910954371d0230828e-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:24:24,185 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/155/tool_script.sh] for tool command [set -o | grep -q pipefail && set -o pipefail; ln -s '/galaxy/server/database/objects/8/6/a/dataset_86a852c0-322b-4204-ad4e-e305ea2cc15f.dat' 'localref.fa' && bwa index 'localref.fa' && bwa aln -t "${GALAXY_SLOTS:-1}" -b -1 'localref.fa' '/galaxy/server/database/objects/f/5/4/dataset_f544c714-2316-4665-af54-671b2dc53035.dat' > first.sai && bwa aln -t "${GALAXY_SLOTS:-1}" -b -2 'localref.fa' '/galaxy/server/database/objects/f/5/4/dataset_f544c714-2316-4665-af54-671b2dc53035.dat' > second.sai && bwa sampe 'localref.fa' first.sai second.sai '/galaxy/server/database/objects/f/5/4/dataset_f544c714-2316-4665-af54-671b2dc53035.dat' '/galaxy/server/database/objects/f/5/4/dataset_f544c714-2316-4665-af54-671b2dc53035.dat' | samtools sort -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O bam -o '/galaxy/server/database/objects/f/d/e/dataset_fdea253a-657d-4d0b-a14c-b948ecf98859.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:24:24,198 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (155) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/155/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/155/galaxy_155.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:24:24,212 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:24:24,212 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.18: mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:1bd8542a8a0b42e0981337910954371d0230828e +galaxy.tool_util.deps.containers INFO 2024-12-30 01:24:24,232 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:1bd8542a8a0b42e0981337910954371d0230828e-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 01:24:30,012 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 155: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:24:34,963 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 155 finished +galaxy.model.metadata DEBUG 2024-12-30 01:24:35,031 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 155 +galaxy.jobs INFO 2024-12-30 01:24:35,113 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 155 in /galaxy/server/database/jobs_directory/000/155 +galaxy.jobs DEBUG 2024-12-30 01:24:35,169 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 155 executed (175.470 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:24:36,324 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 157, 156 +tpv.core.entities DEBUG 2024-12-30 01:24:36,366 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:24:36,367 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (156) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:24:36,373 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (156) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:24:36,392 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (156) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:24:36,413 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (156) Working directory for job is: /galaxy/server/database/jobs_directory/000/156 +galaxy.jobs.runners DEBUG 2024-12-30 01:24:36,421 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [156] queued (47.863 ms) +galaxy.jobs.handler INFO 2024-12-30 01:24:36,427 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (156) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:24:36,432 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 156 +tpv.core.entities DEBUG 2024-12-30 01:24:36,445 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:24:36,446 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (157) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:24:36,453 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (157) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:24:36,471 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (157) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:24:36,498 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (157) Working directory for job is: /galaxy/server/database/jobs_directory/000/157 +galaxy.jobs.runners DEBUG 2024-12-30 01:24:36,506 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [157] queued (52.634 ms) +galaxy.jobs.handler INFO 2024-12-30 01:24:36,512 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (157) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:24:36,518 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 157 +galaxy.jobs DEBUG 2024-12-30 01:24:36,562 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [156] prepared (106.425 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:24:36,594 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/156/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/156/registry.xml' '/galaxy/server/database/jobs_directory/000/156/upload_params.json' '156:/galaxy/server/database/objects/a/f/5/dataset_af532a71-8f4f-4540-903d-9f85c201a615_files:/galaxy/server/database/objects/a/f/5/dataset_af532a71-8f4f-4540-903d-9f85c201a615.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:24:36,608 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (156) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/156/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/156/galaxy_156.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-12-30 01:24:36,646 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [157] prepared (103.144 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:24:36,669 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/157/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/157/registry.xml' '/galaxy/server/database/jobs_directory/000/157/upload_params.json' '157:/galaxy/server/database/objects/6/2/2/dataset_6220af1a-6be9-4252-9598-5c85c3625797_files:/galaxy/server/database/objects/6/2/2/dataset_6220af1a-6be9-4252-9598-5c85c3625797.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:24:36,685 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (157) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/157/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/157/galaxy_157.ec; sh -c "exit $return_code" +galaxy.jobs.handler DEBUG 2024-12-30 01:24:37,514 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 158 +tpv.core.entities DEBUG 2024-12-30 01:24:37,560 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:24:37,560 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (158) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:24:37,566 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (158) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:24:37,585 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (158) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:24:37,604 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (158) Working directory for job is: /galaxy/server/database/jobs_directory/000/158 +galaxy.jobs.runners DEBUG 2024-12-30 01:24:37,611 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [158] queued (44.283 ms) +galaxy.jobs.handler INFO 2024-12-30 01:24:37,614 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (158) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:24:37,619 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 158 +galaxy.jobs DEBUG 2024-12-30 01:24:37,739 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [158] prepared (97.648 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:24:37,761 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/158/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/158/registry.xml' '/galaxy/server/database/jobs_directory/000/158/upload_params.json' '158:/galaxy/server/database/objects/c/b/f/dataset_cbfa711d-b371-43d3-9dc1-3d279ecde592_files:/galaxy/server/database/objects/c/b/f/dataset_cbfa711d-b371-43d3-9dc1-3d279ecde592.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:24:37,777 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (158) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/158/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/158/galaxy_158.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:24:45,701 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 156: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:24:45,750 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 157: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:24:45,773 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 158: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:24:53,458 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 158 finished +galaxy.model.metadata DEBUG 2024-12-30 01:24:53,549 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 158 +galaxy.jobs.runners DEBUG 2024-12-30 01:24:53,550 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 156 finished +galaxy.jobs.runners DEBUG 2024-12-30 01:24:53,554 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 157 finished +galaxy.jobs INFO 2024-12-30 01:24:53,613 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 158 in /galaxy/server/database/jobs_directory/000/158 +galaxy.model.metadata DEBUG 2024-12-30 01:24:53,650 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 157 +galaxy.model.metadata DEBUG 2024-12-30 01:24:53,650 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 156 +galaxy.jobs INFO 2024-12-30 01:24:53,708 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 157 in /galaxy/server/database/jobs_directory/000/157 +galaxy.jobs INFO 2024-12-30 01:24:53,715 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 156 in /galaxy/server/database/jobs_directory/000/156 +galaxy.jobs DEBUG 2024-12-30 01:24:53,724 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 158 executed (234.958 ms) +galaxy.jobs DEBUG 2024-12-30 01:24:53,791 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 157 executed (190.439 ms) +galaxy.jobs DEBUG 2024-12-30 01:24:53,793 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 156 executed (195.842 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:24:55,178 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 159 +tpv.core.entities DEBUG 2024-12-30 01:24:55,226 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/.*, abstract=False, cores=8, mem=20, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:24:55,227 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (159) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:24:55,233 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (159) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:24:55,252 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (159) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:24:55,275 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (159) Working directory for job is: /galaxy/server/database/jobs_directory/000/159 +galaxy.jobs.runners DEBUG 2024-12-30 01:24:55,285 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [159] queued (51.756 ms) +galaxy.jobs.handler INFO 2024-12-30 01:24:55,290 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (159) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:24:55,295 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 159 +galaxy.jobs DEBUG 2024-12-30 01:24:55,391 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [159] prepared (75.635 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:24:55,392 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:24:55,392 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.18: mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:1bd8542a8a0b42e0981337910954371d0230828e +galaxy.tool_util.deps.containers INFO 2024-12-30 01:24:55,413 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:1bd8542a8a0b42e0981337910954371d0230828e-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:24:55,437 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/159/tool_script.sh] for tool command [set -o | grep -q pipefail && set -o pipefail; ln -s '/galaxy/server/database/objects/a/f/5/dataset_af532a71-8f4f-4540-903d-9f85c201a615.dat' 'localref.fa' && bwa index 'localref.fa' && bwa aln -t "${GALAXY_SLOTS:-1}" 'localref.fa' '/galaxy/server/database/objects/6/2/2/dataset_6220af1a-6be9-4252-9598-5c85c3625797.dat' > first.sai && bwa aln -t "${GALAXY_SLOTS:-1}" 'localref.fa' '/galaxy/server/database/objects/c/b/f/dataset_cbfa711d-b371-43d3-9dc1-3d279ecde592.dat' > second.sai && bwa sampe -r '@RG\tID:rg1\tPL:CAPILLARY' 'localref.fa' first.sai second.sai '/galaxy/server/database/objects/6/2/2/dataset_6220af1a-6be9-4252-9598-5c85c3625797.dat' '/galaxy/server/database/objects/c/b/f/dataset_cbfa711d-b371-43d3-9dc1-3d279ecde592.dat' | samtools sort -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O bam -o '/galaxy/server/database/objects/7/a/8/dataset_7a8f6c70-5e53-4249-938b-34405b3fd34a.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:24:55,453 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (159) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/159/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/159/galaxy_159.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:24:55,467 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:24:55,467 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.18: mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:1bd8542a8a0b42e0981337910954371d0230828e +galaxy.tool_util.deps.containers INFO 2024-12-30 01:24:55,485 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:1bd8542a8a0b42e0981337910954371d0230828e-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 01:25:00,906 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 159: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:25:06,141 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 159 finished +galaxy.model.metadata DEBUG 2024-12-30 01:25:06,207 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 159 +galaxy.jobs INFO 2024-12-30 01:25:06,298 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 159 in /galaxy/server/database/jobs_directory/000/159 +galaxy.jobs DEBUG 2024-12-30 01:25:06,369 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 159 executed (195.573 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:25:09,631 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 160 +tpv.core.entities DEBUG 2024-12-30 01:25:09,674 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:25:09,674 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (160) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:25:09,681 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (160) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:25:09,700 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (160) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:25:09,721 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (160) Working directory for job is: /galaxy/server/database/jobs_directory/000/160 +galaxy.jobs.runners DEBUG 2024-12-30 01:25:09,730 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [160] queued (48.983 ms) +galaxy.jobs.handler INFO 2024-12-30 01:25:09,734 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (160) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:25:09,737 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 160 +galaxy.jobs DEBUG 2024-12-30 01:25:09,853 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [160] prepared (97.670 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:25:09,879 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/160/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/160/registry.xml' '/galaxy/server/database/jobs_directory/000/160/upload_params.json' '160:/galaxy/server/database/objects/2/f/b/dataset_2fb9db02-dcb0-4e08-b0f9-1c6d905ef642_files:/galaxy/server/database/objects/2/f/b/dataset_2fb9db02-dcb0-4e08-b0f9-1c6d905ef642.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:25:09,893 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (160) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/160/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/160/galaxy_160.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:25:18,060 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 160: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:25:22,990 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 160 finished +galaxy.model.metadata DEBUG 2024-12-30 01:25:23,069 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 160 +galaxy.jobs INFO 2024-12-30 01:25:23,110 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 160 in /galaxy/server/database/jobs_directory/000/160 +galaxy.jobs DEBUG 2024-12-30 01:25:23,171 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 160 executed (153.203 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:25:24,068 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 161 +tpv.core.entities DEBUG 2024-12-30 01:25:24,110 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/.*, abstract=False, cores=1, mem=4, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:25:24,111 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (161) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:25:24,117 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (161) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:25:24,136 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (161) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:25:24,155 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (161) Working directory for job is: /galaxy/server/database/jobs_directory/000/161 +galaxy.jobs.runners DEBUG 2024-12-30 01:25:24,164 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [161] queued (46.509 ms) +galaxy.jobs.handler INFO 2024-12-30 01:25:24,169 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (161) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:25:24,171 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 161 +galaxy.jobs DEBUG 2024-12-30 01:25:24,276 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [161] prepared (84.584 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:25:24,277 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:25:24,277 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.58.1+galaxy0: mulled-v2-3d571fed05a48eb8af17dbc6c8ed632143702ac1:c5763bb5f3402fc75fc6c0fa6c38d545d78e0e67 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:25:24,491 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-3d571fed05a48eb8af17dbc6c8ed632143702ac1:c5763bb5f3402fc75fc6c0fa6c38d545d78e0e67-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:25:24,516 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/161/tool_script.sh] for tool command [echo $(R --version | grep version | grep -v GNU)", limma version" $(R --vanilla --slave -e "library(limma); cat(sessionInfo()\$otherPkgs\$limma\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", edgeR version" $(R --vanilla --slave -e "library(edgeR); cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", statmod version" $(R --vanilla --slave -e "library(statmod); cat(sessionInfo()\$otherPkgs\$statmod\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", scales version" $(R --vanilla --slave -e "library(scales); cat(sessionInfo()\$otherPkgs\$scales\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", rjson version" $(R --vanilla --slave -e "library(rjson); cat(sessionInfo()\$otherPkgs\$rjson\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", getopt version" $(R --vanilla --slave -e "library(getopt); cat(sessionInfo()\$otherPkgs\$getopt\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", gplots version" $(R --vanilla --slave -e "library(gplots); cat(sessionInfo()\$otherPkgs\$gplots\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", Glimma version" $(R --vanilla --slave -e "library(Glimma); cat(sessionInfo()\$otherPkgs\$Glimma\$Version)" 2> /dev/null | grep -v -i "WARNING: ") > /galaxy/server/database/jobs_directory/000/161/outputs/COMMAND_VERSION 2>&1; +Rscript '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/119b069fc845/limma_voom/limma_voom.R' -R '/galaxy/server/database/objects/7/f/7/dataset_7f715ea6-e455-4a10-b65e-bcf263b52f36.dat' -o '/galaxy/server/database/objects/7/f/7/dataset_7f715ea6-e455-4a10-b65e-bcf263b52f36_files' -m '/galaxy/server/database/objects/2/f/b/dataset_2fb9db02-dcb0-4e08-b0f9-1c6d905ef642.dat' -i 'Genotype::Mut,Mut,Mut,WT,WT,WT' -D 'Mut-WT,WT-Mut' -P i -l '0.0' -p '0.05' -d 'BH' -G '6' -n 'TMM' -b && mkdir ./output_dir && cp '/galaxy/server/database/objects/7/f/7/dataset_7f715ea6-e455-4a10-b65e-bcf263b52f36_files'/*tsv output_dir/ && cp -r ./glimma* '/galaxy/server/database/objects/7/f/7/dataset_7f715ea6-e455-4a10-b65e-bcf263b52f36_files'] +galaxy.jobs.runners DEBUG 2024-12-30 01:25:24,528 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (161) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/161/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/161/galaxy_161.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:25:24,542 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:25:24,542 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.58.1+galaxy0: mulled-v2-3d571fed05a48eb8af17dbc6c8ed632143702ac1:c5763bb5f3402fc75fc6c0fa6c38d545d78e0e67 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:25:24,561 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-3d571fed05a48eb8af17dbc6c8ed632143702ac1:c5763bb5f3402fc75fc6c0fa6c38d545d78e0e67-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 01:26:22,159 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 161: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:26:27,077 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 161 finished +galaxy.model.store.discover DEBUG 2024-12-30 01:26:27,140 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (161) Created dynamic collection dataset for path [/galaxy/server/database/jobs_directory/000/161/working/output_dir/limma-voom_Mut-WT.tsv] with element identifier [limma-voom_Mut-WT] for output [outTables] (5.749 ms) +galaxy.model.store.discover DEBUG 2024-12-30 01:26:27,141 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (161) Created dynamic collection dataset for path [/galaxy/server/database/jobs_directory/000/161/working/output_dir/limma-voom_WT-Mut.tsv] with element identifier [limma-voom_WT-Mut] for output [outTables] (0.693 ms) +galaxy.model.store.discover DEBUG 2024-12-30 01:26:27,168 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (161) Add dynamic collection datasets to history for output [outTables] (26.973 ms) +galaxy.model.metadata DEBUG 2024-12-30 01:26:27,211 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 161 +galaxy.jobs INFO 2024-12-30 01:26:27,277 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 161 in /galaxy/server/database/jobs_directory/000/161 +galaxy.objectstore CRITICAL 2024-12-30 01:26:27,330 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] None delete error [Errno 13] Permission denied: 'MDS-Plot.html' +galaxy.jobs DEBUG 2024-12-30 01:26:27,330 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 161 executed (223.459 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:26:28,631 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 162 +tpv.core.entities DEBUG 2024-12-30 01:26:28,667 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:26:28,668 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (162) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:26:28,673 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (162) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:26:28,692 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (162) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:26:28,709 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (162) Working directory for job is: /galaxy/server/database/jobs_directory/000/162 +galaxy.jobs.runners DEBUG 2024-12-30 01:26:28,717 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [162] queued (43.738 ms) +galaxy.jobs.handler INFO 2024-12-30 01:26:28,721 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (162) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:26:28,725 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 162 +galaxy.jobs DEBUG 2024-12-30 01:26:28,839 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [162] prepared (94.477 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:26:28,863 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/162/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/162/registry.xml' '/galaxy/server/database/jobs_directory/000/162/upload_params.json' '164:/galaxy/server/database/objects/2/c/d/dataset_2cddd2c8-3f23-4b52-a70e-5d3ec3cf6ed9_files:/galaxy/server/database/objects/2/c/d/dataset_2cddd2c8-3f23-4b52-a70e-5d3ec3cf6ed9.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:26:28,877 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (162) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/162/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/162/galaxy_162.ec; sh -c "exit $return_code" +galaxy.jobs.handler DEBUG 2024-12-30 01:26:29,724 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 163 +tpv.core.entities DEBUG 2024-12-30 01:26:29,756 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:26:29,757 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (163) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:26:29,761 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (163) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:26:29,776 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (163) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:26:29,793 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (163) Working directory for job is: /galaxy/server/database/jobs_directory/000/163 +galaxy.jobs.runners DEBUG 2024-12-30 01:26:29,801 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [163] queued (40.095 ms) +galaxy.jobs.handler INFO 2024-12-30 01:26:29,806 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (163) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:26:29,810 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 163 +galaxy.jobs DEBUG 2024-12-30 01:26:29,935 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [163] prepared (103.099 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:26:29,960 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/163/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/163/registry.xml' '/galaxy/server/database/jobs_directory/000/163/upload_params.json' '165:/galaxy/server/database/objects/b/d/c/dataset_bdc101e8-15af-4c90-825c-24da0f07ce44_files:/galaxy/server/database/objects/b/d/c/dataset_bdc101e8-15af-4c90-825c-24da0f07ce44.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:26:29,974 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (163) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/163/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/163/galaxy_163.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:26:37,588 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 162: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:26:38,765 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 163: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:26:42,746 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 162 finished +galaxy.model.metadata DEBUG 2024-12-30 01:26:42,822 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 164 +galaxy.jobs INFO 2024-12-30 01:26:42,876 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 162 in /galaxy/server/database/jobs_directory/000/162 +galaxy.jobs DEBUG 2024-12-30 01:26:42,957 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 162 executed (176.156 ms) +galaxy.jobs.runners DEBUG 2024-12-30 01:26:43,828 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 163 finished +galaxy.model.metadata DEBUG 2024-12-30 01:26:43,882 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 165 +galaxy.jobs INFO 2024-12-30 01:26:43,918 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 163 in /galaxy/server/database/jobs_directory/000/163 +galaxy.jobs DEBUG 2024-12-30 01:26:43,978 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 163 executed (122.663 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:26:45,166 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 164 +tpv.core.entities DEBUG 2024-12-30 01:26:45,211 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/.*, abstract=False, cores=1, mem=4, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:26:45,212 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (164) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:26:45,218 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (164) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:26:45,236 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (164) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:26:45,255 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (164) Working directory for job is: /galaxy/server/database/jobs_directory/000/164 +galaxy.jobs.runners DEBUG 2024-12-30 01:26:45,263 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [164] queued (43.858 ms) +galaxy.jobs.handler INFO 2024-12-30 01:26:45,266 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (164) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:26:45,271 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 164 +galaxy.jobs DEBUG 2024-12-30 01:26:45,370 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [164] prepared (76.689 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:26:45,370 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:26:45,371 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.58.1+galaxy0: mulled-v2-3d571fed05a48eb8af17dbc6c8ed632143702ac1:c5763bb5f3402fc75fc6c0fa6c38d545d78e0e67 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:26:45,565 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-3d571fed05a48eb8af17dbc6c8ed632143702ac1:c5763bb5f3402fc75fc6c0fa6c38d545d78e0e67-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:26:45,590 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/164/tool_script.sh] for tool command [echo $(R --version | grep version | grep -v GNU)", limma version" $(R --vanilla --slave -e "library(limma); cat(sessionInfo()\$otherPkgs\$limma\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", edgeR version" $(R --vanilla --slave -e "library(edgeR); cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", statmod version" $(R --vanilla --slave -e "library(statmod); cat(sessionInfo()\$otherPkgs\$statmod\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", scales version" $(R --vanilla --slave -e "library(scales); cat(sessionInfo()\$otherPkgs\$scales\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", rjson version" $(R --vanilla --slave -e "library(rjson); cat(sessionInfo()\$otherPkgs\$rjson\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", getopt version" $(R --vanilla --slave -e "library(getopt); cat(sessionInfo()\$otherPkgs\$getopt\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", gplots version" $(R --vanilla --slave -e "library(gplots); cat(sessionInfo()\$otherPkgs\$gplots\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", Glimma version" $(R --vanilla --slave -e "library(Glimma); cat(sessionInfo()\$otherPkgs\$Glimma\$Version)" 2> /dev/null | grep -v -i "WARNING: ") > /galaxy/server/database/jobs_directory/000/164/outputs/COMMAND_VERSION 2>&1; +Rscript '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/119b069fc845/limma_voom/limma_voom.R' -R '/galaxy/server/database/objects/8/e/5/dataset_8e5dfc77-e362-4f92-8aa0-e585585c6541.dat' -o '/galaxy/server/database/objects/8/e/5/dataset_8e5dfc77-e362-4f92-8aa0-e585585c6541_files' -m '/galaxy/server/database/objects/2/c/d/dataset_2cddd2c8-3f23-4b52-a70e-5d3ec3cf6ed9.dat' -i 'Genotype::Mut,Mut,Mut,WT,WT,WT' -a '/galaxy/server/database/objects/b/d/c/dataset_bdc101e8-15af-4c90-825c-24da0f07ce44.dat' -D 'Mut-WT' -P i -l '0.0' -p '0.05' -d 'BH' -G '6' -n 'TMM' -b && mkdir ./output_dir && cp '/galaxy/server/database/objects/8/e/5/dataset_8e5dfc77-e362-4f92-8aa0-e585585c6541_files'/*tsv output_dir/ && cp -r ./glimma* '/galaxy/server/database/objects/8/e/5/dataset_8e5dfc77-e362-4f92-8aa0-e585585c6541_files'] +galaxy.jobs.runners DEBUG 2024-12-30 01:26:45,603 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (164) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/164/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/164/galaxy_164.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:26:45,616 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:26:45,617 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.58.1+galaxy0: mulled-v2-3d571fed05a48eb8af17dbc6c8ed632143702ac1:c5763bb5f3402fc75fc6c0fa6c38d545d78e0e67 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:26:45,652 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-3d571fed05a48eb8af17dbc6c8ed632143702ac1:c5763bb5f3402fc75fc6c0fa6c38d545d78e0e67-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 01:27:09,045 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 164: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:27:14,019 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 164 finished +galaxy.model.store.discover DEBUG 2024-12-30 01:27:14,085 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (164) Created dynamic collection dataset for path [/galaxy/server/database/jobs_directory/000/164/working/output_dir/limma-voom_Mut-WT.tsv] with element identifier [limma-voom_Mut-WT] for output [outTables] (6.929 ms) +galaxy.model.store.discover DEBUG 2024-12-30 01:27:14,104 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (164) Add dynamic collection datasets to history for output [outTables] (18.624 ms) +galaxy.model.metadata DEBUG 2024-12-30 01:27:14,161 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 166 +galaxy.jobs INFO 2024-12-30 01:27:14,223 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 164 in /galaxy/server/database/jobs_directory/000/164 +galaxy.objectstore CRITICAL 2024-12-30 01:27:14,276 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] None delete error [Errno 13] Permission denied: 'MD-Plot.html' +galaxy.jobs DEBUG 2024-12-30 01:27:14,277 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 164 executed (227.603 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:27:15,962 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 165 +tpv.core.entities DEBUG 2024-12-30 01:27:16,006 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:27:16,006 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (165) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:27:16,013 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (165) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:27:16,030 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (165) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:27:16,047 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (165) Working directory for job is: /galaxy/server/database/jobs_directory/000/165 +galaxy.jobs.runners DEBUG 2024-12-30 01:27:16,055 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [165] queued (41.661 ms) +galaxy.jobs.handler INFO 2024-12-30 01:27:16,059 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (165) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:27:16,064 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 165 +galaxy.jobs DEBUG 2024-12-30 01:27:16,195 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [165] prepared (107.901 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:27:16,221 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/165/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/165/registry.xml' '/galaxy/server/database/jobs_directory/000/165/upload_params.json' '168:/galaxy/server/database/objects/1/e/3/dataset_1e35e768-597b-4781-960c-0d323070f9a3_files:/galaxy/server/database/objects/1/e/3/dataset_1e35e768-597b-4781-960c-0d323070f9a3.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:27:16,237 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (165) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/165/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/165/galaxy_165.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:27:24,203 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 165: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:27:29,261 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 165 finished +galaxy.model.metadata DEBUG 2024-12-30 01:27:29,331 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 168 +galaxy.jobs INFO 2024-12-30 01:27:29,386 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 165 in /galaxy/server/database/jobs_directory/000/165 +galaxy.jobs DEBUG 2024-12-30 01:27:29,447 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 165 executed (153.568 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:27:30,380 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 166 +tpv.core.entities DEBUG 2024-12-30 01:27:30,415 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/.*, abstract=False, cores=1, mem=4, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:27:30,415 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (166) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:27:30,421 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (166) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:27:30,437 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (166) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:27:30,456 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (166) Working directory for job is: /galaxy/server/database/jobs_directory/000/166 +galaxy.jobs.runners DEBUG 2024-12-30 01:27:30,464 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [166] queued (43.007 ms) +galaxy.jobs.handler INFO 2024-12-30 01:27:30,467 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (166) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:27:30,472 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 166 +galaxy.jobs DEBUG 2024-12-30 01:27:30,554 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [166] prepared (63.638 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:27:30,555 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:27:30,555 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.58.1+galaxy0: mulled-v2-3d571fed05a48eb8af17dbc6c8ed632143702ac1:c5763bb5f3402fc75fc6c0fa6c38d545d78e0e67 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:27:30,576 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-3d571fed05a48eb8af17dbc6c8ed632143702ac1:c5763bb5f3402fc75fc6c0fa6c38d545d78e0e67-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:27:30,599 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/166/tool_script.sh] for tool command [echo $(R --version | grep version | grep -v GNU)", limma version" $(R --vanilla --slave -e "library(limma); cat(sessionInfo()\$otherPkgs\$limma\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", edgeR version" $(R --vanilla --slave -e "library(edgeR); cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", statmod version" $(R --vanilla --slave -e "library(statmod); cat(sessionInfo()\$otherPkgs\$statmod\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", scales version" $(R --vanilla --slave -e "library(scales); cat(sessionInfo()\$otherPkgs\$scales\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", rjson version" $(R --vanilla --slave -e "library(rjson); cat(sessionInfo()\$otherPkgs\$rjson\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", getopt version" $(R --vanilla --slave -e "library(getopt); cat(sessionInfo()\$otherPkgs\$getopt\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", gplots version" $(R --vanilla --slave -e "library(gplots); cat(sessionInfo()\$otherPkgs\$gplots\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", Glimma version" $(R --vanilla --slave -e "library(Glimma); cat(sessionInfo()\$otherPkgs\$Glimma\$Version)" 2> /dev/null | grep -v -i "WARNING: ") > /galaxy/server/database/jobs_directory/000/166/outputs/COMMAND_VERSION 2>&1; +Rscript '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/119b069fc845/limma_voom/limma_voom.R' -R '/galaxy/server/database/objects/e/5/e/dataset_e5e4e009-f6ea-408f-b0ab-61b0ada185f0.dat' -o '/galaxy/server/database/objects/e/5/e/dataset_e5e4e009-f6ea-408f-b0ab-61b0ada185f0_files' -m '/galaxy/server/database/objects/1/e/3/dataset_1e35e768-597b-4781-960c-0d323070f9a3.dat' -i 'Genotype::Mut,Mut,Mut,WT,WT,WT' -D 'Mut-WT' -P i -r -l '0.0' -p '0.05' -d 'BH' -G '6' -n 'TMM' -b && mkdir ./output_dir && cp '/galaxy/server/database/objects/e/5/e/dataset_e5e4e009-f6ea-408f-b0ab-61b0ada185f0_files'/*tsv output_dir/ && cp -r ./glimma* '/galaxy/server/database/objects/e/5/e/dataset_e5e4e009-f6ea-408f-b0ab-61b0ada185f0_files' && cp '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/119b069fc845/limma_voom/limma_voom.R' '/galaxy/server/database/objects/1/4/5/dataset_14508b95-fd03-476a-9462-02e228f5b3a0.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:27:30,618 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (166) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/166/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/166/galaxy_166.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:27:30,631 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:27:30,632 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.58.1+galaxy0: mulled-v2-3d571fed05a48eb8af17dbc6c8ed632143702ac1:c5763bb5f3402fc75fc6c0fa6c38d545d78e0e67 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:27:30,649 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-3d571fed05a48eb8af17dbc6c8ed632143702ac1:c5763bb5f3402fc75fc6c0fa6c38d545d78e0e67-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 01:27:54,722 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 166: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:27:59,877 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 166 finished +galaxy.model.store.discover DEBUG 2024-12-30 01:27:59,947 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (166) Created dynamic collection dataset for path [/galaxy/server/database/jobs_directory/000/166/working/output_dir/limma-voom_Mut-WT.tsv] with element identifier [limma-voom_Mut-WT] for output [outTables] (5.460 ms) +galaxy.model.store.discover DEBUG 2024-12-30 01:27:59,966 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (166) Add dynamic collection datasets to history for output [outTables] (18.525 ms) +galaxy.model.metadata DEBUG 2024-12-30 01:28:00,000 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 169 +galaxy.model.metadata DEBUG 2024-12-30 01:28:00,009 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 170 +galaxy.util WARNING 2024-12-30 01:28:00,019 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/1/4/5/dataset_14508b95-fd03-476a-9462-02e228f5b3a0.dat, group remains grp.struct_group(gr_name='nogroup', gr_passwd='x', gr_gid=65534, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/1/4/5/dataset_14508b95-fd03-476a-9462-02e228f5b3a0.dat' +galaxy.jobs INFO 2024-12-30 01:28:00,068 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 166 in /galaxy/server/database/jobs_directory/000/166 +galaxy.objectstore CRITICAL 2024-12-30 01:28:00,138 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] None delete error [Errno 13] Permission denied: 'MDS-Plot.html' +galaxy.jobs DEBUG 2024-12-30 01:28:00,138 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 166 executed (227.597 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:28:01,157 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 167 +tpv.core.entities DEBUG 2024-12-30 01:28:01,194 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:28:01,195 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (167) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:28:01,200 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (167) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:28:01,220 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (167) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:28:01,239 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (167) Working directory for job is: /galaxy/server/database/jobs_directory/000/167 +galaxy.jobs.runners DEBUG 2024-12-30 01:28:01,248 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [167] queued (47.789 ms) +galaxy.jobs.handler INFO 2024-12-30 01:28:01,253 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (167) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:28:01,259 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 167 +galaxy.jobs DEBUG 2024-12-30 01:28:01,380 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [167] prepared (100.981 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:28:01,405 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/167/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/167/registry.xml' '/galaxy/server/database/jobs_directory/000/167/upload_params.json' '172:/galaxy/server/database/objects/9/8/a/dataset_98a17782-41ba-42f1-a24d-1c23e46265d2_files:/galaxy/server/database/objects/9/8/a/dataset_98a17782-41ba-42f1-a24d-1c23e46265d2.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:28:01,417 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (167) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/167/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/167/galaxy_167.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:28:09,878 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 167: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:28:14,854 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 167 finished +galaxy.model.metadata DEBUG 2024-12-30 01:28:14,931 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 172 +galaxy.jobs INFO 2024-12-30 01:28:14,980 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 167 in /galaxy/server/database/jobs_directory/000/167 +galaxy.jobs DEBUG 2024-12-30 01:28:15,044 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 167 executed (154.958 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:28:15,558 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 168 +tpv.core.entities DEBUG 2024-12-30 01:28:15,605 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/.*, abstract=False, cores=1, mem=4, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:28:15,605 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (168) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:28:15,611 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (168) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:28:15,647 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (168) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:28:15,667 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (168) Working directory for job is: /galaxy/server/database/jobs_directory/000/168 +galaxy.jobs.runners DEBUG 2024-12-30 01:28:15,677 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [168] queued (65.129 ms) +galaxy.jobs.handler INFO 2024-12-30 01:28:15,681 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (168) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:28:15,686 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 168 +galaxy.jobs DEBUG 2024-12-30 01:28:15,804 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [168] prepared (97.223 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:28:15,805 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:28:15,805 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.58.1+galaxy0: mulled-v2-3d571fed05a48eb8af17dbc6c8ed632143702ac1:c5763bb5f3402fc75fc6c0fa6c38d545d78e0e67 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:28:15,830 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-3d571fed05a48eb8af17dbc6c8ed632143702ac1:c5763bb5f3402fc75fc6c0fa6c38d545d78e0e67-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:28:15,854 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/168/tool_script.sh] for tool command [echo $(R --version | grep version | grep -v GNU)", limma version" $(R --vanilla --slave -e "library(limma); cat(sessionInfo()\$otherPkgs\$limma\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", edgeR version" $(R --vanilla --slave -e "library(edgeR); cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", statmod version" $(R --vanilla --slave -e "library(statmod); cat(sessionInfo()\$otherPkgs\$statmod\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", scales version" $(R --vanilla --slave -e "library(scales); cat(sessionInfo()\$otherPkgs\$scales\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", rjson version" $(R --vanilla --slave -e "library(rjson); cat(sessionInfo()\$otherPkgs\$rjson\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", getopt version" $(R --vanilla --slave -e "library(getopt); cat(sessionInfo()\$otherPkgs\$getopt\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", gplots version" $(R --vanilla --slave -e "library(gplots); cat(sessionInfo()\$otherPkgs\$gplots\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", Glimma version" $(R --vanilla --slave -e "library(Glimma); cat(sessionInfo()\$otherPkgs\$Glimma\$Version)" 2> /dev/null | grep -v -i "WARNING: ") > /galaxy/server/database/jobs_directory/000/168/outputs/COMMAND_VERSION 2>&1; +Rscript '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/119b069fc845/limma_voom/limma_voom.R' -R '/galaxy/server/database/objects/f/9/3/dataset_f93a51db-78ad-4c8d-b9b1-4c3c48aaf706.dat' -o '/galaxy/server/database/objects/f/9/3/dataset_f93a51db-78ad-4c8d-b9b1-4c3c48aaf706_files' -m '/galaxy/server/database/objects/9/8/a/dataset_98a17782-41ba-42f1-a24d-1c23e46265d2.dat' -i 'Genotype::Mut,Mut,Mut,WT,WT,WT|Batch::b1,b2,b3,b1,b2,b3' -D 'Mut-WT' -P i -l '0.0' -p '0.05' -d 'BH' -G '6' -n 'TMM' -b && mkdir ./output_dir && cp '/galaxy/server/database/objects/f/9/3/dataset_f93a51db-78ad-4c8d-b9b1-4c3c48aaf706_files'/*tsv output_dir/ && cp -r ./glimma* '/galaxy/server/database/objects/f/9/3/dataset_f93a51db-78ad-4c8d-b9b1-4c3c48aaf706_files'] +galaxy.jobs.runners DEBUG 2024-12-30 01:28:15,871 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (168) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/168/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/168/galaxy_168.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:28:15,886 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:28:15,886 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.58.1+galaxy0: mulled-v2-3d571fed05a48eb8af17dbc6c8ed632143702ac1:c5763bb5f3402fc75fc6c0fa6c38d545d78e0e67 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:28:15,905 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-3d571fed05a48eb8af17dbc6c8ed632143702ac1:c5763bb5f3402fc75fc6c0fa6c38d545d78e0e67-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 01:28:38,347 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 168: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:28:43,266 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 168 finished +galaxy.model.store.discover DEBUG 2024-12-30 01:28:43,328 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (168) Created dynamic collection dataset for path [/galaxy/server/database/jobs_directory/000/168/working/output_dir/limma-voom_Mut-WT.tsv] with element identifier [limma-voom_Mut-WT] for output [outTables] (9.132 ms) +galaxy.model.store.discover DEBUG 2024-12-30 01:28:43,347 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (168) Add dynamic collection datasets to history for output [outTables] (19.073 ms) +galaxy.model.metadata DEBUG 2024-12-30 01:28:43,379 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 173 +galaxy.jobs INFO 2024-12-30 01:28:43,428 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 168 in /galaxy/server/database/jobs_directory/000/168 +galaxy.objectstore CRITICAL 2024-12-30 01:28:43,476 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] None delete error [Errno 13] Permission denied: 'MDS-Plot.html' +galaxy.jobs DEBUG 2024-12-30 01:28:43,476 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 168 executed (181.298 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:28:44,345 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 169 +tpv.core.entities DEBUG 2024-12-30 01:28:44,384 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:28:44,385 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (169) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:28:44,391 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (169) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:28:44,410 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (169) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:28:44,429 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (169) Working directory for job is: /galaxy/server/database/jobs_directory/000/169 +galaxy.jobs.runners DEBUG 2024-12-30 01:28:44,436 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [169] queued (45.036 ms) +galaxy.jobs.handler INFO 2024-12-30 01:28:44,441 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (169) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:28:44,446 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 169 +galaxy.jobs DEBUG 2024-12-30 01:28:44,562 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [169] prepared (95.756 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:28:44,586 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/169/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/169/registry.xml' '/galaxy/server/database/jobs_directory/000/169/upload_params.json' '175:/galaxy/server/database/objects/5/0/7/dataset_5079b547-6f62-440f-b6be-37cee67a2794_files:/galaxy/server/database/objects/5/0/7/dataset_5079b547-6f62-440f-b6be-37cee67a2794.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:28:44,598 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (169) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/169/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/169/galaxy_169.ec; sh -c "exit $return_code" +galaxy.jobs.handler DEBUG 2024-12-30 01:28:45,444 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 170 +tpv.core.entities DEBUG 2024-12-30 01:28:45,483 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:28:45,484 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (170) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:28:45,490 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (170) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:28:45,508 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (170) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:28:45,529 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (170) Working directory for job is: /galaxy/server/database/jobs_directory/000/170 +galaxy.jobs.runners DEBUG 2024-12-30 01:28:45,542 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [170] queued (52.033 ms) +galaxy.jobs.handler INFO 2024-12-30 01:28:45,546 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (170) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:28:45,551 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 170 +galaxy.jobs DEBUG 2024-12-30 01:28:45,688 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [170] prepared (115.702 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:28:45,707 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/170/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/170/registry.xml' '/galaxy/server/database/jobs_directory/000/170/upload_params.json' '176:/galaxy/server/database/objects/5/9/6/dataset_59637351-43db-440d-baf0-7eae2ce85afc_files:/galaxy/server/database/objects/5/9/6/dataset_59637351-43db-440d-baf0-7eae2ce85afc.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:28:45,740 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (170) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/170/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/170/galaxy_170.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:28:54,671 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 169: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:28:54,697 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 170: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:29:00,113 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 169 finished +galaxy.jobs.runners DEBUG 2024-12-30 01:29:00,118 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 170 finished +galaxy.model.metadata DEBUG 2024-12-30 01:29:00,190 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 175 +galaxy.model.metadata DEBUG 2024-12-30 01:29:00,191 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 176 +galaxy.jobs INFO 2024-12-30 01:29:00,240 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 170 in /galaxy/server/database/jobs_directory/000/170 +galaxy.jobs INFO 2024-12-30 01:29:00,249 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 169 in /galaxy/server/database/jobs_directory/000/169 +galaxy.jobs DEBUG 2024-12-30 01:29:00,301 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 170 executed (152.913 ms) +galaxy.jobs DEBUG 2024-12-30 01:29:00,315 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 169 executed (169.452 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:29:00,964 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 171 +tpv.core.entities DEBUG 2024-12-30 01:29:01,008 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/.*, abstract=False, cores=1, mem=4, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:29:01,009 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (171) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:29:01,015 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (171) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:29:01,035 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (171) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:29:01,056 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (171) Working directory for job is: /galaxy/server/database/jobs_directory/000/171 +galaxy.jobs.runners DEBUG 2024-12-30 01:29:01,065 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [171] queued (49.625 ms) +galaxy.jobs.handler INFO 2024-12-30 01:29:01,069 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (171) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:29:01,073 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 171 +galaxy.jobs DEBUG 2024-12-30 01:29:01,150 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [171] prepared (60.540 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:29:01,151 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:29:01,151 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.58.1+galaxy0: mulled-v2-3d571fed05a48eb8af17dbc6c8ed632143702ac1:c5763bb5f3402fc75fc6c0fa6c38d545d78e0e67 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:29:01,170 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-3d571fed05a48eb8af17dbc6c8ed632143702ac1:c5763bb5f3402fc75fc6c0fa6c38d545d78e0e67-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:29:01,193 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/171/tool_script.sh] for tool command [echo $(R --version | grep version | grep -v GNU)", limma version" $(R --vanilla --slave -e "library(limma); cat(sessionInfo()\$otherPkgs\$limma\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", edgeR version" $(R --vanilla --slave -e "library(edgeR); cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", statmod version" $(R --vanilla --slave -e "library(statmod); cat(sessionInfo()\$otherPkgs\$statmod\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", scales version" $(R --vanilla --slave -e "library(scales); cat(sessionInfo()\$otherPkgs\$scales\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", rjson version" $(R --vanilla --slave -e "library(rjson); cat(sessionInfo()\$otherPkgs\$rjson\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", getopt version" $(R --vanilla --slave -e "library(getopt); cat(sessionInfo()\$otherPkgs\$getopt\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", gplots version" $(R --vanilla --slave -e "library(gplots); cat(sessionInfo()\$otherPkgs\$gplots\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", Glimma version" $(R --vanilla --slave -e "library(Glimma); cat(sessionInfo()\$otherPkgs\$Glimma\$Version)" 2> /dev/null | grep -v -i "WARNING: ") > /galaxy/server/database/jobs_directory/000/171/outputs/COMMAND_VERSION 2>&1; +Rscript '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/119b069fc845/limma_voom/limma_voom.R' -R '/galaxy/server/database/objects/1/a/6/dataset_1a6ee646-65d3-4f29-b438-e30b6a4d5638.dat' -o '/galaxy/server/database/objects/1/a/6/dataset_1a6ee646-65d3-4f29-b438-e30b6a4d5638_files' -m '/galaxy/server/database/objects/5/0/7/dataset_5079b547-6f62-440f-b6be-37cee67a2794.dat' -f '/galaxy/server/database/objects/5/9/6/dataset_59637351-43db-440d-baf0-7eae2ce85afc.dat' -D 'Mut-WT' -P i -l '0.0' -p '0.05' -d 'BH' -G '6' -n 'TMM' -b && mkdir ./output_dir && cp '/galaxy/server/database/objects/1/a/6/dataset_1a6ee646-65d3-4f29-b438-e30b6a4d5638_files'/*tsv output_dir/ && cp -r ./glimma* '/galaxy/server/database/objects/1/a/6/dataset_1a6ee646-65d3-4f29-b438-e30b6a4d5638_files'] +galaxy.jobs.runners DEBUG 2024-12-30 01:29:01,208 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (171) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/171/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/171/galaxy_171.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:29:01,224 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:29:01,224 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.58.1+galaxy0: mulled-v2-3d571fed05a48eb8af17dbc6c8ed632143702ac1:c5763bb5f3402fc75fc6c0fa6c38d545d78e0e67 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:29:01,244 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-3d571fed05a48eb8af17dbc6c8ed632143702ac1:c5763bb5f3402fc75fc6c0fa6c38d545d78e0e67-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 01:29:26,192 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 171: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:29:31,042 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 171 finished +galaxy.model.store.discover DEBUG 2024-12-30 01:29:31,105 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (171) Created dynamic collection dataset for path [/galaxy/server/database/jobs_directory/000/171/working/output_dir/limma-voom_Mut-WT.tsv] with element identifier [limma-voom_Mut-WT] for output [outTables] (6.340 ms) +galaxy.model.store.discover DEBUG 2024-12-30 01:29:31,121 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (171) Add dynamic collection datasets to history for output [outTables] (15.847 ms) +galaxy.model.metadata DEBUG 2024-12-30 01:29:31,153 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 177 +galaxy.jobs INFO 2024-12-30 01:29:31,204 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 171 in /galaxy/server/database/jobs_directory/000/171 +galaxy.objectstore CRITICAL 2024-12-30 01:29:31,262 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] None delete error [Errno 13] Permission denied: 'MDS-Plot.html' +galaxy.jobs DEBUG 2024-12-30 01:29:31,263 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 171 executed (192.742 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:29:32,789 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 172 +tpv.core.entities DEBUG 2024-12-30 01:29:32,822 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:29:32,823 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (172) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:29:32,827 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (172) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:29:32,840 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (172) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:29:32,859 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (172) Working directory for job is: /galaxy/server/database/jobs_directory/000/172 +galaxy.jobs.runners DEBUG 2024-12-30 01:29:32,867 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [172] queued (39.839 ms) +galaxy.jobs.handler INFO 2024-12-30 01:29:32,871 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (172) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:29:32,875 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 172 +galaxy.jobs DEBUG 2024-12-30 01:29:32,984 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [172] prepared (90.800 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:29:33,007 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/172/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/172/registry.xml' '/galaxy/server/database/jobs_directory/000/172/upload_params.json' '179:/galaxy/server/database/objects/5/9/b/dataset_59bd7131-9a57-498f-bc95-2fd0fb0c0269_files:/galaxy/server/database/objects/5/9/b/dataset_59bd7131-9a57-498f-bc95-2fd0fb0c0269.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:29:33,022 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (172) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/172/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/172/galaxy_172.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:29:41,359 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 172: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:29:46,263 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 172 finished +galaxy.model.metadata DEBUG 2024-12-30 01:29:46,326 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 179 +galaxy.jobs INFO 2024-12-30 01:29:46,365 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 172 in /galaxy/server/database/jobs_directory/000/172 +galaxy.jobs DEBUG 2024-12-30 01:29:46,419 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 172 executed (126.719 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:29:47,167 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 173 +tpv.core.entities DEBUG 2024-12-30 01:29:47,208 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/.*, abstract=False, cores=1, mem=4, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:29:47,208 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (173) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:29:47,215 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (173) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:29:47,235 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (173) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:29:47,260 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (173) Working directory for job is: /galaxy/server/database/jobs_directory/000/173 +galaxy.jobs.runners DEBUG 2024-12-30 01:29:47,269 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [173] queued (53.975 ms) +galaxy.jobs.handler INFO 2024-12-30 01:29:47,272 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (173) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:29:47,277 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 173 +galaxy.jobs DEBUG 2024-12-30 01:29:47,366 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [173] prepared (70.461 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:29:47,366 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:29:47,366 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.58.1+galaxy0: mulled-v2-3d571fed05a48eb8af17dbc6c8ed632143702ac1:c5763bb5f3402fc75fc6c0fa6c38d545d78e0e67 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:29:47,390 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-3d571fed05a48eb8af17dbc6c8ed632143702ac1:c5763bb5f3402fc75fc6c0fa6c38d545d78e0e67-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:29:47,411 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/173/tool_script.sh] for tool command [echo $(R --version | grep version | grep -v GNU)", limma version" $(R --vanilla --slave -e "library(limma); cat(sessionInfo()\$otherPkgs\$limma\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", edgeR version" $(R --vanilla --slave -e "library(edgeR); cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", statmod version" $(R --vanilla --slave -e "library(statmod); cat(sessionInfo()\$otherPkgs\$statmod\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", scales version" $(R --vanilla --slave -e "library(scales); cat(sessionInfo()\$otherPkgs\$scales\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", rjson version" $(R --vanilla --slave -e "library(rjson); cat(sessionInfo()\$otherPkgs\$rjson\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", getopt version" $(R --vanilla --slave -e "library(getopt); cat(sessionInfo()\$otherPkgs\$getopt\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", gplots version" $(R --vanilla --slave -e "library(gplots); cat(sessionInfo()\$otherPkgs\$gplots\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", Glimma version" $(R --vanilla --slave -e "library(Glimma); cat(sessionInfo()\$otherPkgs\$Glimma\$Version)" 2> /dev/null | grep -v -i "WARNING: ") > /galaxy/server/database/jobs_directory/000/173/outputs/COMMAND_VERSION 2>&1; +Rscript '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/119b069fc845/limma_voom/limma_voom.R' -R '/galaxy/server/database/objects/d/7/1/dataset_d7181054-7395-454b-9487-57739a522b9c.dat' -o '/galaxy/server/database/objects/d/7/1/dataset_d7181054-7395-454b-9487-57739a522b9c_files' -m '/galaxy/server/database/objects/5/9/b/dataset_59bd7131-9a57-498f-bc95-2fd0fb0c0269.dat' -i 'Genotype::Mut,Mut,Mut,WT,WT,WT' -D 'Mut-WT' -z '10' -s '3' -P i -F -x -l '0.0' -p '0.05' -d 'BH' -G '6' -n 'TMM' -b && mkdir ./output_dir && cp '/galaxy/server/database/objects/d/7/1/dataset_d7181054-7395-454b-9487-57739a522b9c_files'/*tsv output_dir/ && cp -r ./glimma* '/galaxy/server/database/objects/d/7/1/dataset_d7181054-7395-454b-9487-57739a522b9c_files' && cp '/galaxy/server/database/objects/d/7/1/dataset_d7181054-7395-454b-9487-57739a522b9c_files'/*counts output_dir/] +galaxy.jobs.runners DEBUG 2024-12-30 01:29:47,442 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (173) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/173/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/173/galaxy_173.ec; +if [ -f "/galaxy/server/database/jobs_directory/000/173/working/output_dir/"*"_filtcounts" ] ; then cp "/galaxy/server/database/jobs_directory/000/173/working/output_dir/"*"_filtcounts" "/galaxy/server/database/objects/8/f/a/dataset_8fa91a89-bcaf-48d3-b414-fbc033ee16e4.dat" ; fi; +if [ -f "/galaxy/server/database/jobs_directory/000/173/working/output_dir/"*"_normcounts" ] ; then cp "/galaxy/server/database/jobs_directory/000/173/working/output_dir/"*"_normcounts" "/galaxy/server/database/objects/e/a/9/dataset_ea9951b0-4ec7-4388-bf71-36b41c927e62.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:29:47,454 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:29:47,454 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.58.1+galaxy0: mulled-v2-3d571fed05a48eb8af17dbc6c8ed632143702ac1:c5763bb5f3402fc75fc6c0fa6c38d545d78e0e67 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:29:47,474 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-3d571fed05a48eb8af17dbc6c8ed632143702ac1:c5763bb5f3402fc75fc6c0fa6c38d545d78e0e67-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 01:30:10,977 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 173: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:30:16,267 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 173 finished +galaxy.model.store.discover DEBUG 2024-12-30 01:30:16,350 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (173) Created dynamic collection dataset for path [/galaxy/server/database/jobs_directory/000/173/working/output_dir/limma-voom_Mut-WT.tsv] with element identifier [limma-voom_Mut-WT] for output [outTables] (6.794 ms) +galaxy.model.store.discover DEBUG 2024-12-30 01:30:16,374 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (173) Add dynamic collection datasets to history for output [outTables] (23.644 ms) +galaxy.model.metadata DEBUG 2024-12-30 01:30:16,418 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 180 +galaxy.model.metadata DEBUG 2024-12-30 01:30:16,432 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 181 +galaxy.model.metadata DEBUG 2024-12-30 01:30:16,449 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 182 +galaxy.util WARNING 2024-12-30 01:30:16,468 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/8/f/a/dataset_8fa91a89-bcaf-48d3-b414-fbc033ee16e4.dat, group remains grp.struct_group(gr_name='nogroup', gr_passwd='x', gr_gid=65534, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/8/f/a/dataset_8fa91a89-bcaf-48d3-b414-fbc033ee16e4.dat' +galaxy.util WARNING 2024-12-30 01:30:16,469 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/e/a/9/dataset_ea9951b0-4ec7-4388-bf71-36b41c927e62.dat, group remains grp.struct_group(gr_name='nogroup', gr_passwd='x', gr_gid=65534, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/e/a/9/dataset_ea9951b0-4ec7-4388-bf71-36b41c927e62.dat' +galaxy.jobs INFO 2024-12-30 01:30:16,522 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 173 in /galaxy/server/database/jobs_directory/000/173 +galaxy.objectstore CRITICAL 2024-12-30 01:30:16,600 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] None delete error [Errno 13] Permission denied: 'MDS-Plot.html' +galaxy.jobs DEBUG 2024-12-30 01:30:16,600 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 173 executed (294.552 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:30:18,029 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 174 +tpv.core.entities DEBUG 2024-12-30 01:30:18,069 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:30:18,070 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (174) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:30:18,076 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (174) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:30:18,097 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (174) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:30:18,120 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (174) Working directory for job is: /galaxy/server/database/jobs_directory/000/174 +galaxy.jobs.runners DEBUG 2024-12-30 01:30:18,129 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [174] queued (52.183 ms) +galaxy.jobs.handler INFO 2024-12-30 01:30:18,134 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (174) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:30:18,140 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 174 +galaxy.jobs DEBUG 2024-12-30 01:30:18,274 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [174] prepared (108.689 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:30:18,302 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/174/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/174/registry.xml' '/galaxy/server/database/jobs_directory/000/174/upload_params.json' '184:/galaxy/server/database/objects/e/b/9/dataset_eb9dfbb9-8890-492e-9204-8ef71f8f856b_files:/galaxy/server/database/objects/e/b/9/dataset_eb9dfbb9-8890-492e-9204-8ef71f8f856b.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:30:18,317 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (174) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/174/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/174/galaxy_174.ec; sh -c "exit $return_code" +galaxy.jobs.handler DEBUG 2024-12-30 01:30:19,137 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 178, 175, 177, 176 +tpv.core.entities DEBUG 2024-12-30 01:30:19,179 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:30:19,179 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (175) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:30:19,186 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (175) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:30:19,209 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (175) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:30:19,230 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (175) Working directory for job is: /galaxy/server/database/jobs_directory/000/175 +galaxy.jobs.runners DEBUG 2024-12-30 01:30:19,237 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [175] queued (50.989 ms) +galaxy.jobs.handler INFO 2024-12-30 01:30:19,242 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (175) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:30:19,249 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 175 +tpv.core.entities DEBUG 2024-12-30 01:30:19,268 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:30:19,268 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (176) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:30:19,276 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (176) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:30:19,295 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (176) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:30:19,325 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (176) Working directory for job is: /galaxy/server/database/jobs_directory/000/176 +galaxy.jobs.runners DEBUG 2024-12-30 01:30:19,334 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [176] queued (57.439 ms) +galaxy.jobs.handler INFO 2024-12-30 01:30:19,338 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (176) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:30:19,345 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 176 +tpv.core.entities DEBUG 2024-12-30 01:30:19,367 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:30:19,368 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (177) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:30:19,375 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (177) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:30:19,399 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (177) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:30:19,408 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [175] prepared (128.567 ms) +galaxy.jobs DEBUG 2024-12-30 01:30:19,445 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (177) Working directory for job is: /galaxy/server/database/jobs_directory/000/177 +galaxy.jobs.runners DEBUG 2024-12-30 01:30:19,454 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [177] queued (78.695 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:30:19,457 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/175/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/175/registry.xml' '/galaxy/server/database/jobs_directory/000/175/upload_params.json' '185:/galaxy/server/database/objects/8/2/3/dataset_823c12df-cf6b-4a63-ba84-0a6f885e6126_files:/galaxy/server/database/objects/8/2/3/dataset_823c12df-cf6b-4a63-ba84-0a6f885e6126.dat'] +galaxy.jobs.handler INFO 2024-12-30 01:30:19,465 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (177) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:30:19,470 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 177 +galaxy.jobs.runners DEBUG 2024-12-30 01:30:19,488 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (175) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/175/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/175/galaxy_175.ec; sh -c "exit $return_code" +tpv.core.entities DEBUG 2024-12-30 01:30:19,505 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:30:19,505 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (178) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:30:19,528 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (178) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:30:19,561 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [176] prepared (186.368 ms) +galaxy.jobs DEBUG 2024-12-30 01:30:19,565 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (178) Persisting job destination (destination id: k8s) +galaxy.jobs.command_factory INFO 2024-12-30 01:30:19,610 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/176/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/176/registry.xml' '/galaxy/server/database/jobs_directory/000/176/upload_params.json' '186:/galaxy/server/database/objects/b/4/1/dataset_b4139d36-f02c-4fdb-a716-b936df960d2e_files:/galaxy/server/database/objects/b/4/1/dataset_b4139d36-f02c-4fdb-a716-b936df960d2e.dat'] +galaxy.jobs DEBUG 2024-12-30 01:30:19,613 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (178) Working directory for job is: /galaxy/server/database/jobs_directory/000/178 +galaxy.jobs.runners DEBUG 2024-12-30 01:30:19,623 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [178] queued (95.257 ms) +galaxy.jobs.handler INFO 2024-12-30 01:30:19,631 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (178) Job dispatched +galaxy.jobs.runners DEBUG 2024-12-30 01:30:19,637 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (176) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/176/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/176/galaxy_176.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:30:19,639 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 178 +galaxy.jobs DEBUG 2024-12-30 01:30:19,682 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [177] prepared (167.600 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:30:19,718 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/177/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/177/registry.xml' '/galaxy/server/database/jobs_directory/000/177/upload_params.json' '187:/galaxy/server/database/objects/7/8/6/dataset_786d6f0f-fef3-436b-9dab-20ee29af478a_files:/galaxy/server/database/objects/7/8/6/dataset_786d6f0f-fef3-436b-9dab-20ee29af478a.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:30:19,741 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (177) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/177/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/177/galaxy_177.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-12-30 01:30:19,810 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [178] prepared (137.759 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:30:19,836 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/178/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/178/registry.xml' '/galaxy/server/database/jobs_directory/000/178/upload_params.json' '188:/galaxy/server/database/objects/c/5/2/dataset_c52f211d-0b7b-4a12-8b3a-2e7212a53054_files:/galaxy/server/database/objects/c/5/2/dataset_c52f211d-0b7b-4a12-8b3a-2e7212a53054.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:30:19,856 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (178) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/178/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/178/galaxy_178.ec; sh -c "exit $return_code" +galaxy.jobs.handler DEBUG 2024-12-30 01:30:20,634 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 181, 180, 179, 183, 182 +tpv.core.entities DEBUG 2024-12-30 01:30:20,680 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:30:20,681 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (179) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:30:20,687 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (179) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:30:20,706 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (179) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:30:20,729 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (179) Working directory for job is: /galaxy/server/database/jobs_directory/000/179 +galaxy.jobs.runners DEBUG 2024-12-30 01:30:20,738 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [179] queued (50.323 ms) +galaxy.jobs.handler INFO 2024-12-30 01:30:20,741 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (179) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:30:20,747 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 179 +tpv.core.entities DEBUG 2024-12-30 01:30:20,766 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:30:20,766 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (180) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:30:20,773 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (180) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:30:20,804 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (180) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:30:20,842 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (180) Working directory for job is: /galaxy/server/database/jobs_directory/000/180 +galaxy.jobs.runners DEBUG 2024-12-30 01:30:20,851 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [180] queued (77.388 ms) +galaxy.jobs.handler INFO 2024-12-30 01:30:20,856 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (180) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:30:20,864 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 180 +tpv.core.entities DEBUG 2024-12-30 01:30:20,885 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:30:20,886 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (181) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:30:20,898 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (181) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:30:20,923 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [179] prepared (140.171 ms) +galaxy.jobs DEBUG 2024-12-30 01:30:20,925 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (181) Persisting job destination (destination id: k8s) +galaxy.jobs.command_factory INFO 2024-12-30 01:30:20,962 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/179/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/179/registry.xml' '/galaxy/server/database/jobs_directory/000/179/upload_params.json' '189:/galaxy/server/database/objects/b/0/3/dataset_b03b7810-92a2-4726-854d-b99d755ca5a1_files:/galaxy/server/database/objects/b/0/3/dataset_b03b7810-92a2-4726-854d-b99d755ca5a1.dat'] +galaxy.jobs DEBUG 2024-12-30 01:30:20,969 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (181) Working directory for job is: /galaxy/server/database/jobs_directory/000/181 +galaxy.jobs.runners DEBUG 2024-12-30 01:30:20,978 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [181] queued (80.017 ms) +galaxy.jobs.handler INFO 2024-12-30 01:30:20,986 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (181) Job dispatched +galaxy.jobs.runners DEBUG 2024-12-30 01:30:20,990 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (179) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/179/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/179/galaxy_179.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:30:20,999 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 181 +tpv.core.entities DEBUG 2024-12-30 01:30:21,028 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:30:21,028 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (182) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:30:21,043 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (182) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:30:21,066 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (182) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:30:21,077 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [180] prepared (172.707 ms) +galaxy.jobs DEBUG 2024-12-30 01:30:21,125 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (182) Working directory for job is: /galaxy/server/database/jobs_directory/000/182 +galaxy.jobs.command_factory INFO 2024-12-30 01:30:21,128 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/180/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/180/registry.xml' '/galaxy/server/database/jobs_directory/000/180/upload_params.json' '190:/galaxy/server/database/objects/9/6/9/dataset_969b0812-4aec-4760-bdba-1252a15b0217_files:/galaxy/server/database/objects/9/6/9/dataset_969b0812-4aec-4760-bdba-1252a15b0217.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:30:21,136 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [182] queued (92.182 ms) +galaxy.jobs.handler INFO 2024-12-30 01:30:21,141 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (182) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:30:21,159 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 182 +galaxy.jobs.runners DEBUG 2024-12-30 01:30:21,176 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (180) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/180/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/180/galaxy_180.ec; sh -c "exit $return_code" +tpv.core.entities DEBUG 2024-12-30 01:30:21,211 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:30:21,211 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (183) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:30:21,221 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (183) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:30:21,264 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (183) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:30:21,275 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [181] prepared (228.742 ms) +galaxy.jobs DEBUG 2024-12-30 01:30:21,335 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (183) Working directory for job is: /galaxy/server/database/jobs_directory/000/183 +galaxy.jobs.command_factory INFO 2024-12-30 01:30:21,343 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/181/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/181/registry.xml' '/galaxy/server/database/jobs_directory/000/181/upload_params.json' '191:/galaxy/server/database/objects/6/3/1/dataset_63181f94-2825-4bdf-b1f2-970c9312e385_files:/galaxy/server/database/objects/6/3/1/dataset_63181f94-2825-4bdf-b1f2-970c9312e385.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:30:21,347 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [183] queued (125.419 ms) +galaxy.jobs.handler INFO 2024-12-30 01:30:21,354 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (183) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:30:21,364 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 183 +galaxy.jobs.runners DEBUG 2024-12-30 01:30:21,379 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (181) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/181/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/181/galaxy_181.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-12-30 01:30:21,439 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [182] prepared (216.336 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:30:21,490 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/182/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/182/registry.xml' '/galaxy/server/database/jobs_directory/000/182/upload_params.json' '192:/galaxy/server/database/objects/e/8/0/dataset_e802b3ce-8c23-4942-aa2b-584f3e8b9b1b_files:/galaxy/server/database/objects/e/8/0/dataset_e802b3ce-8c23-4942-aa2b-584f3e8b9b1b.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:30:21,513 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (182) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/182/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/182/galaxy_182.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-12-30 01:30:21,573 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [183] prepared (162.110 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:30:21,603 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/183/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/183/registry.xml' '/galaxy/server/database/jobs_directory/000/183/upload_params.json' '193:/galaxy/server/database/objects/e/2/e/dataset_e2e73402-0cbe-4b8d-b768-526f10b8c10e_files:/galaxy/server/database/objects/e/2/e/dataset_e2e73402-0cbe-4b8d-b768-526f10b8c10e.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:30:21,632 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (183) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/183/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/183/galaxy_183.ec; sh -c "exit $return_code" +galaxy.jobs.handler DEBUG 2024-12-30 01:30:22,357 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 186, 185, 184 +tpv.core.entities DEBUG 2024-12-30 01:30:22,400 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:30:22,401 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (184) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:30:22,406 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (184) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:30:22,429 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (184) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:30:22,450 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (184) Working directory for job is: /galaxy/server/database/jobs_directory/000/184 +galaxy.jobs.runners DEBUG 2024-12-30 01:30:22,459 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [184] queued (52.263 ms) +galaxy.jobs.handler INFO 2024-12-30 01:30:22,463 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (184) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:30:22,470 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 184 +tpv.core.entities DEBUG 2024-12-30 01:30:22,490 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:30:22,491 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (185) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:30:22,500 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (185) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:30:22,537 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (185) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:30:22,603 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (185) Working directory for job is: /galaxy/server/database/jobs_directory/000/185 +galaxy.jobs.runners DEBUG 2024-12-30 01:30:22,618 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [185] queued (118.138 ms) +galaxy.jobs.handler INFO 2024-12-30 01:30:22,627 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (185) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:30:22,636 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 185 +tpv.core.entities DEBUG 2024-12-30 01:30:22,679 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:30:22,680 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (186) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:30:22,697 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (186) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:30:22,732 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [184] prepared (229.573 ms) +galaxy.jobs DEBUG 2024-12-30 01:30:22,740 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (186) Persisting job destination (destination id: k8s) +galaxy.jobs.command_factory INFO 2024-12-30 01:30:22,786 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/184/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/184/registry.xml' '/galaxy/server/database/jobs_directory/000/184/upload_params.json' '194:/galaxy/server/database/objects/8/e/8/dataset_8e8cdca4-aa93-40d9-976c-f561b5805be8_files:/galaxy/server/database/objects/8/e/8/dataset_8e8cdca4-aa93-40d9-976c-f561b5805be8.dat'] +galaxy.jobs DEBUG 2024-12-30 01:30:22,805 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (186) Working directory for job is: /galaxy/server/database/jobs_directory/000/186 +galaxy.jobs.runners DEBUG 2024-12-30 01:30:22,821 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (184) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/184/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/184/galaxy_184.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:30:22,825 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [186] queued (127.039 ms) +galaxy.jobs.handler INFO 2024-12-30 01:30:22,832 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (186) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:30:22,845 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 186 +galaxy.jobs DEBUG 2024-12-30 01:30:22,901 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [185] prepared (219.187 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:30:22,943 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/185/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/185/registry.xml' '/galaxy/server/database/jobs_directory/000/185/upload_params.json' '195:/galaxy/server/database/objects/9/7/5/dataset_9757be5b-53ae-4964-ac3f-6d12e447bf18_files:/galaxy/server/database/objects/9/7/5/dataset_9757be5b-53ae-4964-ac3f-6d12e447bf18.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:30:22,982 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (185) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/185/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/185/galaxy_185.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-12-30 01:30:23,101 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [186] prepared (215.883 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:30:23,126 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/186/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/186/registry.xml' '/galaxy/server/database/jobs_directory/000/186/upload_params.json' '196:/galaxy/server/database/objects/4/f/2/dataset_4f2db28a-ba74-4816-b953-87e49f57d140_files:/galaxy/server/database/objects/4/f/2/dataset_4f2db28a-ba74-4816-b953-87e49f57d140.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:30:23,144 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (186) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/186/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/186/galaxy_186.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes ERROR 2024-12-30 01:30:29,700 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Could not clean up k8s batch job. Ignoring... +Traceback (most recent call last): + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/http.py", line 437, in raise_for_status + resp.raise_for_status() + File "/galaxy/server/.venv/lib/python3.10/site-packages/requests/models.py", line 1021, in raise_for_status + raise HTTPError(http_error_msg, response=self) +requests.exceptions.HTTPError: 409 Client Error: Conflict for url: https://10.107.32.1:443/apis/batch/v1/namespaces/prod-24-12-30-00-37-1/jobs/gxy-xsfmx + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 817, in _handle_job_failure + self.__cleanup_k8s_job(job) + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 824, in __cleanup_k8s_job + delete_job(job, k8s_cleanup_job) + File "/galaxy/server/lib/galaxy/jobs/runners/util/pykube_util.py", line 107, in delete_job + job.scale(replicas=0) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/mixins.py", line 30, in scale + self.update() + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 165, in update + self.patch(self.obj, subresource=subresource) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 157, in patch + self.api.raise_for_status(r) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/http.py", line 444, in raise_for_status + raise HTTPError(resp.status_code, payload["message"]) +pykube.exceptions.HTTPError: Operation cannot be fulfilled on jobs.batch "gxy-xsfmx": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners DEBUG 2024-12-30 01:30:29,767 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 174: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:30:29,786 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (177/gxy-xsfmx) Terminated at user's request +galaxy.jobs.runners DEBUG 2024-12-30 01:30:31,258 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 175: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:30:31,278 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 176: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:30:31,295 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 178: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:30:40,149 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 174 finished +galaxy.model.metadata DEBUG 2024-12-30 01:30:40,269 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 184 +galaxy.jobs INFO 2024-12-30 01:30:40,358 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 174 in /galaxy/server/database/jobs_directory/000/174 +galaxy.jobs DEBUG 2024-12-30 01:30:40,464 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 174 executed (281.718 ms) +galaxy.jobs.runners DEBUG 2024-12-30 01:30:40,801 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 180: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:30:42,465 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 178 finished +galaxy.jobs.runners DEBUG 2024-12-30 01:30:42,543 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 175 finished +galaxy.jobs.runners DEBUG 2024-12-30 01:30:42,577 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 176 finished +galaxy.model.metadata DEBUG 2024-12-30 01:30:42,595 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 188 +galaxy.model.metadata DEBUG 2024-12-30 01:30:42,653 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 185 +galaxy.jobs INFO 2024-12-30 01:30:42,867 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 178 in /galaxy/server/database/jobs_directory/000/178 +galaxy.model.metadata DEBUG 2024-12-30 01:30:42,874 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 186 +galaxy.jobs INFO 2024-12-30 01:30:42,891 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 175 in /galaxy/server/database/jobs_directory/000/175 +galaxy.jobs INFO 2024-12-30 01:30:42,931 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 176 in /galaxy/server/database/jobs_directory/000/176 +galaxy.jobs DEBUG 2024-12-30 01:30:42,971 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 178 executed (426.449 ms) +galaxy.jobs DEBUG 2024-12-30 01:30:42,994 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 175 executed (414.199 ms) +galaxy.jobs DEBUG 2024-12-30 01:30:43,030 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 176 executed (389.086 ms) +galaxy.jobs.runners DEBUG 2024-12-30 01:30:43,247 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 179: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:30:43,295 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 181: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:30:43,444 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 182: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.handler DEBUG 2024-12-30 01:30:43,870 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 187 +tpv.core.entities DEBUG 2024-12-30 01:30:43,970 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:30:43,970 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (187) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:30:43,977 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (187) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:30:44,056 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (187) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:30:44,082 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (187) Working directory for job is: /galaxy/server/database/jobs_directory/000/187 +galaxy.jobs.runners DEBUG 2024-12-30 01:30:44,147 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [187] queued (169.518 ms) +galaxy.jobs.handler INFO 2024-12-30 01:30:44,151 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (187) Job dispatched +galaxy.jobs.runners DEBUG 2024-12-30 01:30:51,741 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 180 finished +galaxy.model.metadata DEBUG 2024-12-30 01:30:51,865 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 190 +galaxy.jobs INFO 2024-12-30 01:30:51,956 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 180 in /galaxy/server/database/jobs_directory/000/180 +galaxy.jobs DEBUG 2024-12-30 01:30:52,066 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 180 executed (290.260 ms) +galaxy.jobs.runners DEBUG 2024-12-30 01:30:52,395 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 183: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:30:54,442 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 179 finished +galaxy.model.metadata DEBUG 2024-12-30 01:30:54,586 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 189 +galaxy.jobs INFO 2024-12-30 01:30:54,681 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 179 in /galaxy/server/database/jobs_directory/000/179 +galaxy.jobs.runners DEBUG 2024-12-30 01:30:54,743 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 181 finished +galaxy.model.metadata DEBUG 2024-12-30 01:30:54,844 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 191 +galaxy.jobs DEBUG 2024-12-30 01:30:54,845 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 179 executed (296.646 ms) +galaxy.jobs.runners DEBUG 2024-12-30 01:30:54,852 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 182 finished +galaxy.jobs INFO 2024-12-30 01:30:54,930 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 181 in /galaxy/server/database/jobs_directory/000/181 +galaxy.model.metadata DEBUG 2024-12-30 01:30:54,987 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 192 +galaxy.jobs INFO 2024-12-30 01:30:55,036 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 182 in /galaxy/server/database/jobs_directory/000/182 +galaxy.jobs DEBUG 2024-12-30 01:30:55,044 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 181 executed (270.343 ms) +galaxy.jobs.runners DEBUG 2024-12-30 01:30:55,119 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 184: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs DEBUG 2024-12-30 01:30:55,153 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 182 executed (228.185 ms) +galaxy.jobs.runners DEBUG 2024-12-30 01:30:55,344 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 185: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:30:55,540 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 186: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:31:03,284 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 183 finished +galaxy.model.metadata DEBUG 2024-12-30 01:31:03,459 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 193 +galaxy.jobs INFO 2024-12-30 01:31:03,556 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 183 in /galaxy/server/database/jobs_directory/000/183 +galaxy.jobs DEBUG 2024-12-30 01:31:03,664 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 183 executed (288.907 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:31:03,771 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 187 +galaxy.jobs DEBUG 2024-12-30 01:31:04,040 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [187] prepared (199.014 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:31:04,065 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/187/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/187/registry.xml' '/galaxy/server/database/jobs_directory/000/187/upload_params.json' '197:/galaxy/server/database/objects/d/9/0/dataset_d903e634-7047-45ab-9df8-5eb22cad9f4a_files:/galaxy/server/database/objects/d/9/0/dataset_d903e634-7047-45ab-9df8-5eb22cad9f4a.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:31:04,079 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (187) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/187/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/187/galaxy_187.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:31:06,064 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 184 finished +galaxy.jobs.runners DEBUG 2024-12-30 01:31:06,165 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 185 finished +galaxy.model.metadata DEBUG 2024-12-30 01:31:06,186 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 194 +galaxy.jobs INFO 2024-12-30 01:31:06,241 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 184 in /galaxy/server/database/jobs_directory/000/184 +galaxy.model.metadata DEBUG 2024-12-30 01:31:06,264 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 195 +galaxy.jobs.runners DEBUG 2024-12-30 01:31:06,283 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 186 finished +galaxy.jobs INFO 2024-12-30 01:31:06,314 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 185 in /galaxy/server/database/jobs_directory/000/185 +galaxy.jobs DEBUG 2024-12-30 01:31:06,355 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 184 executed (259.350 ms) +galaxy.model.metadata DEBUG 2024-12-30 01:31:06,386 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 196 +galaxy.jobs DEBUG 2024-12-30 01:31:06,430 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 185 executed (222.641 ms) +galaxy.jobs INFO 2024-12-30 01:31:06,435 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 186 in /galaxy/server/database/jobs_directory/000/186 +galaxy.jobs DEBUG 2024-12-30 01:31:06,506 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 186 executed (182.164 ms) +galaxy.jobs.runners DEBUG 2024-12-30 01:31:13,621 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 187: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:31:18,887 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 187 finished +galaxy.model.metadata DEBUG 2024-12-30 01:31:18,953 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 197 +galaxy.jobs INFO 2024-12-30 01:31:18,998 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 187 in /galaxy/server/database/jobs_directory/000/187 +galaxy.jobs DEBUG 2024-12-30 01:31:19,060 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 187 executed (142.313 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:31:19,871 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 188 +tpv.core.entities DEBUG 2024-12-30 01:31:19,915 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/.*, abstract=False, cores=1, mem=4, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:31:19,916 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (188) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:31:19,922 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (188) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:31:19,943 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (188) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:31:19,965 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (188) Working directory for job is: /galaxy/server/database/jobs_directory/000/188 +galaxy.jobs.runners DEBUG 2024-12-30 01:31:19,973 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [188] queued (50.176 ms) +galaxy.jobs.handler INFO 2024-12-30 01:31:19,977 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (188) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:31:19,982 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 188 +galaxy.jobs DEBUG 2024-12-30 01:31:20,080 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [188] prepared (74.708 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:31:20,080 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:31:20,080 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.58.1+galaxy0: mulled-v2-3d571fed05a48eb8af17dbc6c8ed632143702ac1:c5763bb5f3402fc75fc6c0fa6c38d545d78e0e67 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:31:20,104 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-3d571fed05a48eb8af17dbc6c8ed632143702ac1:c5763bb5f3402fc75fc6c0fa6c38d545d78e0e67-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:31:20,129 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/188/tool_script.sh] for tool command [echo $(R --version | grep version | grep -v GNU)", limma version" $(R --vanilla --slave -e "library(limma); cat(sessionInfo()\$otherPkgs\$limma\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", edgeR version" $(R --vanilla --slave -e "library(edgeR); cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", statmod version" $(R --vanilla --slave -e "library(statmod); cat(sessionInfo()\$otherPkgs\$statmod\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", scales version" $(R --vanilla --slave -e "library(scales); cat(sessionInfo()\$otherPkgs\$scales\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", rjson version" $(R --vanilla --slave -e "library(rjson); cat(sessionInfo()\$otherPkgs\$rjson\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", getopt version" $(R --vanilla --slave -e "library(getopt); cat(sessionInfo()\$otherPkgs\$getopt\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", gplots version" $(R --vanilla --slave -e "library(gplots); cat(sessionInfo()\$otherPkgs\$gplots\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", Glimma version" $(R --vanilla --slave -e "library(Glimma); cat(sessionInfo()\$otherPkgs\$Glimma\$Version)" 2> /dev/null | grep -v -i "WARNING: ") > /galaxy/server/database/jobs_directory/000/188/outputs/COMMAND_VERSION 2>&1; +Rscript '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/119b069fc845/limma_voom/limma_voom.R' -R '/galaxy/server/database/objects/5/f/b/dataset_5fb6d6c2-6094-482a-b760-4ea34f11fc75.dat' -o '/galaxy/server/database/objects/5/f/b/dataset_5fb6d6c2-6094-482a-b760-4ea34f11fc75_files' -m '/galaxy/server/database/objects/d/9/0/dataset_d903e634-7047-45ab-9df8-5eb22cad9f4a.dat' -i 'Genotype::Mut,Mut,Mut,WT,WT,WT' -D 'Mut-WT' -P i -l '0.0' -p '0.05' -d 'BH' -G '6' -t 3.0 -n 'TMM' -b && mkdir ./output_dir && cp '/galaxy/server/database/objects/5/f/b/dataset_5fb6d6c2-6094-482a-b760-4ea34f11fc75_files'/*tsv output_dir/ && cp -r ./glimma* '/galaxy/server/database/objects/5/f/b/dataset_5fb6d6c2-6094-482a-b760-4ea34f11fc75_files'] +galaxy.jobs.runners DEBUG 2024-12-30 01:31:20,146 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (188) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/188/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/188/galaxy_188.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:31:20,161 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:31:20,161 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.58.1+galaxy0: mulled-v2-3d571fed05a48eb8af17dbc6c8ed632143702ac1:c5763bb5f3402fc75fc6c0fa6c38d545d78e0e67 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:31:20,184 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-3d571fed05a48eb8af17dbc6c8ed632143702ac1:c5763bb5f3402fc75fc6c0fa6c38d545d78e0e67-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 01:31:45,139 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 188: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:31:50,490 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 188 finished +galaxy.model.store.discover DEBUG 2024-12-30 01:31:50,562 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (188) Created dynamic collection dataset for path [/galaxy/server/database/jobs_directory/000/188/working/output_dir/limma-trend_Mut-WT.tsv] with element identifier [limma-trend_Mut-WT] for output [outTables] (5.510 ms) +galaxy.model.store.discover DEBUG 2024-12-30 01:31:50,581 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (188) Add dynamic collection datasets to history for output [outTables] (17.964 ms) +galaxy.model.metadata DEBUG 2024-12-30 01:31:50,613 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 198 +galaxy.jobs INFO 2024-12-30 01:31:50,668 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 188 in /galaxy/server/database/jobs_directory/000/188 +galaxy.objectstore CRITICAL 2024-12-30 01:31:50,738 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] None delete error [Errno 13] Permission denied: 'MDS-Plot.html' +galaxy.jobs DEBUG 2024-12-30 01:31:50,738 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 188 executed (213.970 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:31:52,732 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 190, 189 +tpv.core.entities DEBUG 2024-12-30 01:31:52,773 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:31:52,774 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (189) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:31:52,779 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (189) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:31:52,796 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (189) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:31:52,813 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (189) Working directory for job is: /galaxy/server/database/jobs_directory/000/189 +galaxy.jobs.runners DEBUG 2024-12-30 01:31:52,820 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [189] queued (40.874 ms) +galaxy.jobs.handler INFO 2024-12-30 01:31:52,823 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (189) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:31:52,829 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 189 +tpv.core.entities DEBUG 2024-12-30 01:31:52,843 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:31:52,843 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (190) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:31:52,851 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (190) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:31:52,871 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (190) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:31:52,905 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (190) Working directory for job is: /galaxy/server/database/jobs_directory/000/190 +galaxy.jobs.runners DEBUG 2024-12-30 01:31:52,914 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [190] queued (62.431 ms) +galaxy.jobs.handler INFO 2024-12-30 01:31:52,918 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (190) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:31:52,924 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 190 +galaxy.jobs DEBUG 2024-12-30 01:31:52,986 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [189] prepared (131.783 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:31:53,020 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/189/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/189/registry.xml' '/galaxy/server/database/jobs_directory/000/189/upload_params.json' '200:/galaxy/server/database/objects/2/c/b/dataset_2cb770f2-6d4d-4ba6-910b-c692bc348e64_files:/galaxy/server/database/objects/2/c/b/dataset_2cb770f2-6d4d-4ba6-910b-c692bc348e64.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:31:53,057 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (189) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/189/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/189/galaxy_189.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-12-30 01:31:53,081 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [190] prepared (130.467 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:31:53,109 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/190/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/190/registry.xml' '/galaxy/server/database/jobs_directory/000/190/upload_params.json' '201:/galaxy/server/database/objects/5/3/8/dataset_53890e8f-2ca0-443f-b576-be0255b29fd3_files:/galaxy/server/database/objects/5/3/8/dataset_53890e8f-2ca0-443f-b576-be0255b29fd3.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:31:53,127 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (190) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/190/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/190/galaxy_190.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:32:01,506 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 190: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:32:02,619 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 189: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:32:07,071 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 190 finished +galaxy.model.metadata DEBUG 2024-12-30 01:32:07,144 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 201 +galaxy.jobs INFO 2024-12-30 01:32:07,189 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 190 in /galaxy/server/database/jobs_directory/000/190 +galaxy.jobs DEBUG 2024-12-30 01:32:07,255 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 190 executed (148.028 ms) +galaxy.jobs.runners DEBUG 2024-12-30 01:32:08,063 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 189 finished +galaxy.model.metadata DEBUG 2024-12-30 01:32:08,128 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 200 +galaxy.jobs INFO 2024-12-30 01:32:08,169 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 189 in /galaxy/server/database/jobs_directory/000/189 +galaxy.jobs DEBUG 2024-12-30 01:32:08,233 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 189 executed (137.220 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:32:09,310 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 191 +tpv.core.entities DEBUG 2024-12-30 01:32:09,358 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/.*, abstract=False, cores=1, mem=4, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:32:09,359 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (191) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:32:09,365 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (191) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:32:09,386 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (191) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:32:09,412 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (191) Working directory for job is: /galaxy/server/database/jobs_directory/000/191 +galaxy.jobs.runners DEBUG 2024-12-30 01:32:09,422 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [191] queued (56.560 ms) +galaxy.jobs.handler INFO 2024-12-30 01:32:09,425 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (191) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:32:09,430 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 191 +galaxy.jobs DEBUG 2024-12-30 01:32:09,540 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [191] prepared (87.022 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:32:09,540 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:32:09,540 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.58.1+galaxy0: mulled-v2-3d571fed05a48eb8af17dbc6c8ed632143702ac1:c5763bb5f3402fc75fc6c0fa6c38d545d78e0e67 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:32:09,734 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-3d571fed05a48eb8af17dbc6c8ed632143702ac1:c5763bb5f3402fc75fc6c0fa6c38d545d78e0e67-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:32:09,758 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/191/tool_script.sh] for tool command [echo $(R --version | grep version | grep -v GNU)", limma version" $(R --vanilla --slave -e "library(limma); cat(sessionInfo()\$otherPkgs\$limma\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", edgeR version" $(R --vanilla --slave -e "library(edgeR); cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", statmod version" $(R --vanilla --slave -e "library(statmod); cat(sessionInfo()\$otherPkgs\$statmod\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", scales version" $(R --vanilla --slave -e "library(scales); cat(sessionInfo()\$otherPkgs\$scales\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", rjson version" $(R --vanilla --slave -e "library(rjson); cat(sessionInfo()\$otherPkgs\$rjson\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", getopt version" $(R --vanilla --slave -e "library(getopt); cat(sessionInfo()\$otherPkgs\$getopt\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", gplots version" $(R --vanilla --slave -e "library(gplots); cat(sessionInfo()\$otherPkgs\$gplots\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", Glimma version" $(R --vanilla --slave -e "library(Glimma); cat(sessionInfo()\$otherPkgs\$Glimma\$Version)" 2> /dev/null | grep -v -i "WARNING: ") > /galaxy/server/database/jobs_directory/000/191/outputs/COMMAND_VERSION 2>&1; +Rscript '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/119b069fc845/limma_voom/limma_voom.R' -R '/galaxy/server/database/objects/7/0/d/dataset_70db7eb5-9187-4e8d-976c-2f85b234332d.dat' -o '/galaxy/server/database/objects/7/0/d/dataset_70db7eb5-9187-4e8d-976c-2f85b234332d_files' -m '/galaxy/server/database/objects/2/c/b/dataset_2cb770f2-6d4d-4ba6-910b-c692bc348e64.dat' -i 'Genotype::Mut,Mut,Mut,WT,WT,WT' -a '/galaxy/server/database/objects/5/3/8/dataset_53890e8f-2ca0-443f-b576-be0255b29fd3.dat' -D 'Mut-WT' -P i -l '0.0' -p '0.05' -d 'BH' -G '6' -t 3.0 -n 'TMM' -b && mkdir ./output_dir && cp '/galaxy/server/database/objects/7/0/d/dataset_70db7eb5-9187-4e8d-976c-2f85b234332d_files'/*tsv output_dir/ && cp -r ./glimma* '/galaxy/server/database/objects/7/0/d/dataset_70db7eb5-9187-4e8d-976c-2f85b234332d_files'] +galaxy.jobs.runners DEBUG 2024-12-30 01:32:09,774 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (191) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/191/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/191/galaxy_191.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:32:09,787 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:32:09,788 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.58.1+galaxy0: mulled-v2-3d571fed05a48eb8af17dbc6c8ed632143702ac1:c5763bb5f3402fc75fc6c0fa6c38d545d78e0e67 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:32:09,808 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-3d571fed05a48eb8af17dbc6c8ed632143702ac1:c5763bb5f3402fc75fc6c0fa6c38d545d78e0e67-0,type=docker]] +galaxy.jobs.runners.kubernetes ERROR 2024-12-30 01:32:34,891 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Could not clean up k8s batch job. Ignoring... +Traceback (most recent call last): + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/http.py", line 437, in raise_for_status + resp.raise_for_status() + File "/galaxy/server/.venv/lib/python3.10/site-packages/requests/models.py", line 1021, in raise_for_status + raise HTTPError(http_error_msg, response=self) +requests.exceptions.HTTPError: 409 Client Error: Conflict for url: https://10.107.32.1:443/apis/batch/v1/namespaces/prod-24-12-30-00-37-1/jobs/gxy-dmg8h + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 817, in _handle_job_failure + self.__cleanup_k8s_job(job) + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 824, in __cleanup_k8s_job + delete_job(job, k8s_cleanup_job) + File "/galaxy/server/lib/galaxy/jobs/runners/util/pykube_util.py", line 107, in delete_job + job.scale(replicas=0) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/mixins.py", line 30, in scale + self.update() + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 165, in update + self.patch(self.obj, subresource=subresource) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 157, in patch + self.api.raise_for_status(r) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/http.py", line 444, in raise_for_status + raise HTTPError(resp.status_code, payload["message"]) +pykube.exceptions.HTTPError: Operation cannot be fulfilled on jobs.batch "gxy-dmg8h": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:32:34,942 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (191/gxy-dmg8h) Terminated at user's request +galaxy.objectstore CRITICAL 2024-12-30 01:32:35,074 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] None delete error [Errno 13] Permission denied: 'MD-Plot.html' +galaxy.jobs.handler DEBUG 2024-12-30 01:32:35,998 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 192 +tpv.core.entities DEBUG 2024-12-30 01:32:36,031 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:32:36,032 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (192) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:32:36,037 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (192) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:32:36,054 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (192) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:32:36,069 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (192) Working directory for job is: /galaxy/server/database/jobs_directory/000/192 +galaxy.jobs.runners DEBUG 2024-12-30 01:32:36,076 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [192] queued (39.146 ms) +galaxy.jobs.handler INFO 2024-12-30 01:32:36,080 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (192) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:32:36,084 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 192 +galaxy.jobs DEBUG 2024-12-30 01:32:36,195 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [192] prepared (92.011 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:32:36,216 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/192/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/192/registry.xml' '/galaxy/server/database/jobs_directory/000/192/upload_params.json' '203:/galaxy/server/database/objects/8/7/5/dataset_87513d1a-cf0f-4f36-812c-9e092872a3ff_files:/galaxy/server/database/objects/8/7/5/dataset_87513d1a-cf0f-4f36-812c-9e092872a3ff.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:32:36,229 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (192) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/192/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/192/galaxy_192.ec; sh -c "exit $return_code" +galaxy.jobs.handler DEBUG 2024-12-30 01:32:37,082 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 193 +tpv.core.entities DEBUG 2024-12-30 01:32:37,119 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:32:37,119 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (193) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:32:37,125 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (193) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:32:37,145 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (193) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:32:37,166 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (193) Working directory for job is: /galaxy/server/database/jobs_directory/000/193 +galaxy.jobs.runners DEBUG 2024-12-30 01:32:37,175 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [193] queued (49.399 ms) +galaxy.jobs.handler INFO 2024-12-30 01:32:37,179 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (193) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:32:37,184 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 193 +galaxy.jobs DEBUG 2024-12-30 01:32:37,310 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [193] prepared (103.748 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:32:37,334 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/193/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/193/registry.xml' '/galaxy/server/database/jobs_directory/000/193/upload_params.json' '204:/galaxy/server/database/objects/8/7/1/dataset_871065b7-5f90-4e95-9410-35ab7f72544d_files:/galaxy/server/database/objects/8/7/1/dataset_871065b7-5f90-4e95-9410-35ab7f72544d.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:32:37,347 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (193) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/193/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/193/galaxy_193.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:32:45,490 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 193: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:32:45,513 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 192: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:32:51,023 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 192 finished +galaxy.jobs.runners DEBUG 2024-12-30 01:32:51,051 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 193 finished +galaxy.model.metadata DEBUG 2024-12-30 01:32:51,096 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 203 +galaxy.model.metadata DEBUG 2024-12-30 01:32:51,125 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 204 +galaxy.jobs INFO 2024-12-30 01:32:51,157 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 192 in /galaxy/server/database/jobs_directory/000/192 +galaxy.jobs INFO 2024-12-30 01:32:51,182 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 193 in /galaxy/server/database/jobs_directory/000/193 +galaxy.jobs DEBUG 2024-12-30 01:32:51,226 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 192 executed (170.303 ms) +galaxy.jobs DEBUG 2024-12-30 01:32:51,252 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 193 executed (169.914 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:32:51,494 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 194 +tpv.core.entities DEBUG 2024-12-30 01:32:51,532 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/.*, abstract=False, cores=1, mem=4, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:32:51,532 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (194) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:32:51,537 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (194) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:32:51,554 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (194) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:32:51,577 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (194) Working directory for job is: /galaxy/server/database/jobs_directory/000/194 +galaxy.jobs.runners DEBUG 2024-12-30 01:32:51,586 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [194] queued (49.656 ms) +galaxy.jobs.handler INFO 2024-12-30 01:32:51,590 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (194) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:32:51,595 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 194 +galaxy.jobs DEBUG 2024-12-30 01:32:51,703 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [194] prepared (86.847 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:32:51,704 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:32:51,704 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.58.1+galaxy0: mulled-v2-3d571fed05a48eb8af17dbc6c8ed632143702ac1:c5763bb5f3402fc75fc6c0fa6c38d545d78e0e67 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:32:51,727 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-3d571fed05a48eb8af17dbc6c8ed632143702ac1:c5763bb5f3402fc75fc6c0fa6c38d545d78e0e67-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:32:51,752 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/194/tool_script.sh] for tool command [echo $(R --version | grep version | grep -v GNU)", limma version" $(R --vanilla --slave -e "library(limma); cat(sessionInfo()\$otherPkgs\$limma\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", edgeR version" $(R --vanilla --slave -e "library(edgeR); cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", statmod version" $(R --vanilla --slave -e "library(statmod); cat(sessionInfo()\$otherPkgs\$statmod\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", scales version" $(R --vanilla --slave -e "library(scales); cat(sessionInfo()\$otherPkgs\$scales\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", rjson version" $(R --vanilla --slave -e "library(rjson); cat(sessionInfo()\$otherPkgs\$rjson\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", getopt version" $(R --vanilla --slave -e "library(getopt); cat(sessionInfo()\$otherPkgs\$getopt\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", gplots version" $(R --vanilla --slave -e "library(gplots); cat(sessionInfo()\$otherPkgs\$gplots\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", Glimma version" $(R --vanilla --slave -e "library(Glimma); cat(sessionInfo()\$otherPkgs\$Glimma\$Version)" 2> /dev/null | grep -v -i "WARNING: ") > /galaxy/server/database/jobs_directory/000/194/outputs/COMMAND_VERSION 2>&1; +Rscript '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/119b069fc845/limma_voom/limma_voom.R' -R '/galaxy/server/database/objects/2/5/f/dataset_25f4bb38-6005-411c-842c-9062d89b9226.dat' -o '/galaxy/server/database/objects/2/5/f/dataset_25f4bb38-6005-411c-842c-9062d89b9226_files' -m '/galaxy/server/database/objects/8/7/5/dataset_87513d1a-cf0f-4f36-812c-9e092872a3ff.dat' -i 'Group::2,2,2,1,1,1' -a '/galaxy/server/database/objects/8/7/1/dataset_871065b7-5f90-4e95-9410-35ab7f72544d.dat' -D '2-1' -z '10' -s '3' -P i -x -l '0.0' -p '0.05' -d 'BH' -G '6' -n 'TMM' -b && mkdir ./output_dir && cp '/galaxy/server/database/objects/2/5/f/dataset_25f4bb38-6005-411c-842c-9062d89b9226_files'/*tsv output_dir/ && cp -r ./glimma* '/galaxy/server/database/objects/2/5/f/dataset_25f4bb38-6005-411c-842c-9062d89b9226_files' && cp '/galaxy/server/database/objects/2/5/f/dataset_25f4bb38-6005-411c-842c-9062d89b9226_files'/*counts output_dir/] +galaxy.jobs.runners DEBUG 2024-12-30 01:32:51,778 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (194) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/194/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/194/galaxy_194.ec; +if [ -f "/galaxy/server/database/jobs_directory/000/194/working/output_dir/"*"_normcounts" ] ; then cp "/galaxy/server/database/jobs_directory/000/194/working/output_dir/"*"_normcounts" "/galaxy/server/database/objects/a/b/5/dataset_ab5af91c-9901-4a9e-938b-3495c4b92588.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:32:51,792 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:32:51,792 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.58.1+galaxy0: mulled-v2-3d571fed05a48eb8af17dbc6c8ed632143702ac1:c5763bb5f3402fc75fc6c0fa6c38d545d78e0e67 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:32:51,812 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-3d571fed05a48eb8af17dbc6c8ed632143702ac1:c5763bb5f3402fc75fc6c0fa6c38d545d78e0e67-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 01:33:16,028 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 194: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:33:21,038 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 194 finished +galaxy.model.store.discover DEBUG 2024-12-30 01:33:21,104 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (194) Created dynamic collection dataset for path [/galaxy/server/database/jobs_directory/000/194/working/output_dir/limma-voom_X2-X1.tsv] with element identifier [limma-voom_X2-X1] for output [outTables] (8.695 ms) +galaxy.model.store.discover DEBUG 2024-12-30 01:33:21,122 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (194) Add dynamic collection datasets to history for output [outTables] (17.614 ms) +galaxy.model.metadata DEBUG 2024-12-30 01:33:21,184 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 205 +galaxy.model.metadata DEBUG 2024-12-30 01:33:21,195 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 206 +galaxy.util WARNING 2024-12-30 01:33:21,217 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/a/b/5/dataset_ab5af91c-9901-4a9e-938b-3495c4b92588.dat, group remains grp.struct_group(gr_name='nogroup', gr_passwd='x', gr_gid=65534, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/a/b/5/dataset_ab5af91c-9901-4a9e-938b-3495c4b92588.dat' +galaxy.jobs INFO 2024-12-30 01:33:21,271 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 194 in /galaxy/server/database/jobs_directory/000/194 +galaxy.objectstore CRITICAL 2024-12-30 01:33:21,336 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] None delete error [Errno 13] Permission denied: 'XY-Plot.html' +galaxy.jobs DEBUG 2024-12-30 01:33:21,337 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 194 executed (272.675 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:33:23,318 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 196, 195 +tpv.core.entities DEBUG 2024-12-30 01:33:23,356 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:33:23,356 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (195) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:33:23,364 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (195) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:33:23,382 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (195) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:33:23,403 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (195) Working directory for job is: /galaxy/server/database/jobs_directory/000/195 +galaxy.jobs.runners DEBUG 2024-12-30 01:33:23,410 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [195] queued (45.822 ms) +galaxy.jobs.handler INFO 2024-12-30 01:33:23,414 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (195) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:33:23,418 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 195 +tpv.core.entities DEBUG 2024-12-30 01:33:23,430 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:33:23,431 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (196) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:33:23,437 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (196) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:33:23,456 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (196) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:33:23,488 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (196) Working directory for job is: /galaxy/server/database/jobs_directory/000/196 +galaxy.jobs.runners DEBUG 2024-12-30 01:33:23,497 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [196] queued (59.338 ms) +galaxy.jobs.handler INFO 2024-12-30 01:33:23,502 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (196) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:33:23,509 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 196 +galaxy.jobs DEBUG 2024-12-30 01:33:23,558 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [195] prepared (113.383 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:33:23,592 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/195/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/195/registry.xml' '/galaxy/server/database/jobs_directory/000/195/upload_params.json' '208:/galaxy/server/database/objects/0/8/6/dataset_086eca7a-bc0a-4ce2-8bc5-d52353a59deb_files:/galaxy/server/database/objects/0/8/6/dataset_086eca7a-bc0a-4ce2-8bc5-d52353a59deb.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:33:23,609 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (195) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/195/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/195/galaxy_195.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-12-30 01:33:23,650 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [196] prepared (113.970 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:33:23,678 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/196/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/196/registry.xml' '/galaxy/server/database/jobs_directory/000/196/upload_params.json' '209:/galaxy/server/database/objects/3/9/7/dataset_39768aaa-5ccf-4ebe-858b-4c02f167040d_files:/galaxy/server/database/objects/3/9/7/dataset_39768aaa-5ccf-4ebe-858b-4c02f167040d.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:33:23,694 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (196) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/196/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/196/galaxy_196.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:33:33,444 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 196: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:33:33,461 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 195: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:33:39,107 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 196 finished +galaxy.jobs.runners DEBUG 2024-12-30 01:33:39,135 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 195 finished +galaxy.model.metadata DEBUG 2024-12-30 01:33:39,188 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 209 +galaxy.model.metadata DEBUG 2024-12-30 01:33:39,219 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 208 +galaxy.jobs INFO 2024-12-30 01:33:39,241 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 196 in /galaxy/server/database/jobs_directory/000/196 +galaxy.jobs INFO 2024-12-30 01:33:39,260 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 195 in /galaxy/server/database/jobs_directory/000/195 +galaxy.jobs DEBUG 2024-12-30 01:33:39,312 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 196 executed (174.535 ms) +galaxy.jobs DEBUG 2024-12-30 01:33:39,335 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 195 executed (162.609 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:33:39,946 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 197 +tpv.core.entities DEBUG 2024-12-30 01:33:39,987 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/.*, abstract=False, cores=1, mem=4, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:33:39,987 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (197) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:33:39,993 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (197) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:33:40,014 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (197) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:33:40,036 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (197) Working directory for job is: /galaxy/server/database/jobs_directory/000/197 +galaxy.jobs.runners DEBUG 2024-12-30 01:33:40,047 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [197] queued (54.100 ms) +galaxy.jobs.handler INFO 2024-12-30 01:33:40,051 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (197) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:33:40,056 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 197 +galaxy.jobs DEBUG 2024-12-30 01:33:40,163 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [197] prepared (84.185 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:33:40,163 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:33:40,164 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.58.1+galaxy0: mulled-v2-3d571fed05a48eb8af17dbc6c8ed632143702ac1:c5763bb5f3402fc75fc6c0fa6c38d545d78e0e67 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:33:40,189 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-3d571fed05a48eb8af17dbc6c8ed632143702ac1:c5763bb5f3402fc75fc6c0fa6c38d545d78e0e67-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:33:40,216 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/197/tool_script.sh] for tool command [echo $(R --version | grep version | grep -v GNU)", limma version" $(R --vanilla --slave -e "library(limma); cat(sessionInfo()\$otherPkgs\$limma\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", edgeR version" $(R --vanilla --slave -e "library(edgeR); cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", statmod version" $(R --vanilla --slave -e "library(statmod); cat(sessionInfo()\$otherPkgs\$statmod\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", scales version" $(R --vanilla --slave -e "library(scales); cat(sessionInfo()\$otherPkgs\$scales\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", rjson version" $(R --vanilla --slave -e "library(rjson); cat(sessionInfo()\$otherPkgs\$rjson\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", getopt version" $(R --vanilla --slave -e "library(getopt); cat(sessionInfo()\$otherPkgs\$getopt\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", gplots version" $(R --vanilla --slave -e "library(gplots); cat(sessionInfo()\$otherPkgs\$gplots\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", Glimma version" $(R --vanilla --slave -e "library(Glimma); cat(sessionInfo()\$otherPkgs\$Glimma\$Version)" 2> /dev/null | grep -v -i "WARNING: ") > /galaxy/server/database/jobs_directory/000/197/outputs/COMMAND_VERSION 2>&1; +Rscript '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/119b069fc845/limma_voom/limma_voom.R' -R '/galaxy/server/database/objects/9/5/c/dataset_95ca4a1c-4321-4b3d-ba7c-022a6225ae4a.dat' -o '/galaxy/server/database/objects/9/5/c/dataset_95ca4a1c-4321-4b3d-ba7c-022a6225ae4a_files' -m '/galaxy/server/database/objects/0/8/6/dataset_086eca7a-bc0a-4ce2-8bc5-d52353a59deb.dat' -i 'Genotype::Mut,Mut,Mut,WT,WT,WT' -C '/galaxy/server/database/objects/3/9/7/dataset_39768aaa-5ccf-4ebe-858b-4c02f167040d.dat' -P i -l '0.0' -p '0.05' -d 'BH' -G '6' -n 'TMM' -b && mkdir ./output_dir && cp '/galaxy/server/database/objects/9/5/c/dataset_95ca4a1c-4321-4b3d-ba7c-022a6225ae4a_files'/*tsv output_dir/ && cp -r ./glimma* '/galaxy/server/database/objects/9/5/c/dataset_95ca4a1c-4321-4b3d-ba7c-022a6225ae4a_files'] +galaxy.jobs.runners DEBUG 2024-12-30 01:33:40,235 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (197) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/197/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/197/galaxy_197.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:33:40,251 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:33:40,251 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.58.1+galaxy0: mulled-v2-3d571fed05a48eb8af17dbc6c8ed632143702ac1:c5763bb5f3402fc75fc6c0fa6c38d545d78e0e67 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:33:40,274 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-3d571fed05a48eb8af17dbc6c8ed632143702ac1:c5763bb5f3402fc75fc6c0fa6c38d545d78e0e67-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 01:34:04,958 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 197: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:34:10,164 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 197 finished +galaxy.model.store.discover DEBUG 2024-12-30 01:34:10,238 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (197) Created dynamic collection dataset for path [/galaxy/server/database/jobs_directory/000/197/working/output_dir/limma-voom_Mut-WT-WT-Mut.tsv] with element identifier [limma-voom_Mut-WT-WT-Mut] for output [outTables] (7.688 ms) +galaxy.model.store.discover DEBUG 2024-12-30 01:34:10,238 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (197) Created dynamic collection dataset for path [/galaxy/server/database/jobs_directory/000/197/working/output_dir/limma-voom_Mut-WT.tsv] with element identifier [limma-voom_Mut-WT] for output [outTables] (0.754 ms) +galaxy.model.store.discover DEBUG 2024-12-30 01:34:10,239 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (197) Created dynamic collection dataset for path [/galaxy/server/database/jobs_directory/000/197/working/output_dir/limma-voom_WT-Mut.tsv] with element identifier [limma-voom_WT-Mut] for output [outTables] (0.576 ms) +galaxy.model.store.discover DEBUG 2024-12-30 01:34:10,279 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (197) Add dynamic collection datasets to history for output [outTables] (39.115 ms) +galaxy.model.metadata DEBUG 2024-12-30 01:34:10,331 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 210 +galaxy.jobs INFO 2024-12-30 01:34:10,395 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 197 in /galaxy/server/database/jobs_directory/000/197 +galaxy.objectstore CRITICAL 2024-12-30 01:34:10,450 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] None delete error [Errno 13] Permission denied: 'MDS-Plot.html' +galaxy.jobs DEBUG 2024-12-30 01:34:10,450 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 197 executed (253.694 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:34:12,834 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 198 +tpv.core.entities DEBUG 2024-12-30 01:34:12,870 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:34:12,870 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (198) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:34:12,874 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (198) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:34:12,892 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (198) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:34:12,918 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (198) Working directory for job is: /galaxy/server/database/jobs_directory/000/198 +galaxy.jobs.runners DEBUG 2024-12-30 01:34:12,926 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [198] queued (51.143 ms) +galaxy.jobs.handler INFO 2024-12-30 01:34:12,931 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (198) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:34:12,936 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 198 +galaxy.jobs DEBUG 2024-12-30 01:34:13,063 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [198] prepared (104.689 ms) +galaxy.jobs.command_factory INFO 2024-12-30 01:34:13,090 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/198/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/198/registry.xml' '/galaxy/server/database/jobs_directory/000/198/upload_params.json' '214:/galaxy/server/database/objects/2/0/3/dataset_2036bd5b-de43-4d9b-a043-e864c269b8f7_files:/galaxy/server/database/objects/2/0/3/dataset_2036bd5b-de43-4d9b-a043-e864c269b8f7.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:34:13,108 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (198) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/198/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/198/galaxy_198.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-12-30 01:34:22,134 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 198: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:34:27,519 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 198 finished +galaxy.model.metadata DEBUG 2024-12-30 01:34:27,597 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 214 +galaxy.jobs INFO 2024-12-30 01:34:27,643 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 198 in /galaxy/server/database/jobs_directory/000/198 +galaxy.jobs DEBUG 2024-12-30 01:34:27,705 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 198 executed (153.544 ms) +galaxy.jobs.handler DEBUG 2024-12-30 01:34:28,371 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 199 +tpv.core.entities DEBUG 2024-12-30 01:34:28,412 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-12-30 01:34:28,413 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (199) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-12-30 01:34:28,418 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (199) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-12-30 01:34:28,436 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (199) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-12-30 01:34:28,456 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (199) Working directory for job is: /galaxy/server/database/jobs_directory/000/199 +galaxy.jobs.runners DEBUG 2024-12-30 01:34:28,466 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [199] queued (47.204 ms) +galaxy.jobs.handler INFO 2024-12-30 01:34:28,470 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (199) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-12-30 01:34:28,476 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 199 +galaxy.jobs DEBUG 2024-12-30 01:34:28,570 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [199] prepared (73.757 ms) +galaxy.tool_util.deps.containers INFO 2024-12-30 01:34:28,570 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:34:28,571 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0rc1+galaxy3: mulled-v2-94c12e128fff0e4d1d34a43f778cdcdbfaba4960:f01f2bb89bd4c09e7ac156d4371df2eb495534e5 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:34:28,901 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-94c12e128fff0e4d1d34a43f778cdcdbfaba4960:f01f2bb89bd4c09e7ac156d4371df2eb495534e5-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-12-30 01:34:28,927 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/199/tool_script.sh] for tool command [delta-filter -m -i '0.0' -l '0' -q -u '0.0' -o '100.0' '/galaxy/server/database/objects/2/0/3/dataset_2036bd5b-de43-4d9b-a043-e864c269b8f7.dat' > '/galaxy/server/database/objects/d/7/0/dataset_d709912c-4428-4d00-ab3c-7f8af360b073.dat'] +galaxy.jobs.runners DEBUG 2024-12-30 01:34:28,944 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (199) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/199/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/199/galaxy_199.ec; +if [ -f "/galaxy/server/database/jobs_directory/000/199/working/delta-filter.txt" ] ; then cp "/galaxy/server/database/jobs_directory/000/199/working/delta-filter.txt" "/galaxy/server/database/objects/d/7/0/dataset_d709912c-4428-4d00-ab3c-7f8af360b073.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-12-30 01:34:28,957 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-12-30 01:34:28,958 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0rc1+galaxy3: mulled-v2-94c12e128fff0e4d1d34a43f778cdcdbfaba4960:f01f2bb89bd4c09e7ac156d4371df2eb495534e5 +galaxy.tool_util.deps.containers INFO 2024-12-30 01:34:28,978 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-94c12e128fff0e4d1d34a43f778cdcdbfaba4960:f01f2bb89bd4c09e7ac156d4371df2eb495534e5-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-12-30 01:34:40,406 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 199: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-12-30 01:34:45,583 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 199 finished +galaxy.model.metadata DEBUG 2024-12-30 01:34:45,689 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 215 +galaxy.jobs INFO 2024-12-30 01:34:45,760 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 199 in /galaxy/server/database/jobs_directory/000/199 +galaxy.jobs DEBUG 2024-12-30 01:34:45,818 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 199 executed (167.134 ms) diff --git a/reports/anvil-production/tool-tests/prod-24-12-30-00-37-1/jobs.txt b/reports/anvil-production/tool-tests/prod-24-12-30-00-37-1/jobs.txt new file mode 100644 index 000000000..d1a4d4845 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-12-30-00-37-1/jobs.txt @@ -0,0 +1,199 @@ +87e45c46f7283ad0 ok 2024-12-30T01:34:45.765466 toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0rc1+galaxy3 +365c84298ee31b03 ok 2024-12-30T01:34:27.646905 upload1 +935606a73f55d869 ok 2024-12-30T01:34:10.398816 toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.58.1+galaxy0 +4476541a8ae8e89b ok 2024-12-30T01:33:39.264771 upload1 +9100e72d6759a2a1 ok 2024-12-30T01:33:39.245395 upload1 +61327fb60674d557 ok 2024-12-30T01:33:21.276465 toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.58.1+galaxy0 +fd99a2ed81aad668 ok 2024-12-30T01:32:51.186136 upload1 +0d0f164547f8c84e ok 2024-12-30T01:32:51.161633 upload1 +f2cc7012ce9ef9eb error 2024-12-30T01:32:35.024142 toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.58.1+galaxy0 +408a2bfc1af55d9e ok 2024-12-30T01:32:08.172640 upload1 +2a3b1def3dc5d6e0 ok 2024-12-30T01:32:07.194017 upload1 +1e92894b0aa06402 ok 2024-12-30T01:31:50.672234 toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.58.1+galaxy0 +a5874df6dbd01444 ok 2024-12-30T01:31:19.002532 upload1 +0a0e634990133030 ok 2024-12-30T01:31:06.439103 upload1 +a5d60cb032fdc4ef ok 2024-12-30T01:31:06.319025 upload1 +4bee00657e0e71bf ok 2024-12-30T01:31:06.246174 upload1 +e644d97e8e35fce2 ok 2024-12-30T01:31:03.560015 upload1 +de5fe91328addd71 ok 2024-12-30T01:30:55.039688 upload1 +c81c340ac1b1db4a ok 2024-12-30T01:30:54.946606 upload1 +fe862782b9d94df9 ok 2024-12-30T01:30:54.686165 upload1 +6dfd83583e16855b ok 2024-12-30T01:30:51.960090 upload1 +d4289a12a4802052 ok 2024-12-30T01:30:42.944426 upload1 +0b4b4d92232ad17f ok 2024-12-30T01:30:42.898596 upload1 +d88e8580f2de0ee6 ok 2024-12-30T01:30:42.873550 upload1 +02186832019a3f3c ok 2024-12-30T01:30:40.362285 upload1 +bf46a3337c78fbae error 2024-12-30T01:30:29.874464 upload1 +de2a21e9166bfce0 ok 2024-12-30T01:30:16.527272 toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.58.1+galaxy0 +d6ebe976b2aab76e ok 2024-12-30T01:29:46.368279 upload1 +aec302a3294f1532 ok 2024-12-30T01:29:31.208586 toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.58.1+galaxy0 +514b23a59a5aabcf ok 2024-12-30T01:29:00.253636 upload1 +5aa4b71787a9342e ok 2024-12-30T01:29:00.244461 upload1 +85efb25904cc4bd9 ok 2024-12-30T01:28:43.431686 toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.58.1+galaxy0 +d0df8636558cb0d9 ok 2024-12-30T01:28:14.983953 upload1 +51d680a76a4e5d82 ok 2024-12-30T01:28:00.071995 toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.58.1+galaxy0 +3d5138a6b4b0ad06 ok 2024-12-30T01:27:29.390289 upload1 +3cd19557b8337cca ok 2024-12-30T01:27:14.227331 toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.58.1+galaxy0 +8f2b1c61faf29b98 ok 2024-12-30T01:26:43.921344 upload1 +2d818e9b3880a45c ok 2024-12-30T01:26:42.882012 upload1 +4ab292ba862179d8 ok 2024-12-30T01:26:27.280694 toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.58.1+galaxy0 +8e91e8737cee903f ok 2024-12-30T01:25:23.115021 upload1 +5e0a58b814e449e7 ok 2024-12-30T01:25:06.301297 toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.18 +acb31e04834d1552 ok 2024-12-30T01:24:53.719234 upload1 +1a46ae39a1533e33 ok 2024-12-30T01:24:53.712965 upload1 +ef0423079d291afd ok 2024-12-30T01:24:53.620631 upload1 +4f97579405063640 ok 2024-12-30T01:24:35.117005 toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.18 +00205c8c505c46b6 ok 2024-12-30T01:24:23.129753 upload1 +e09d38ac2ec8c55c ok 2024-12-30T01:24:23.126342 upload1 +6b8e6812c494129b ok 2024-12-30T01:24:14.579287 upload1 +ed577906d445815f ok 2024-12-30T01:24:13.487137 upload1 +18d63872b3269485 error 2024-12-30T01:24:07.030917 upload1 +4fafbc5467932c94 ok 2024-12-30T01:23:57.614229 toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.18 +1c85cb4b1429bce5 ok 2024-12-30T01:23:45.224776 upload1 +8bcbbbc7eb8bb479 ok 2024-12-30T01:23:45.178358 upload1 +7a2d1bbf6938011d ok 2024-12-30T01:23:45.042119 upload1 +70f4a40ee2dd73ac ok 2024-12-30T01:23:25.937888 toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.18 +869f33a53e53131b ok 2024-12-30T01:23:07.037888 upload1 +27d38c2acb093f4f ok 2024-12-30T01:23:06.997607 upload1 +0f2a57d83e08c260 ok 2024-12-30T01:22:50.158897 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/3.5.4+galaxy0 +c82bbc66a620ae76 ok 2024-12-30T01:22:21.101767 upload1 +0e19f8b845668869 ok 2024-12-30T01:22:21.033566 upload1 +9fbbcd7e53eeecb6 ok 2024-12-30T01:22:02.222451 toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0 +2549e2abd59b5ab2 ok 2024-12-30T01:21:49.084400 upload1 +30849d827d0b87e9 ok 2024-12-30T01:21:32.849325 toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0 +599abfd6fe8206a3 ok 2024-12-30T01:21:20.731238 upload1 +98ba3f43b2ec1f79 ok 2024-12-30T01:21:04.273182 toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0 +65776e38c288081b ok 2024-12-30T01:20:52.231010 upload1 +5eec17c7711e2db5 ok 2024-12-30T01:20:37.090202 toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0 +92d6b7f9fa68a9ec ok 2024-12-30T01:20:24.738289 upload1 +254e9a522d7e7a58 ok 2024-12-30T01:20:09.945744 toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0 +a6742216c12826b8 ok 2024-12-30T01:19:57.802701 upload1 +7b54e7fe9b136d43 ok 2024-12-30T01:19:42.356857 toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0 +9efbec2a30985c3f ok 2024-12-30T01:19:23.976900 upload1 +798ce302529f6e3f ok 2024-12-30T01:19:08.759922 toolshed.g2.bx.psu.edu/repos/devteam/vcftools_annotate/vcftools_annotate/0.1 +63ec486a59172927 ok 2024-12-30T01:18:52.326464 upload1 +b199453d55d1008b ok 2024-12-30T01:18:36.177580 toolshed.g2.bx.psu.edu/repos/devteam/vcffixup/vcffixup/1.0.0_rc3+galaxy0 +a1103d5912b69db6 ok 2024-12-30T01:18:18.033537 upload1 +9d9743b4b8ce0c75 error 2024-12-30T01:18:02.671700 upload1 +0c18b428e393303f ok 2024-12-30T01:17:53.506739 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4 +3337f974be7abfa8 ok 2024-12-30T01:17:41.375497 upload1 +abb0c83d687376d2 ok 2024-12-30T01:17:25.180920 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4 +ba3d5d7e2e1e072b ok 2024-12-30T01:17:13.079575 upload1 +a31a92347d5b7b07 ok 2024-12-30T01:16:57.934748 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4 +fbf7a30547f983b1 ok 2024-12-30T01:16:46.723857 upload1 +50bc257ec42392c1 ok 2024-12-30T01:16:32.437058 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4 +4e22fed0e573e2bf ok 2024-12-30T01:16:21.621806 upload1 +8aaa620134da4b3f ok 2024-12-30T01:16:21.541283 upload1 +b64308614a80387a ok 2024-12-30T01:16:04.932211 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4 +fa76d05568187d5a ok 2024-12-30T01:15:52.910655 upload1 +b44fb3047a023ae0 ok 2024-12-30T01:15:52.901464 upload1 +5c8707f919a70182 ok 2024-12-30T01:15:36.456881 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4 +6bf55f0095bdcf52 ok 2024-12-30T01:15:24.799369 upload1 +4fa6353e1475b8e8 ok 2024-12-30T01:15:24.514918 upload1 +906a346bd90cbb09 ok 2024-12-30T01:15:08.982763 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4 +4aaa5ab690473dd8 ok 2024-12-30T01:14:56.893146 upload1 +17ae9a3f6937c023 ok 2024-12-30T01:14:56.882911 upload1 +3486ef5567398f96 ok 2024-12-30T01:14:40.198729 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4 +b06c5949985caf75 ok 2024-12-30T01:14:29.265122 upload1 +155a90d52bb4a79c ok 2024-12-30T01:14:29.247053 upload1 +d04284554dc99baa ok 2024-12-30T01:14:28.127734 upload1 +991b6756fcfc001a ok 2024-12-30T01:14:09.141447 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4 +0e40df125b95de6b ok 2024-12-30T01:13:56.169966 upload1 +9f786fde84d3b8dc ok 2024-12-30T01:13:54.518364 upload1 +85a33a94c6429486 ok 2024-12-30T01:13:54.382507 upload1 +6d6dbf16b1195332 ok 2024-12-30T01:13:35.969805 upload1 +1e2ca038c6fae50b error 2024-12-30T01:13:29.734171 upload1 +9765e6866d45e244 ok 2024-12-30T01:13:20.559356 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.15.1+galaxy4 +35dbb8216ed2c60c ok 2024-12-30T01:13:08.792214 upload1 +e49fa79d982a2e0e ok 2024-12-30T01:13:08.736296 upload1 +f9ab8bc17d513f45 ok 2024-12-30T01:12:56.913113 upload1 +8d426062260e5599 error 2024-12-30T01:12:51.637365 upload1 +fccdf7c99d58ccb9 ok 2024-12-30T01:12:41.150408 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.15.1+galaxy4 +ce812daebfa4cb32 ok 2024-12-30T01:12:28.200658 upload1 +121cbf44a773e05b ok 2024-12-30T01:12:21.816230 upload1 +db057033ea142ec9 ok 2024-12-30T01:12:07.545662 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.15.1+galaxy4 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toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3 +c52e9dc71b5d2484 ok 2024-12-30T01:09:30.963808 upload1 +7a82f5a57734dfaa ok 2024-12-30T01:09:15.812245 toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3 +cef1ef233d649e68 ok 2024-12-30T01:09:03.391384 upload1 +844808caf7756563 ok 2024-12-30T01:08:47.149690 toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3 +9b0aace47f069df0 ok 2024-12-30T01:08:36.022798 upload1 +7411613e1a6fc733 ok 2024-12-30T01:08:21.046622 toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3 +87d7d1c2fb9d83f3 ok 2024-12-30T01:08:09.830963 upload1 +aae1891d4b88b804 ok 2024-12-30T01:07:53.201986 toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3 +8764eb2d79202145 ok 2024-12-30T01:07:41.268493 upload1 +3a4309e493a64a5f ok 2024-12-30T01:07:25.039006 toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3 +e3a4941fedae6737 ok 2024-12-30T01:07:12.885116 upload1 +55446d6113bb19bb ok 2024-12-30T01:06:57.718051 toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3 +c74eab4166fbb65c ok 2024-12-30T01:06:46.547156 upload1 +65e560fe91597247 ok 2024-12-30T01:06:30.544421 toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3 +6c57b686e8db6b8e ok 2024-12-30T01:06:18.830982 upload1 +7b986663b792e971 ok 2024-12-30T01:06:17.903592 upload1 +7c12007f05f1af25 ok 2024-12-30T01:06:17.889945 upload1 +d127a80372ea6698 ok 2024-12-30T01:05:58.583185 toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3 +dd71cca156f1390f ok 2024-12-30T01:05:46.767572 upload1 +a12eb6ea508f124b ok 2024-12-30T01:05:46.660222 upload1 +3467a254fce916da ok 2024-12-30T01:05:30.936308 toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3 +724900be56f9469b ok 2024-12-30T01:05:18.135471 upload1 +46173ea66ac5197a ok 2024-12-30T01:05:17.078704 upload1 +8fb60f5115b6f92c ok 2024-12-30T01:05:00.344717 toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3 +9efb84aa16c06c86 ok 2024-12-30T01:04:47.705690 upload1 +afbc9e957401521f ok 2024-12-30T01:04:47.691086 upload1 +627114804621566b ok 2024-12-30T01:04:30.734705 toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3 +a842bb8a80bc64df ok 2024-12-30T01:04:17.929072 upload1 +81557b37ce6f097c ok 2024-12-30T01:04:17.905814 upload1 +11d61bdc0121fdce ok 2024-12-30T01:04:00.497973 toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3 +1716993f2d8bea0f ok 2024-12-30T01:03:47.927181 upload1 +c932bf8ced6c313e error 2024-12-30T01:03:31.288002 upload1 +70c3cb9feabad675 ok 2024-12-30T01:03:21.106739 toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3 +1958bb756aa56d25 ok 2024-12-30T01:03:09.254559 upload1 +c6df0a97b5b7e3be ok 2024-12-30T01:02:52.772411 toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3 +5b8b9eb8992c0fc5 ok 2024-12-30T01:02:41.748733 upload1 +611a05f0e2887df6 ok 2024-12-30T01:02:24.296825 toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3 +37aec2ce0608f047 ok 2024-12-30T01:02:12.260152 upload1 +5382d35a68c9df5e ok 2024-12-30T01:01:57.000580 toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3 +bd160df99ae4cf99 ok 2024-12-30T01:01:45.000575 upload1 +91ba9c0545237ea2 ok 2024-12-30T01:01:30.227883 toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3 +4aaf880e0f6f3a5c ok 2024-12-30T01:01:17.900276 upload1 +48bb38aa499c3a0b ok 2024-12-30T01:01:02.359397 toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3 +fca20421263140dc ok 2024-12-30T01:00:50.225710 upload1 +18e5c9145b338dad ok 2024-12-30T01:00:34.982862 toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3 +3c170082823cf887 ok 2024-12-30T01:00:22.859716 upload1 +7e3077fb34b289c9 ok 2024-12-30T01:00:05.188721 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cloud.google.com/gke-logging-variant=DEFAULT + cloud.google.com/gke-max-pods-per-node=110 + cloud.google.com/gke-nodepool=default-pool + cloud.google.com/gke-os-distribution=cos + cloud.google.com/gke-provisioning=standard + cloud.google.com/gke-stack-type=IPV4 + cloud.google.com/machine-family=e2 + cloud.google.com/private-node=false + failure-domain.beta.kubernetes.io/region=us-east1 + failure-domain.beta.kubernetes.io/zone=us-east1-b + kubernetes.io/arch=amd64 + kubernetes.io/hostname=gke-prod-24-12-30-00-37-default-pool-8624e8fb-t1vw + kubernetes.io/os=linux + node.kubernetes.io/instance-type=e2-custom-20-81920 + topology.gke.io/zone=us-east1-b + topology.kubernetes.io/region=us-east1 + topology.kubernetes.io/zone=us-east1-b +Annotations: container.googleapis.com/instance_id: 4587531103998072104 + csi.volume.kubernetes.io/nodeid: + {"cvmfs.csi.cern.ch":"gke-prod-24-12-30-00-37-default-pool-8624e8fb-t1vw","pd.csi.storage.gke.io":"projects/anvil-and-terra-development/zo... + node.alpha.kubernetes.io/ttl: 0 + node.gke.io/last-applied-node-labels: + cloud.google.com/gke-boot-disk=pd-balanced,cloud.google.com/gke-container-runtime=containerd,cloud.google.com/gke-cpu-scaling-level=20,clo... + node.gke.io/last-applied-node-taints: + volumes.kubernetes.io/controller-managed-attach-detach: true +CreationTimestamp: Mon, 30 Dec 2024 00:44:08 +0000 +Taints: +Unschedulable: false +Lease: + HolderIdentity: gke-prod-24-12-30-00-37-default-pool-8624e8fb-t1vw + AcquireTime: + RenewTime: Mon, 30 Dec 2024 01:35:16 +0000 +Conditions: + Type Status LastHeartbeatTime LastTransitionTime Reason Message + ---- ------ ----------------- ------------------ ------ ------- + KernelDeadlock False Mon, 30 Dec 2024 01:34:20 +0000 Mon, 30 Dec 2024 00:44:12 +0000 KernelHasNoDeadlock kernel has no deadlock + DeprecatedOtherContainerdFeatures False Mon, 30 Dec 2024 01:34:20 +0000 Mon, 30 Dec 2024 00:44:12 +0000 DeprecatedOtherContainerdFeaturesNotDetected No deprecation risk: did not find any deprecations other than 3 configs fields (auths/configs/mirrors), pulling schema v1 images and using v1alpha2 CRI. + DeprecatedUsingV1Alpha2Cri False Mon, 30 Dec 2024 01:34:20 +0000 Mon, 30 Dec 2024 00:44:12 +0000 DeprecatedUsingV1Alpha2CriNotDetected No deprecation risk: did not use v1alpha2 CRI + DeprecatedAuthsFieldInContainerdConfiguration False Mon, 30 Dec 2024 01:34:20 +0000 Mon, 30 Dec 2024 00:44:12 +0000 DeprecatedAuthsFieldInContainerdConfigurationNotDetected No deprecation risk: did not find any deprecated 'auths' field in containerd's config + DeprecatedConfigsFieldInContainerdConfiguration False Mon, 30 Dec 2024 01:34:20 +0000 Mon, 30 Dec 2024 00:44:12 +0000 DeprecatedConfigsFieldInContainerdConfigurationNotDetected No deprecation risk: did not find any deprecated 'configs' field in containerd's config + SysctlChanged False Mon, 30 Dec 2024 01:34:20 +0000 Mon, 30 Dec 2024 00:44:12 +0000 SysctlNotChanged Default sysctls are in effect, no unexpected sysctl changes + CorruptDockerOverlay2 False Mon, 30 Dec 2024 01:34:20 +0000 Mon, 30 Dec 2024 00:44:12 +0000 NoCorruptDockerOverlay2 docker overlay2 is functioning properly + FrequentContainerdRestart False Mon, 30 Dec 2024 01:34:20 +0000 Mon, 30 Dec 2024 00:44:12 +0000 NoFrequentContainerdRestart containerd is functioning properly + FrequentDockerRestart False Mon, 30 Dec 2024 01:34:20 +0000 Mon, 30 Dec 2024 00:44:12 +0000 NoFrequentDockerRestart docker is functioning properly + FrequentKubeletRestart False Mon, 30 Dec 2024 01:34:20 +0000 Mon, 30 Dec 2024 00:44:12 +0000 NoFrequentKubeletRestart kubelet is functioning properly + FrequentUnregisterNetDevice False Mon, 30 Dec 2024 01:34:20 +0000 Mon, 30 Dec 2024 00:44:12 +0000 NoFrequentUnregisterNetDevice node is functioning properly + DeprecatedMirrorsFieldInContainerdConfiguration False Mon, 30 Dec 2024 01:34:20 +0000 Mon, 30 Dec 2024 00:44:12 +0000 DeprecatedMirrorsFieldInContainerdConfigurationNotDetected No deprecation risk: did not find any deprecated 'mirrors' field in containerd's config + DeprecatedPullingSchemaV1Image False Mon, 30 Dec 2024 01:34:20 +0000 Mon, 30 Dec 2024 00:44:12 +0000 DeprecatedPullingSchemaV1ImageDetected No deprecation risk: did not pull any schema v1 images + ReadonlyFilesystem False Mon, 30 Dec 2024 01:34:20 +0000 Mon, 30 Dec 2024 00:44:12 +0000 FilesystemIsNotReadOnly Filesystem is not read-only + NetworkUnavailable False Mon, 30 Dec 2024 00:44:09 +0000 Mon, 30 Dec 2024 00:44:08 +0000 RouteCreated NodeController create implicit route + MemoryPressure False Mon, 30 Dec 2024 01:34:42 +0000 Mon, 30 Dec 2024 00:43:40 +0000 KubeletHasSufficientMemory kubelet has sufficient memory available + DiskPressure False Mon, 30 Dec 2024 01:34:42 +0000 Mon, 30 Dec 2024 00:43:40 +0000 KubeletHasNoDiskPressure kubelet has no disk pressure + PIDPressure False Mon, 30 Dec 2024 01:34:42 +0000 Mon, 30 Dec 2024 00:43:40 +0000 KubeletHasSufficientPID kubelet has sufficient PID available + Ready True Mon, 30 Dec 2024 01:34:42 +0000 Mon, 30 Dec 2024 00:44:28 +0000 KubeletReady kubelet is posting ready status. AppArmor enabled +Addresses: + InternalIP: 10.142.0.45 + ExternalIP: 35.231.222.35 + Hostname: gke-prod-24-12-30-00-37-default-pool-8624e8fb-t1vw +Capacity: + cpu: 20 + ephemeral-storage: 98831908Ki + hugepages-1Gi: 0 + hugepages-2Mi: 0 + memory: 82369068Ki + pods: 110 +Allocatable: + cpu: 19880m + ephemeral-storage: 47060071478 + hugepages-1Gi: 0 + hugepages-2Mi: 0 + memory: 75554348Ki + pods: 110 +System Info: + Machine ID: 0fb8921560c195bf94eacff9c507d103 + System UUID: 0fb89215-60c1-95bf-94ea-cff9c507d103 + Boot ID: 4946f7a1-539d-497f-8192-bd88e7dcbdb8 + Kernel Version: 6.1.112+ + OS Image: Container-Optimized OS from Google + Operating System: linux + Architecture: amd64 + Container Runtime Version: containerd://1.7.23 + Kubelet Version: v1.28.15-gke.1020000 + Kube-Proxy Version: v1.28.15-gke.1020000 +PodCIDR: 10.92.0.0/24 +PodCIDRs: 10.92.0.0/24 +ProviderID: gce://anvil-and-terra-development/us-east1-b/gke-prod-24-12-30-00-37-default-pool-8624e8fb-t1vw +Non-terminated Pods: (26 in total) + Namespace Name CPU Requests CPU Limits Memory Requests Memory Limits Age + --------- ---- ------------ ---------- --------------- ------------- --- + gmp-system collector-sql69 5m (0%) 0 (0%) 36M (0%) 3032M (3%) 50m + gmp-system gmp-operator-7d6f64c77c-56gq5 1m (0%) 0 (0%) 16M (0%) 2G (2%) 51m + kube-system event-exporter-gke-85885bd8fc-8x9lm 3m (0%) 0 (0%) 100Mi (0%) 0 (0%) 52m + kube-system fluentbit-gke-wdcsb 100m (0%) 0 (0%) 200Mi (0%) 500Mi (0%) 51m + kube-system gke-metrics-agent-ghtht 9m (0%) 0 (0%) 110Mi (0%) 110Mi (0%) 51m + kube-system konnectivity-agent-78674bd795-xjv9n 15m (0%) 1 (5%) 60Mi (0%) 155Mi (0%) 52m + kube-system konnectivity-agent-autoscaler-7ccc577975-v49k6 10m (0%) 0 (0%) 10M (0%) 0 (0%) 51m + kube-system kube-dns-7944cfdbbf-mlk9l 260m (1%) 0 (0%) 110Mi (0%) 210Mi (0%) 52m + kube-system kube-dns-autoscaler-755c7dfdf5-b5qn5 20m (0%) 0 (0%) 10Mi (0%) 0 (0%) 52m + kube-system kube-proxy-gke-prod-24-12-30-00-37-default-pool-8624e8fb-t1vw 100m (0%) 0 (0%) 0 (0%) 0 (0%) 50m + kube-system l7-default-backend-6886579dfd-j75vl 10m (0%) 0 (0%) 20Mi (0%) 0 (0%) 51m + kube-system metrics-server-v0.7.0-8657cbfc4b-7cs2k 48m (0%) 43m (0%) 105Mi (0%) 355Mi (0%) 50m + kube-system pdcsi-node-txqck 10m (0%) 0 (0%) 20Mi (0%) 100Mi (0%) 51m + prod-24-12-30-00-37-1 prod-24-12-30-00-37-1-cvmfscsi-controllerplugin-b8d59b9d4-7mswz 0 (0%) 0 (0%) 0 (0%) 0 (0%) 48m + prod-24-12-30-00-37-1 prod-24-12-30-00-37-1-cvmfscsi-nodeplugin-j9s9p 0 (0%) 0 (0%) 0 (0%) 0 (0%) 43m + prod-24-12-30-00-37-1 prod-24-12-30-00-37-1-galaxy-celery-58f78d588c-ww622 500m (2%) 2 (10%) 2G (2%) 8G (10%) 48m + prod-24-12-30-00-37-1 prod-24-12-30-00-37-1-galaxy-celery-beat-7d45c58548-wkpmc 500m (2%) 2 (10%) 2G (2%) 8G (10%) 48m + prod-24-12-30-00-37-1 prod-24-12-30-00-37-1-galaxy-galaxy-postgres-0 250m (1%) 0 (0%) 256Mi (0%) 0 (0%) 48m + prod-24-12-30-00-37-1 prod-24-12-30-00-37-1-galaxy-job-0-79c5668dfd-ppcng 500m (2%) 2 (10%) 2G (2%) 8G (10%) 48m + prod-24-12-30-00-37-1 prod-24-12-30-00-37-1-galaxy-nginx-f8b78cb88-k9bk2 100m (0%) 2 (10%) 500M (0%) 3G (3%) 48m + prod-24-12-30-00-37-1 prod-24-12-30-00-37-1-galaxy-rabbitmq-server-server-0 1 (5%) 2 (10%) 2Gi (2%) 2Gi (2%) 48m + prod-24-12-30-00-37-1 prod-24-12-30-00-37-1-galaxy-web-7fdd77c8bb-m8jg4 500m (2%) 2 (10%) 2G (2%) 8G (10%) 48m + prod-24-12-30-00-37-1 prod-24-12-30-00-37-1-galaxy-workflow-756fdd9c5b-6x7jd 500m (2%) 2 (10%) 2G (2%) 8G (10%) 48m + prod-24-12-30-00-37-1 prod-24-12-30-00-37-1-nfs-0 0 (0%) 0 (0%) 0 (0%) 0 (0%) 48m + prod-24-12-30-00-37-1 prod-24-12-30-00-37-1-rabbitmq-d6559cf9f-r9c2p 0 (0%) 0 (0%) 0 (0%) 0 (0%) 48m + prod-24-12-30-00-37-1 prod-24-12-30-00-37-1-rabbitmq-messaging-topology-operatorclp9s 0 (0%) 0 (0%) 0 (0%) 0 (0%) 48m +Allocated resources: + (Total limits may be over 100 percent, i.e., overcommitted.) + Resource Requests Limits + -------- -------- ------ + cpu 4441m (22%) 15043m (75%) + memory 13748622464 (17%) 51678947328 (66%) + ephemeral-storage 35Gi (79%) 200Gi (456%) + hugepages-1Gi 0 (0%) 0 (0%) + hugepages-2Mi 0 (0%) 0 (0%) +Events: + Type Reason Age From Message + ---- ------ ---- ---- ------- + Normal Starting 51m kube-proxy + Normal Starting 55m kubelet Starting kubelet. + Warning InvalidDiskCapacity 55m kubelet invalid capacity 0 on image filesystem + Normal NodeAllocatableEnforced 55m kubelet Updated Node Allocatable limit across pods + Normal NodeHasNoDiskPressure 53m (x7 over 55m) kubelet Node gke-prod-24-12-30-00-37-default-pool-8624e8fb-t1vw status is now: NodeHasNoDiskPressure + Normal NodeHasSufficientPID 53m (x7 over 55m) kubelet Node gke-prod-24-12-30-00-37-default-pool-8624e8fb-t1vw status is now: NodeHasSufficientPID + Normal NodeHasSufficientMemory 52m (x8 over 55m) kubelet Node gke-prod-24-12-30-00-37-default-pool-8624e8fb-t1vw status is now: NodeHasSufficientMemory + Normal Synced 51m cloud-node-controller Node synced successfully + Normal RegisteredNode 51m node-controller Node gke-prod-24-12-30-00-37-default-pool-8624e8fb-t1vw event: Registered Node gke-prod-24-12-30-00-37-default-pool-8624e8fb-t1vw in Controller + Warning NodeRegistrationCheckerStart 51m node-registration-checker-monitor Mon Dec 30 00:40:04 UTC 2024 - ** Starting Node Registration Checker ** + Warning NodeRegistrationCheckerDidNotRunChecks 48m node-registration-checker-monitor Mon Dec 30 00:47:05 UTC 2024 - ** Node ready and registered. ** diff --git a/reports/anvil-production/tool-tests/prod-24-12-30-00-37-1/results.html b/reports/anvil-production/tool-tests/prod-24-12-30-00-37-1/results.html new file mode 100644 index 000000000..9315e6a6f --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-12-30-00-37-1/results.html @@ -0,0 +1,291 @@ + + + + + + + Test Results (powered by Planemo) + + + + + + + + + + +
+
+
+
+ + + + + + + \ No newline at end of file diff --git a/reports/anvil-production/tool-tests/prod-24-12-30-00-37-1/results.json b/reports/anvil-production/tool-tests/prod-24-12-30-00-37-1/results.json new file mode 100644 index 000000000..6e49d8338 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-12-30-00-37-1/results.json @@ -0,0 +1 @@ +{"version": "0.1", "suitename": "Galaxy Tool Tests", "results": {"total": 81, "errors": 7, "failures": 28, "skips": 2}, "tests": [{"id": "bcftools_annotate/1.15.1+galaxy4-0", "has_data": true, "data": {"tool_id": "bcftools_annotate", "tool_version": "1.15.1+galaxy4", "test_index": 0, "time_seconds": 32.382657051086426, "inputs": {"input_file": {"src": "hda", "id": "85a33a94c6429486"}, "sec_annofile|columns": "CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL", "sec_annofile|annofile|annotations": {"src": "hda", "id": "9f786fde84d3b8dc"}, "sec_annofile|annofile|header_file": {"src": "hda", "id": "0e40df125b95de6b"}, "sec_annofile|annofile|anno_fmt": "tab", "output_type": "v"}, "job": {"model_class": "Job", "id": "991b6756fcfc001a", "state": "ok", "exit_code": 0, "update_time": "2024-12-30T01:14:09.141447", "create_time": "2024-12-30T01:13:56.501204", "galaxy_version": "23.1", "command_version": "Version: 1.15.1 (using htslib 1.15.1)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4", "history_id": "1262154bdd2f9614", "external_id": "gxy-nvqwg", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/8/7/e/dataset_87e83e9b-e659-4ed7-b098-a7cf77a18af8.dat' > input.vcf.gz && bcftools index input.vcf.gz && bgzip -c '/galaxy/server/database/objects/7/8/0/dataset_78060287-94ab-411f-b691-b171e383ab24.dat' > annotations.tab.gz && tabix -s 1 -b 2 -e 2 annotations.tab.gz && bcftools annotate --columns 'CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL' --annotations 'annotations.tab.gz' --header-lines '/galaxy/server/database/objects/3/e/1/dataset_3e145f34-9981-4c90-a2fe-113fb30a839d.dat' --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/8/6/f/dataset_86f508c9-6efd-4be4-87a8-bc2649422f61.dat'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "sec_restrict": "{\"collapse\": null, \"exclude\": null, \"include\": null, \"invert_samples\": false, \"invert_samples_file\": false, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"samples\": \"\", \"samples_file\": null}", "sec_annotate": "{\"remove\": \"\", \"rename_annots\": null, \"rename_chrs\": null}", "sec_annofile": "{\"annofile\": {\"__current_case__\": 2, \"anno_fmt\": \"tab\", \"annotations\": {\"values\": [{\"id\": 98, \"src\": \"hda\"}]}, \"header_file\": {\"values\": [{\"id\": 99, \"src\": \"hda\"}]}, \"header_lines\": null}, \"columns\": \"CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL\", \"mark_sites\": \"\", \"min_overlap\": \"\", \"set_id\": \"\"}"}, "inputs": {"input_file": {"id": "85a33a94c6429486", "src": "hda", "uuid": "87e83e9b-e659-4ed7-b098-a7cf77a18af8"}, "sec_annofile|annofile|annotations": {"id": "9f786fde84d3b8dc", "src": "hda", "uuid": "78060287-94ab-411f-b691-b171e383ab24"}, "sec_annofile|annofile|header_file": {"id": "0e40df125b95de6b", "src": "hda", "uuid": "3e145f34-9981-4c90-a2fe-113fb30a839d"}}, "outputs": {"output_file": {"id": "991b6756fcfc001a", "src": "hda", "uuid": "86f508c9-6efd-4be4-87a8-bc2649422f61"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-12-30 01:13:59", "plugin": "core", "name": "end_epoch", "raw_value": "1735521239.0000000"}, {"title": "Job Start Time", "value": "2024-12-30 01:13:58", "plugin": "core", "name": "start_epoch", "raw_value": "1735521238.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "bcftools_annotate/1.15.1+galaxy4-1", "has_data": true, "data": {"tool_id": "bcftools_annotate", "tool_version": "1.15.1+galaxy4", "test_index": 1, "time_seconds": 31.04396939277649, "inputs": {"input_file": {"src": "hda", "id": "d04284554dc99baa"}, "sec_annofile|columns": "CHROM,FROM,TO,T_STR", "sec_annofile|annofile|annotations": {"src": "hda", "id": "b06c5949985caf75"}, "sec_annofile|annofile|header_file": {"src": "hda", "id": "155a90d52bb4a79c"}, "sec_annofile|annofile|anno_fmt": "tab", "sec_annofile|set_id": "%CHROM\\_%POS\\_%REF\\_%FIRST_ALT", "output_type": "v"}, "job": {"model_class": "Job", "id": "3486ef5567398f96", "state": "ok", "exit_code": 0, "update_time": "2024-12-30T01:14:40.198729", "create_time": "2024-12-30T01:14:29.495626", "galaxy_version": "23.1", "command_version": "Version: 1.15.1 (using htslib 1.15.1)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4", "history_id": "1262154bdd2f9614", "external_id": "gxy-v4mc5", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/7/6/e/dataset_76e03c9a-ada9-488b-a8f7-0dc3e745b284.dat' > input.vcf.gz && bcftools index input.vcf.gz && bgzip -c '/galaxy/server/database/objects/1/1/9/dataset_11957baa-fd8d-4e9e-992b-50cc5182b2b3.dat' > annotations.bed.gz && tabix -s 1 -b 2 -e 3 annotations.bed.gz && bcftools annotate --columns 'CHROM,FROM,TO,T_STR' --annotations 'annotations.bed.gz' --header-lines '/galaxy/server/database/objects/8/c/7/dataset_8c7883fa-b4ef-4e56-8831-21952c8b7155.dat' --set-id '%CHROM\\_%POS\\_%REF\\_%FIRST_ALT' --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/4/2/a/dataset_42ae429f-2974-4975-a633-248bf9c8ebe0.dat'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "sec_restrict": "{\"collapse\": null, \"exclude\": null, \"include\": null, \"invert_samples\": false, \"invert_samples_file\": false, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"samples\": \"\", \"samples_file\": null}", "sec_annotate": "{\"remove\": \"\", \"rename_annots\": null, \"rename_chrs\": null}", "sec_annofile": "{\"annofile\": {\"__current_case__\": 2, \"anno_fmt\": \"tab\", \"annotations\": {\"values\": [{\"id\": 102, \"src\": \"hda\"}]}, \"header_file\": {\"values\": [{\"id\": 103, \"src\": \"hda\"}]}, \"header_lines\": null}, \"columns\": \"CHROM,FROM,TO,T_STR\", \"mark_sites\": \"\", \"min_overlap\": \"\", \"set_id\": \"%CHROM\\\\_%POS\\\\_%REF\\\\_%FIRST_ALT\"}"}, "inputs": {"input_file": {"id": "d04284554dc99baa", "src": "hda", "uuid": "76e03c9a-ada9-488b-a8f7-0dc3e745b284"}, "sec_annofile|annofile|annotations": {"id": "b06c5949985caf75", "src": "hda", "uuid": "11957baa-fd8d-4e9e-992b-50cc5182b2b3"}, "sec_annofile|annofile|header_file": {"id": "155a90d52bb4a79c", "src": "hda", "uuid": "8c7883fa-b4ef-4e56-8831-21952c8b7155"}}, "outputs": {"output_file": {"id": "3486ef5567398f96", "src": "hda", "uuid": "42ae429f-2974-4975-a633-248bf9c8ebe0"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-12-30 01:14:31", "plugin": "core", "name": "end_epoch", "raw_value": "1735521271.0000000"}, {"title": "Job Start Time", "value": "2024-12-30 01:14:30", "plugin": "core", "name": "start_epoch", "raw_value": "1735521270.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "bcftools_annotate/1.15.1+galaxy4-2", "has_data": true, "data": {"tool_id": "bcftools_annotate", "tool_version": "1.15.1+galaxy4", "test_index": 2, "time_seconds": 28.75369644165039, "inputs": {"input_file": {"src": "hda", "id": "17ae9a3f6937c023"}, "sec_annofile|columns": "STR,ID,QUAL,FILTER", "sec_annofile|annofile|annotations": {"src": "hda", "id": "4aaa5ab690473dd8"}, "sec_annofile|annofile|anno_fmt": "vcf", "output_type": "v"}, "job": {"model_class": "Job", "id": "906a346bd90cbb09", "state": "ok", "exit_code": 0, "update_time": "2024-12-30T01:15:08.982763", "create_time": "2024-12-30T01:14:57.091067", "galaxy_version": "23.1", "command_version": "Version: 1.15.1 (using htslib 1.15.1)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4", "history_id": "1262154bdd2f9614", "external_id": "gxy-8b2f7", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/5/2/1/dataset_52180263-b245-42fd-8312-7c1b6ca814b3.dat' > input.vcf.gz && bcftools index input.vcf.gz && bgzip -c '/galaxy/server/database/objects/6/9/2/dataset_6928abe5-e71e-495d-a879-80e778c654de.dat' > annotations.vcf.gz && bcftools index annotations.vcf.gz && bcftools annotate --columns 'STR,ID,QUAL,FILTER' --annotations 'annotations.vcf.gz' --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/2/1/8/dataset_218c8d36-0b8c-49d5-aca2-a09d4e3b004e.dat'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "sec_restrict": "{\"collapse\": null, \"exclude\": null, \"include\": null, \"invert_samples\": false, \"invert_samples_file\": false, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"samples\": \"\", \"samples_file\": null}", "sec_annotate": "{\"remove\": \"\", \"rename_annots\": null, \"rename_chrs\": null}", "sec_annofile": "{\"annofile\": {\"__current_case__\": 1, \"anno_fmt\": \"vcf\", \"annotations\": {\"values\": [{\"id\": 106, \"src\": \"hda\"}]}}, \"columns\": \"STR,ID,QUAL,FILTER\", \"mark_sites\": \"\", \"min_overlap\": \"\", \"set_id\": \"\"}"}, "inputs": {"input_file": {"id": "17ae9a3f6937c023", "src": "hda", "uuid": "52180263-b245-42fd-8312-7c1b6ca814b3"}, "sec_annofile|annofile|annotations": {"id": "4aaa5ab690473dd8", "src": "hda", "uuid": "6928abe5-e71e-495d-a879-80e778c654de"}}, "outputs": {"output_file": {"id": "906a346bd90cbb09", "src": "hda", "uuid": "218c8d36-0b8c-49d5-aca2-a09d4e3b004e"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-12-30 01:15:00", "plugin": "core", "name": "end_epoch", "raw_value": "1735521300.0000000"}, {"title": "Job Start Time", "value": "2024-12-30 01:14:59", "plugin": "core", "name": "start_epoch", "raw_value": "1735521299.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "bcftools_annotate/1.15.1+galaxy4-3", "has_data": true, "data": {"tool_id": "bcftools_annotate", "tool_version": "1.15.1+galaxy4", "test_index": 3, "time_seconds": 27.370021104812622, "inputs": {"input_file": {"src": "hda", "id": "4fa6353e1475b8e8"}, "sec_annofile|columns": "STR,ID,QUAL,FILTER", "sec_annofile|annofile|annotations": {"src": "hda", "id": "6bf55f0095bdcf52"}, "sec_annofile|annofile|anno_fmt": "vcf", "output_type": "v"}, "job": {"model_class": "Job", "id": "5c8707f919a70182", "state": "ok", "exit_code": 0, "update_time": "2024-12-30T01:15:36.456881", "create_time": "2024-12-30T01:15:25.182529", "galaxy_version": "23.1", "command_version": "Version: 1.15.1 (using htslib 1.15.1)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4", "history_id": "1262154bdd2f9614", "external_id": "gxy-dn2nw", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/d/e/5/dataset_de571565-2b7f-4c97-bfe0-49f4e17c0a46.dat' > input.vcf.gz && bcftools index input.vcf.gz && ln -s '/galaxy/server/database/objects/c/b/7/dataset_cb718df6-aa41-462f-8504-9662e3b8ec3f.dat' annotations.bcf && ln -s '/galaxy/server/database/objects/_metadata_files/f/4/7/metadata_f47e915f-0797-4080-b325-d3337d0ee746.dat' annotations.bcf.csi && bcftools annotate --columns 'STR,ID,QUAL,FILTER' --annotations 'annotations.bcf' --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/f/d/1/dataset_fd1002d7-f588-432e-8b88-b83b4a4ce0c2.dat'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "sec_restrict": "{\"collapse\": null, \"exclude\": null, \"include\": null, \"invert_samples\": false, \"invert_samples_file\": false, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"samples\": \"\", \"samples_file\": null}", "sec_annotate": "{\"remove\": \"\", \"rename_annots\": null, \"rename_chrs\": null}", "sec_annofile": "{\"annofile\": {\"__current_case__\": 1, \"anno_fmt\": \"vcf\", \"annotations\": {\"values\": [{\"id\": 109, \"src\": \"hda\"}]}}, \"columns\": \"STR,ID,QUAL,FILTER\", \"mark_sites\": \"\", \"min_overlap\": \"\", \"set_id\": \"\"}"}, "inputs": {"input_file": {"id": "4fa6353e1475b8e8", "src": "hda", "uuid": "de571565-2b7f-4c97-bfe0-49f4e17c0a46"}, "sec_annofile|annofile|annotations": {"id": "6bf55f0095bdcf52", "src": "hda", "uuid": "cb718df6-aa41-462f-8504-9662e3b8ec3f"}}, "outputs": {"output_file": {"id": "5c8707f919a70182", "src": "hda", "uuid": "fd1002d7-f588-432e-8b88-b83b4a4ce0c2"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-12-30 01:15:27", "plugin": "core", "name": "end_epoch", "raw_value": "1735521327.0000000"}, {"title": "Job Start Time", "value": "2024-12-30 01:15:26", "plugin": "core", "name": "start_epoch", "raw_value": "1735521326.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "bcftools_annotate/1.15.1+galaxy4-4", "has_data": true, "data": {"tool_id": "bcftools_annotate", "tool_version": "1.15.1+galaxy4", "test_index": 4, "time_seconds": 28.219101905822754, "inputs": {"input_file": {"src": "hda", "id": "fa76d05568187d5a"}, "sec_annofile|columns": "ID,QUAL,FILTER,INFO,FMT", "sec_annofile|annofile|annotations": {"src": "hda", "id": "b44fb3047a023ae0"}, "sec_annofile|annofile|anno_fmt": "vcf", "output_type": "v"}, "job": {"model_class": "Job", "id": "b64308614a80387a", "state": "ok", "exit_code": 0, "update_time": "2024-12-30T01:16:04.932211", "create_time": "2024-12-30T01:15:53.180093", "galaxy_version": "23.1", "command_version": "Version: 1.15.1 (using htslib 1.15.1)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4", "history_id": "1262154bdd2f9614", "external_id": "gxy-jdw4h", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/0/0/e/dataset_00ef2145-8a3e-461d-8ecd-faba5ac99ac5.dat' > input.vcf.gz && bcftools index input.vcf.gz && bgzip -c '/galaxy/server/database/objects/6/3/c/dataset_63cb5c9c-eaab-477e-b663-1312cf53b120.dat' > annotations.vcf.gz && bcftools index annotations.vcf.gz && bcftools annotate --columns 'ID,QUAL,FILTER,INFO,FMT' --annotations 'annotations.vcf.gz' --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/e/1/6/dataset_e163629d-5e1b-4dc1-a76a-082e01ec5e3b.dat'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "sec_restrict": "{\"collapse\": null, \"exclude\": null, \"include\": null, \"invert_samples\": false, \"invert_samples_file\": false, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"samples\": \"\", \"samples_file\": null}", "sec_annotate": "{\"remove\": \"\", \"rename_annots\": null, \"rename_chrs\": null}", "sec_annofile": "{\"annofile\": {\"__current_case__\": 1, \"anno_fmt\": \"vcf\", \"annotations\": {\"values\": [{\"id\": 112, \"src\": \"hda\"}]}}, \"columns\": \"ID,QUAL,FILTER,INFO,FMT\", \"mark_sites\": \"\", \"min_overlap\": \"\", \"set_id\": \"\"}"}, "inputs": {"input_file": {"id": "fa76d05568187d5a", "src": "hda", "uuid": "00ef2145-8a3e-461d-8ecd-faba5ac99ac5"}, "sec_annofile|annofile|annotations": {"id": "b44fb3047a023ae0", "src": "hda", "uuid": "63cb5c9c-eaab-477e-b663-1312cf53b120"}}, "outputs": {"output_file": {"id": "b64308614a80387a", "src": "hda", "uuid": "e163629d-5e1b-4dc1-a76a-082e01ec5e3b"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-12-30 01:15:55", "plugin": "core", "name": "end_epoch", "raw_value": "1735521355.0000000"}, {"title": "Job Start Time", "value": "2024-12-30 01:15:54", "plugin": "core", "name": "start_epoch", "raw_value": "1735521354.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "bcftools_annotate/1.15.1+galaxy4-5", "has_data": true, "data": {"tool_id": "bcftools_annotate", "tool_version": "1.15.1+galaxy4", "test_index": 5, "time_seconds": 27.540628910064697, "inputs": {"input_file": {"src": "hda", "id": "8aaa620134da4b3f"}, "sec_annofile|columns": "ID,QUAL,FILTER,INFO,FMT", "sec_annofile|annofile|annotations": {"src": "hda", "id": "4e22fed0e573e2bf"}, "sec_annofile|annofile|anno_fmt": "vcf", "sec_restrict|samples": "A", "output_type": "v"}, "job": {"model_class": "Job", "id": "50bc257ec42392c1", "state": "ok", "exit_code": 0, "update_time": "2024-12-30T01:16:32.437058", "create_time": "2024-12-30T01:16:22.061171", "galaxy_version": "23.1", "command_version": "Version: 1.15.1 (using htslib 1.15.1)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4", "history_id": "1262154bdd2f9614", "external_id": "gxy-tqss2", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/f/e/f/dataset_fef346b3-faf2-4ddb-9a09-add15474021c.dat' > input.vcf.gz && bcftools index input.vcf.gz && bgzip -c '/galaxy/server/database/objects/a/d/5/dataset_ad5fca75-0707-4434-8629-004dde032b7c.dat' > annotations.vcf.gz && bcftools index annotations.vcf.gz && bcftools annotate --columns 'ID,QUAL,FILTER,INFO,FMT' --annotations 'annotations.vcf.gz' --samples 'A' --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/a/b/6/dataset_ab6fa7f4-3214-46f3-a764-7ff952535b5e.dat'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "sec_restrict": "{\"collapse\": null, \"exclude\": null, \"include\": null, \"invert_samples\": false, \"invert_samples_file\": false, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"samples\": \"A\", \"samples_file\": null}", "sec_annotate": "{\"remove\": \"\", \"rename_annots\": null, \"rename_chrs\": null}", "sec_annofile": "{\"annofile\": {\"__current_case__\": 1, \"anno_fmt\": \"vcf\", \"annotations\": {\"values\": [{\"id\": 115, \"src\": \"hda\"}]}}, \"columns\": \"ID,QUAL,FILTER,INFO,FMT\", \"mark_sites\": \"\", \"min_overlap\": \"\", \"set_id\": \"\"}"}, "inputs": {"input_file": {"id": "8aaa620134da4b3f", "src": "hda", "uuid": "fef346b3-faf2-4ddb-9a09-add15474021c"}, "sec_annofile|annofile|annotations": {"id": "4e22fed0e573e2bf", "src": "hda", "uuid": "ad5fca75-0707-4434-8629-004dde032b7c"}}, "outputs": {"output_file": {"id": "50bc257ec42392c1", "src": "hda", "uuid": "ab6fa7f4-3214-46f3-a764-7ff952535b5e"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-12-30 01:16:24", "plugin": "core", "name": "end_epoch", "raw_value": "1735521384.0000000"}, {"title": "Job Start Time", "value": "2024-12-30 01:16:23", "plugin": "core", "name": "start_epoch", "raw_value": "1735521383.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "bcftools_annotate/1.15.1+galaxy4-6", "has_data": true, "data": {"tool_id": "bcftools_annotate", "tool_version": "1.15.1+galaxy4", "test_index": 6, "time_seconds": 25.431042671203613, "inputs": {"input_file": {"src": "hda", "id": "fbf7a30547f983b1"}, "sec_annofile|annofile|anno_fmt": "none", "sec_annotate|remove": "ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL", "output_type": "v"}, "job": {"model_class": "Job", "id": "a31a92347d5b7b07", "state": "ok", "exit_code": 0, "update_time": "2024-12-30T01:16:57.934748", "create_time": "2024-12-30T01:16:47.149549", "galaxy_version": "23.1", "command_version": "Version: 1.15.1 (using htslib 1.15.1)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4", "history_id": "1262154bdd2f9614", "external_id": "gxy-prqhw", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/1/f/6/dataset_1f68ac62-bc3b-4e01-bcee-dda9316a409b.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools annotate --remove 'ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL' --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/9/4/f/dataset_94ff8681-6038-4a0a-950f-c9da043d66ad.dat'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "sec_restrict": "{\"collapse\": null, \"exclude\": null, \"include\": null, \"invert_samples\": false, \"invert_samples_file\": false, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"samples\": \"\", \"samples_file\": null}", "sec_annotate": "{\"remove\": \"ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL\", \"rename_annots\": null, \"rename_chrs\": null}", "sec_annofile": "{\"annofile\": {\"__current_case__\": 0, \"anno_fmt\": \"none\"}, \"columns\": \"\", \"mark_sites\": \"\", \"min_overlap\": \"\", \"set_id\": \"\"}"}, "inputs": {"input_file": {"id": "fbf7a30547f983b1", "src": "hda", "uuid": "1f68ac62-bc3b-4e01-bcee-dda9316a409b"}}, "outputs": {"output_file": {"id": "a31a92347d5b7b07", "src": "hda", "uuid": "94ff8681-6038-4a0a-950f-c9da043d66ad"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-12-30 01:16:49", "plugin": "core", "name": "end_epoch", "raw_value": "1735521409.0000000"}, {"title": "Job Start Time", "value": "2024-12-30 01:16:48", "plugin": "core", "name": "start_epoch", "raw_value": "1735521408.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "bcftools_annotate/1.15.1+galaxy4-7", "has_data": true, "data": {"tool_id": "bcftools_annotate", "tool_version": "1.15.1+galaxy4", "test_index": 7, "time_seconds": 27.1191725730896, "inputs": {"input_file": {"src": "hda", "id": "ba3d5d7e2e1e072b"}, "sec_annofile|annofile|anno_fmt": "none", "sec_annotate|remove": "FORMAT", "output_type": "v"}, "job": {"model_class": "Job", "id": "abb0c83d687376d2", "state": "ok", "exit_code": 0, "update_time": "2024-12-30T01:17:25.180920", "create_time": "2024-12-30T01:17:13.347898", "galaxy_version": "23.1", "command_version": "Version: 1.15.1 (using htslib 1.15.1)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4", "history_id": "1262154bdd2f9614", "external_id": "gxy-26rkh", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/3/f/8/dataset_3f8dc32a-c3d3-43f6-a19a-f44ca1f2544e.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools annotate --remove 'FORMAT' --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/8/0/2/dataset_8022584c-4e18-4a38-b23e-be1f18c0ca0f.dat'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "sec_restrict": "{\"collapse\": null, \"exclude\": null, \"include\": null, \"invert_samples\": false, \"invert_samples_file\": false, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"samples\": \"\", \"samples_file\": null}", "sec_annotate": "{\"remove\": \"FORMAT\", \"rename_annots\": null, \"rename_chrs\": null}", "sec_annofile": "{\"annofile\": {\"__current_case__\": 0, \"anno_fmt\": \"none\"}, \"columns\": \"\", \"mark_sites\": \"\", \"min_overlap\": \"\", \"set_id\": \"\"}"}, "inputs": {"input_file": {"id": "ba3d5d7e2e1e072b", "src": "hda", "uuid": "3f8dc32a-c3d3-43f6-a19a-f44ca1f2544e"}}, "outputs": {"output_file": {"id": "abb0c83d687376d2", "src": "hda", "uuid": "8022584c-4e18-4a38-b23e-be1f18c0ca0f"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-12-30 01:17:15", "plugin": "core", "name": "end_epoch", "raw_value": "1735521435.0000000"}, {"title": "Job Start Time", "value": "2024-12-30 01:17:15", "plugin": "core", "name": "start_epoch", "raw_value": "1735521435.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "bcftools_annotate/1.15.1+galaxy4-8", "has_data": true, "data": {"tool_id": "bcftools_annotate", "tool_version": "1.15.1+galaxy4", "test_index": 8, "time_seconds": 28.286183834075928, "inputs": {"input_file": {"src": "hda", "id": "3337f974be7abfa8"}, "sec_annofile|annofile|anno_fmt": "none", "sec_annotate|remove": "FORMAT", "sec_restrict|regions_overlap": "1", "output_type": "v"}, "job": {"model_class": "Job", "id": "0c18b428e393303f", "state": "ok", "exit_code": 0, "update_time": "2024-12-30T01:17:53.506739", "create_time": "2024-12-30T01:17:41.799056", "galaxy_version": "23.1", "command_version": "Version: 1.15.1 (using htslib 1.15.1)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4", "history_id": "1262154bdd2f9614", "external_id": "gxy-7vqwp", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/5/b/0/dataset_5b022d4d-94e5-4fc1-b553-69708d6757e5.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools annotate --remove 'FORMAT' --regions-overlap 1 --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/5/9/7/dataset_597eaa6c-1db4-44f8-af96-6ae2bad7639f.dat'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "sec_restrict": "{\"collapse\": null, \"exclude\": null, \"include\": null, \"invert_samples\": false, \"invert_samples_file\": false, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": \"1\", \"samples\": \"\", \"samples_file\": null}", "sec_annotate": "{\"remove\": \"FORMAT\", \"rename_annots\": null, \"rename_chrs\": null}", "sec_annofile": "{\"annofile\": {\"__current_case__\": 0, \"anno_fmt\": \"none\"}, \"columns\": \"\", \"mark_sites\": \"\", \"min_overlap\": \"\", \"set_id\": \"\"}"}, "inputs": {"input_file": {"id": "3337f974be7abfa8", "src": "hda", "uuid": "5b022d4d-94e5-4fc1-b553-69708d6757e5"}}, "outputs": {"output_file": {"id": "0c18b428e393303f", "src": "hda", "uuid": "597eaa6c-1db4-44f8-af96-6ae2bad7639f"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-12-30 01:17:43", "plugin": "core", "name": "end_epoch", "raw_value": "1735521463.0000000"}, {"title": "Job Start Time", "value": "2024-12-30 01:17:43", "plugin": "core", "name": "start_epoch", "raw_value": "1735521463.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "bcftools_annotate/1.15.1+galaxy4-9", "has_data": true, "data": {"tool_id": "bcftools_annotate", "tool_version": "1.15.1+galaxy4", "test_index": 9, "time_seconds": 8.928919076919556, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "bcftools_concat/1.15.1+galaxy4-0", "has_data": true, "data": {"tool_id": "bcftools_concat", "tool_version": "1.15.1+galaxy4", "test_index": 0, "time_seconds": 33.27296566963196, "inputs": {"input_files": [{"src": "hda", "id": "4f222401df7c1d09"}, {"src": "hda", "id": "77e89a3ca18fd33b"}], "output_type": "v"}, "job": {"model_class": "Job", "id": "bf40b6bef4181fc1", "state": "ok", "exit_code": 0, "update_time": "2024-12-30T01:11:39.035848", "create_time": "2024-12-30T01:11:22.186696", "galaxy_version": "23.1", "command_version": "Version: 1.15.1 (using htslib 1.15.1)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.15.1+galaxy4", "history_id": "1262154bdd2f9614", "external_id": "gxy-9v6h7", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/4/1/a/dataset_41a0c711-dcba-4b9d-8dbf-1aee90e79a98.dat' > input0.vcf.gz && bcftools index input0.vcf.gz && echo 'input0.vcf.gz' >> vcfs_list && bgzip -c '/galaxy/server/database/objects/d/a/2/dataset_da253d4a-6bff-4c68-80c3-bb94a23a44f2.dat' > input1.vcf.gz && bcftools index input1.vcf.gz && echo 'input1.vcf.gz' >> vcfs_list && bcftools concat --allow-overlaps --min-PQ 30 --output-type 'v' --threads ${GALAXY_SLOTS:-4} input0.vcf.gz input1.vcf.gz > '/galaxy/server/database/objects/c/d/4/dataset_cd4b4459-4ca0-4198-b112-0a626a3cac1b.dat'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "sec_default": "{\"compact_PS\": false, \"min_PQ\": \"30\", \"mode\": {\"__current_case__\": 1, \"ligate\": false, \"ligate_mode\": null, \"naive\": \"no\", \"overlaps\": {\"__current_case__\": 0, \"allow_overlaps\": \"yes\", \"rm_dups\": null}}}", "sec_restrict": "{\"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null}"}, "inputs": {"input_files": {"id": "4f222401df7c1d09", "src": "hda", "uuid": "41a0c711-dcba-4b9d-8dbf-1aee90e79a98"}, "input_files1": {"id": "4f222401df7c1d09", "src": "hda", "uuid": "41a0c711-dcba-4b9d-8dbf-1aee90e79a98"}, "input_files2": {"id": "77e89a3ca18fd33b", "src": "hda", "uuid": "da253d4a-6bff-4c68-80c3-bb94a23a44f2"}}, "outputs": {"output_file": {"id": "bf40b6bef4181fc1", "src": "hda", "uuid": "cd4b4459-4ca0-4198-b112-0a626a3cac1b"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Checking the headers and starting positions of 2 files\n", "job_stdout": "", "job_stderr": "", "stderr": "Checking the headers and starting positions of 2 files\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-12-30 01:11:28", "plugin": "core", "name": "end_epoch", "raw_value": "1735521088.0000000"}, {"title": "Job Start Time", "value": "2024-12-30 01:11:27", "plugin": "core", "name": "start_epoch", "raw_value": "1735521087.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "bcftools_concat/1.15.1+galaxy4-1", "has_data": true, "data": {"tool_id": "bcftools_concat", "tool_version": "1.15.1+galaxy4", "test_index": 1, "time_seconds": 28.259020566940308, "inputs": {"input_files": [{"src": "hda", "id": "8c2431ea1521bc61"}, {"src": "hda", "id": "319117df431f01e8"}], "sec_default|mode|naive": "no", "output_type": "v"}, "job": {"model_class": "Job", "id": "db057033ea142ec9", "state": "ok", "exit_code": 0, "update_time": "2024-12-30T01:12:07.545662", "create_time": "2024-12-30T01:11:55.995414", "galaxy_version": "23.1", "command_version": "Version: 1.15.1 (using htslib 1.15.1)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.15.1+galaxy4", "history_id": "1262154bdd2f9614", "external_id": "gxy-kkhdh", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/e/9/0/dataset_e90d19ab-bf2a-447d-b514-61dd6ca213c2.dat' > input0.vcf.gz && bcftools index input0.vcf.gz && echo 'input0.vcf.gz' >> vcfs_list && bgzip -c '/galaxy/server/database/objects/9/1/4/dataset_9145dd52-76ae-445c-8be4-983a4d5d4559.dat' > input1.vcf.gz && bcftools index input1.vcf.gz && echo 'input1.vcf.gz' >> vcfs_list && bcftools concat --allow-overlaps --min-PQ 30 --output-type 'v' --threads ${GALAXY_SLOTS:-4} input0.vcf.gz input1.vcf.gz > '/galaxy/server/database/objects/f/6/0/dataset_f60ca435-7e08-4b25-a5ab-2544c6f5e1f0.dat'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "sec_default": "{\"compact_PS\": false, \"min_PQ\": \"30\", \"mode\": {\"__current_case__\": 1, \"ligate\": false, \"ligate_mode\": null, \"naive\": \"no\", \"overlaps\": {\"__current_case__\": 0, \"allow_overlaps\": \"yes\", \"rm_dups\": null}}}", "sec_restrict": "{\"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null}"}, "inputs": {"input_files": {"id": "8c2431ea1521bc61", "src": "hda", "uuid": "e90d19ab-bf2a-447d-b514-61dd6ca213c2"}, "input_files1": {"id": "8c2431ea1521bc61", "src": "hda", "uuid": "e90d19ab-bf2a-447d-b514-61dd6ca213c2"}, "input_files2": {"id": "319117df431f01e8", "src": "hda", "uuid": "9145dd52-76ae-445c-8be4-983a4d5d4559"}}, "outputs": {"output_file": {"id": "db057033ea142ec9", "src": "hda", "uuid": "f60ca435-7e08-4b25-a5ab-2544c6f5e1f0"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Checking the headers and starting positions of 2 files\n", "job_stdout": "", "job_stderr": "", "stderr": "Checking the headers and starting positions of 2 files\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-12-30 01:11:59", "plugin": "core", "name": "end_epoch", "raw_value": "1735521119.0000000"}, {"title": "Job Start Time", "value": "2024-12-30 01:11:58", "plugin": "core", "name": "start_epoch", "raw_value": "1735521118.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "bcftools_concat/1.15.1+galaxy4-2", "has_data": true, "data": {"tool_id": "bcftools_concat", "tool_version": "1.15.1+galaxy4", "test_index": 2, "time_seconds": 33.82575440406799, "inputs": {"input_files": [{"src": "hda", "id": "ce812daebfa4cb32"}, {"src": "hda", "id": "121cbf44a773e05b"}], "sec_default|mode|overlaps|allow_overlaps": "yes", "output_type": "v"}, "job": {"model_class": "Job", "id": "fccdf7c99d58ccb9", "state": "ok", "exit_code": 0, "update_time": "2024-12-30T01:12:41.150408", "create_time": "2024-12-30T01:12:28.618398", "galaxy_version": "23.1", "command_version": "Version: 1.15.1 (using htslib 1.15.1)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.15.1+galaxy4", "history_id": "1262154bdd2f9614", "external_id": "gxy-rrkwf", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/8/2/3/dataset_8236698a-f809-4b23-b6ef-a17385bdfaa5.dat' > input0.vcf.gz && bcftools index input0.vcf.gz && echo 'input0.vcf.gz' >> vcfs_list && bgzip -c '/galaxy/server/database/objects/2/2/0/dataset_2207c916-be53-48de-98d1-447e01386689.dat' > input1.vcf.gz && bcftools index input1.vcf.gz && echo 'input1.vcf.gz' >> vcfs_list && bcftools concat --allow-overlaps --min-PQ 30 --output-type 'v' --threads ${GALAXY_SLOTS:-4} input0.vcf.gz input1.vcf.gz > '/galaxy/server/database/objects/2/3/0/dataset_2300e8a2-e345-4666-b964-46d2622571d7.dat'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "sec_default": "{\"compact_PS\": false, \"min_PQ\": \"30\", \"mode\": {\"__current_case__\": 1, \"ligate\": false, \"ligate_mode\": null, \"naive\": \"no\", \"overlaps\": {\"__current_case__\": 0, \"allow_overlaps\": \"yes\", \"rm_dups\": null}}}", "sec_restrict": "{\"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null}"}, "inputs": {"input_files": {"id": "ce812daebfa4cb32", "src": "hda", "uuid": "8236698a-f809-4b23-b6ef-a17385bdfaa5"}, "input_files1": {"id": "ce812daebfa4cb32", "src": "hda", "uuid": "8236698a-f809-4b23-b6ef-a17385bdfaa5"}, "input_files2": {"id": "121cbf44a773e05b", "src": "hda", "uuid": "2207c916-be53-48de-98d1-447e01386689"}}, "outputs": {"output_file": {"id": "fccdf7c99d58ccb9", "src": "hda", "uuid": "2300e8a2-e345-4666-b964-46d2622571d7"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Checking the headers and starting positions of 2 files\n", "job_stdout": "", "job_stderr": "", "stderr": "Checking the headers and starting positions of 2 files\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-12-30 01:12:31", "plugin": "core", "name": "end_epoch", "raw_value": "1735521151.0000000"}, {"title": "Job Start Time", "value": "2024-12-30 01:12:30", "plugin": "core", "name": "start_epoch", "raw_value": "1735521150.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "bcftools_concat/1.15.1+galaxy4-3", "has_data": true, "data": {"tool_id": "bcftools_concat", "tool_version": "1.15.1+galaxy4", "test_index": 3, "time_seconds": 10.164400339126587, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "bcftools_concat/1.15.1+galaxy4-4", "has_data": true, "data": {"tool_id": "bcftools_concat", "tool_version": "1.15.1+galaxy4", "test_index": 4, "time_seconds": 29.139310359954834, "inputs": {"input_files": [{"src": "hda", "id": "e49fa79d982a2e0e"}, {"src": "hda", "id": "35dbb8216ed2c60c"}], "sec_restrict|regions_overlap": "1", "output_type": "v"}, "job": {"model_class": "Job", "id": "9765e6866d45e244", "state": "ok", "exit_code": 0, "update_time": "2024-12-30T01:13:20.559356", "create_time": "2024-12-30T01:13:09.239614", "galaxy_version": "23.1", "command_version": "Version: 1.15.1 (using htslib 1.15.1)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.15.1+galaxy4", "history_id": "1262154bdd2f9614", "external_id": "gxy-hq59p", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/5/a/d/dataset_5ad67651-0695-4121-9aec-b46dd9734f02.dat' > input0.vcf.gz && bcftools index input0.vcf.gz && echo 'input0.vcf.gz' >> vcfs_list && bgzip -c '/galaxy/server/database/objects/b/7/0/dataset_b7097205-1559-4f3f-a1d9-53de22150368.dat' > input1.vcf.gz && bcftools index input1.vcf.gz && echo 'input1.vcf.gz' >> vcfs_list && bcftools concat --allow-overlaps --min-PQ 30 --regions-overlap 1 --output-type 'v' --threads ${GALAXY_SLOTS:-4} input0.vcf.gz input1.vcf.gz > '/galaxy/server/database/objects/f/f/e/dataset_ffebfbd5-46f3-44c8-a54c-98b60c9ec0e3.dat'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "sec_default": "{\"compact_PS\": false, \"min_PQ\": \"30\", \"mode\": {\"__current_case__\": 1, \"ligate\": false, \"ligate_mode\": null, \"naive\": \"no\", \"overlaps\": {\"__current_case__\": 0, \"allow_overlaps\": \"yes\", \"rm_dups\": null}}}", "sec_restrict": "{\"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": \"1\"}"}, "inputs": {"input_files": {"id": "e49fa79d982a2e0e", "src": "hda", "uuid": "5ad67651-0695-4121-9aec-b46dd9734f02"}, "input_files1": {"id": "e49fa79d982a2e0e", "src": "hda", "uuid": "5ad67651-0695-4121-9aec-b46dd9734f02"}, "input_files2": {"id": "35dbb8216ed2c60c", "src": "hda", "uuid": "b7097205-1559-4f3f-a1d9-53de22150368"}}, "outputs": {"output_file": {"id": "9765e6866d45e244", "src": "hda", "uuid": "ffebfbd5-46f3-44c8-a54c-98b60c9ec0e3"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Checking the headers and starting positions of 2 files\n", "job_stdout": "", "job_stderr": "", "stderr": "Checking the headers and starting positions of 2 files\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-12-30 01:13:11", "plugin": "core", "name": "end_epoch", "raw_value": "1735521191.0000000"}, {"title": "Job Start Time", "value": "2024-12-30 01:13:10", "plugin": "core", "name": "start_epoch", "raw_value": "1735521190.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "bcftools_concat/1.15.1+galaxy4-5", "has_data": true, "data": {"tool_id": "bcftools_concat", "tool_version": "1.15.1+galaxy4", "test_index": 5, "time_seconds": 15.130417823791504, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "bwa/0.7.18-0", "has_data": true, "data": {"tool_id": "bwa", "tool_version": "0.7.18", "test_index": 0, "time_seconds": 35.030076026916504, "inputs": {"reference_source|ref_file": {"src": "hda", "id": "27d38c2acb093f4f"}, "reference_source|reference_source_selector": "history", "input_type|fastq_input1": {"src": "hda", "id": "869f33a53e53131b"}, "input_type|input_type_selector": "single", "analysis_type|analysis_type_selector": "illumina"}, "job": {"model_class": "Job", "id": "70f4a40ee2dd73ac", "state": "ok", "exit_code": 0, "update_time": "2024-12-30T01:23:25.937888", "create_time": "2024-12-30T01:23:07.488281", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.18", "history_id": "1262154bdd2f9614", "external_id": "gxy-t7tbg", "command_line": "set -o | grep -q pipefail && set -o pipefail; ln -s '/galaxy/server/database/objects/d/6/2/dataset_d62b40cf-3712-410b-af8d-e5caf23bfdf0.dat' 'localref.fa' && bwa index 'localref.fa' && bwa aln -t \"${GALAXY_SLOTS:-1}\" 'localref.fa' '/galaxy/server/database/objects/b/9/b/dataset_b9b211ff-d0df-4c46-b9be-0aa461ad4daf.dat' > first.sai && bwa samse 'localref.fa' first.sai '/galaxy/server/database/objects/b/9/b/dataset_b9b211ff-d0df-4c46-b9be-0aa461ad4daf.dat' | samtools sort -@${GALAXY_SLOTS:-2} -T \"${TMPDIR:-.}\" -O bam -o '/galaxy/server/database/objects/d/1/6/dataset_d16a2d20-8081-493c-94f4-3d02bc894176.dat'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "analysis_type": "{\"__current_case__\": 0, \"analysis_type_selector\": \"illumina\"}", "rg": "{\"__current_case__\": 3, \"rg_selector\": \"do_not_set\"}", "input_type": "{\"__current_case__\": 2, \"adv_se_options\": {\"__current_case__\": 1, \"adv_se_options_selector\": \"do_not_set\"}, \"fastq_input1\": {\"values\": [{\"id\": 144, \"src\": \"hda\"}]}, \"input_type_selector\": \"single\"}", "reference_source": "{\"__current_case__\": 1, \"index_a\": \"auto\", \"ref_file\": {\"values\": [{\"id\": 143, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}"}, "inputs": {"reference_source|ref_file": {"id": "27d38c2acb093f4f", "src": "hda", "uuid": "d62b40cf-3712-410b-af8d-e5caf23bfdf0"}, "input_type|fastq_input1": {"id": "869f33a53e53131b", "src": "hda", "uuid": "b9b211ff-d0df-4c46-b9be-0aa461ad4daf"}}, "outputs": {"bam_output": {"id": "70f4a40ee2dd73ac", "src": "hda", "uuid": "d16a2d20-8081-493c-94f4-3d02bc894176"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "[bwa_index] Pack FASTA... 0.00 sec\n[bwa_index] Construct BWT for the packed sequence...\n[bwa_index] 0.00 seconds elapse.\n[bwa_index] Update BWT... 0.00 sec\n[bwa_index] Pack forward-only FASTA... 0.00 sec\n[bwa_index] Construct SA from BWT and Occ... 0.00 sec\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa index localref.fa\n[main] Real time: 0.052 sec; CPU: 0.009 sec\n[bwa_aln] 17bp reads: max_diff = 2\n[bwa_aln] 38bp reads: max_diff = 3\n[bwa_aln] 64bp reads: max_diff = 4\n[bwa_aln] 93bp reads: max_diff = 5\n[bwa_aln] 124bp reads: max_diff = 6\n[bwa_aln] 157bp reads: max_diff = 7\n[bwa_aln] 190bp reads: max_diff = 8\n[bwa_aln] 225bp reads: max_diff = 9\n[bwa_aln_core] calculate SA coordinate... 0.03 sec\n[bwa_aln_core] write to the disk... 0.00 sec\n[bwa_aln_core] 100 sequences have been processed.\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa aln -t 8 localref.fa /galaxy/server/database/objects/b/9/b/dataset_b9b211ff-d0df-4c46-b9be-0aa461ad4daf.dat\n[main] Real time: 0.020 sec; CPU: 0.037 sec\n[bwa_aln_core] convert to sequence coordinate... 0.00 sec\n[bwa_aln_core] refine gapped alignments... 0.00 sec\n[bwa_aln_core] print alignments... 0.00 sec\n[bwa_aln_core] 100 sequences have been processed.\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa samse localref.fa first.sai /galaxy/server/database/objects/b/9/b/dataset_b9b211ff-d0df-4c46-b9be-0aa461ad4daf.dat\n[main] Real time: 0.008 sec; CPU: 0.003 sec\n", "job_stdout": "", "job_stderr": "", "stderr": "[bwa_index] Pack FASTA... 0.00 sec\n[bwa_index] Construct BWT for the packed sequence...\n[bwa_index] 0.00 seconds elapse.\n[bwa_index] Update BWT... 0.00 sec\n[bwa_index] Pack forward-only FASTA... 0.00 sec\n[bwa_index] Construct SA from BWT and Occ... 0.00 sec\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa index localref.fa\n[main] Real time: 0.052 sec; CPU: 0.009 sec\n[bwa_aln] 17bp reads: max_diff = 2\n[bwa_aln] 38bp reads: max_diff = 3\n[bwa_aln] 64bp reads: max_diff = 4\n[bwa_aln] 93bp reads: max_diff = 5\n[bwa_aln] 124bp reads: max_diff = 6\n[bwa_aln] 157bp reads: max_diff = 7\n[bwa_aln] 190bp reads: max_diff = 8\n[bwa_aln] 225bp reads: max_diff = 9\n[bwa_aln_core] calculate SA coordinate... 0.03 sec\n[bwa_aln_core] write to the disk... 0.00 sec\n[bwa_aln_core] 100 sequences have been processed.\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa aln -t 8 localref.fa /galaxy/server/database/objects/b/9/b/dataset_b9b211ff-d0df-4c46-b9be-0aa461ad4daf.dat\n[main] Real time: 0.020 sec; CPU: 0.037 sec\n[bwa_aln_core] convert to sequence coordinate... 0.00 sec\n[bwa_aln_core] refine gapped alignments... 0.00 sec\n[bwa_aln_core] print alignments... 0.00 sec\n[bwa_aln_core] 100 sequences have been processed.\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa samse localref.fa first.sai /galaxy/server/database/objects/b/9/b/dataset_b9b211ff-d0df-4c46-b9be-0aa461ad4daf.dat\n[main] Real time: 0.008 sec; CPU: 0.003 sec\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-12-30 01:23:14", "plugin": "core", "name": "end_epoch", "raw_value": "1735521794.0000000"}, {"title": "Job Start Time", "value": "2024-12-30 01:23:14", "plugin": "core", "name": "start_epoch", "raw_value": "1735521794.0000000"}, {"title": "Memory Allocated (MB)", "value": "21474", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "21474.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "bwa/0.7.18-1", "has_data": true, "data": {"tool_id": "bwa", "tool_version": "0.7.18", "test_index": 1, "time_seconds": 31.54680609703064, "inputs": {"reference_source|ref_file": {"src": "hda", "id": "7a2d1bbf6938011d"}, "reference_source|reference_source_selector": "history", "input_type|fastq_input1": {"src": "hda", "id": "8bcbbbc7eb8bb479"}, "input_type|fastq_input2": {"src": "hda", "id": "1c85cb4b1429bce5"}, "input_type|input_type_selector": "paired", "analysis_type|analysis_type_selector": "illumina"}, "job": {"model_class": "Job", "id": "4fafbc5467932c94", "state": "ok", "exit_code": 0, "update_time": "2024-12-30T01:23:57.614229", "create_time": "2024-12-30T01:23:45.509376", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.18", "history_id": "1262154bdd2f9614", "external_id": "gxy-jvl9j", "command_line": "set -o | grep -q pipefail && set -o pipefail; ln -s '/galaxy/server/database/objects/b/8/b/dataset_b8b99bf5-7071-4c84-b5f4-3fa44463e901.dat' 'localref.fa' && bwa index 'localref.fa' && bwa aln -t \"${GALAXY_SLOTS:-1}\" 'localref.fa' '/galaxy/server/database/objects/e/2/9/dataset_e29437f7-8a81-4bac-a8fa-dbd9d6a70c43.dat' > first.sai && bwa aln -t \"${GALAXY_SLOTS:-1}\" 'localref.fa' '/galaxy/server/database/objects/e/7/a/dataset_e7aa1d48-72f5-469b-987a-cee73ae4ed9e.dat' > second.sai && bwa sampe 'localref.fa' first.sai second.sai '/galaxy/server/database/objects/e/2/9/dataset_e29437f7-8a81-4bac-a8fa-dbd9d6a70c43.dat' '/galaxy/server/database/objects/e/7/a/dataset_e7aa1d48-72f5-469b-987a-cee73ae4ed9e.dat' | samtools sort -@${GALAXY_SLOTS:-2} -T \"${TMPDIR:-.}\" -O bam -o '/galaxy/server/database/objects/2/6/9/dataset_2690073e-63ff-4898-b73f-fa0f96430ca6.dat'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "analysis_type": "{\"__current_case__\": 0, \"analysis_type_selector\": \"illumina\"}", "rg": "{\"__current_case__\": 3, \"rg_selector\": \"do_not_set\"}", "input_type": "{\"__current_case__\": 0, \"adv_pe_options\": {\"__current_case__\": 1, \"adv_pe_options_selector\": \"do_not_set\"}, \"fastq_input1\": {\"values\": [{\"id\": 147, \"src\": \"hda\"}]}, \"fastq_input2\": {\"values\": [{\"id\": 148, \"src\": \"hda\"}]}, \"input_type_selector\": \"paired\"}", "reference_source": "{\"__current_case__\": 1, \"index_a\": \"auto\", \"ref_file\": {\"values\": [{\"id\": 146, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}"}, "inputs": {"reference_source|ref_file": {"id": "7a2d1bbf6938011d", "src": "hda", "uuid": "b8b99bf5-7071-4c84-b5f4-3fa44463e901"}, "input_type|fastq_input1": {"id": "8bcbbbc7eb8bb479", "src": "hda", "uuid": "e29437f7-8a81-4bac-a8fa-dbd9d6a70c43"}, "input_type|fastq_input2": {"id": "1c85cb4b1429bce5", "src": "hda", "uuid": "e7aa1d48-72f5-469b-987a-cee73ae4ed9e"}}, "outputs": {"bam_output": {"id": "4fafbc5467932c94", "src": "hda", "uuid": "2690073e-63ff-4898-b73f-fa0f96430ca6"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "[bwa_index] Pack FASTA... 0.00 sec\n[bwa_index] Construct BWT for the packed sequence...\n[bwa_index] 0.00 seconds elapse.\n[bwa_index] Update BWT... 0.00 sec\n[bwa_index] Pack forward-only FASTA... 0.00 sec\n[bwa_index] Construct SA from BWT and Occ... 0.00 sec\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa index localref.fa\n[main] Real time: 0.053 sec; CPU: 0.010 sec\n[bwa_aln] 17bp reads: max_diff = 2\n[bwa_aln] 38bp reads: max_diff = 3\n[bwa_aln] 64bp reads: max_diff = 4\n[bwa_aln] 93bp reads: max_diff = 5\n[bwa_aln] 124bp reads: max_diff = 6\n[bwa_aln] 157bp reads: max_diff = 7\n[bwa_aln] 190bp reads: max_diff = 8\n[bwa_aln] 225bp reads: max_diff = 9\n[bwa_aln_core] calculate SA coordinate... 0.04 sec\n[bwa_aln_core] write to the disk... 0.00 sec\n[bwa_aln_core] 100 sequences have been processed.\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa aln -t 8 localref.fa /galaxy/server/database/objects/e/2/9/dataset_e29437f7-8a81-4bac-a8fa-dbd9d6a70c43.dat\n[main] Real time: 0.018 sec; CPU: 0.039 sec\n[bwa_aln] 17bp reads: max_diff = 2\n[bwa_aln] 38bp reads: max_diff = 3\n[bwa_aln] 64bp reads: max_diff = 4\n[bwa_aln] 93bp reads: max_diff = 5\n[bwa_aln] 124bp reads: max_diff = 6\n[bwa_aln] 157bp reads: max_diff = 7\n[bwa_aln] 190bp reads: max_diff = 8\n[bwa_aln] 225bp reads: max_diff = 9\n[bwa_aln_core] calculate SA coordinate... 0.03 sec\n[bwa_aln_core] write to the disk... 0.00 sec\n[bwa_aln_core] 100 sequences have been processed.\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa aln -t 8 localref.fa /galaxy/server/database/objects/e/7/a/dataset_e7aa1d48-72f5-469b-987a-cee73ae4ed9e.dat\n[main] Real time: 0.017 sec; CPU: 0.034 sec\n[bwa_sai2sam_pe_core] convert to sequence coordinate... \n[infer_isize] fail to infer insert size: too few good pairs\n[bwa_sai2sam_pe_core] time elapses: 0.00 sec\n[bwa_sai2sam_pe_core] changing coordinates of 0 alignments.\n[bwa_sai2sam_pe_core] align unmapped mate...\n[bwa_sai2sam_pe_core] time elapses: 0.00 sec\n[bwa_sai2sam_pe_core] refine gapped alignments... 0.00 sec\n[bwa_sai2sam_pe_core] print alignments... 0.00 sec\n[bwa_sai2sam_pe_core] 100 sequences have been processed.\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa sampe localref.fa first.sai second.sai /galaxy/server/database/objects/e/2/9/dataset_e29437f7-8a81-4bac-a8fa-dbd9d6a70c43.dat /galaxy/server/database/objects/e/7/a/dataset_e7aa1d48-72f5-469b-987a-cee73ae4ed9e.dat\n[main] Real time: 0.011 sec; CPU: 0.005 sec\n", "job_stdout": "", "job_stderr": "", "stderr": "[bwa_index] Pack FASTA... 0.00 sec\n[bwa_index] Construct BWT for the packed sequence...\n[bwa_index] 0.00 seconds elapse.\n[bwa_index] Update BWT... 0.00 sec\n[bwa_index] Pack forward-only FASTA... 0.00 sec\n[bwa_index] Construct SA from BWT and Occ... 0.00 sec\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa index localref.fa\n[main] Real time: 0.053 sec; CPU: 0.010 sec\n[bwa_aln] 17bp reads: max_diff = 2\n[bwa_aln] 38bp reads: max_diff = 3\n[bwa_aln] 64bp reads: max_diff = 4\n[bwa_aln] 93bp reads: max_diff = 5\n[bwa_aln] 124bp reads: max_diff = 6\n[bwa_aln] 157bp reads: max_diff = 7\n[bwa_aln] 190bp reads: max_diff = 8\n[bwa_aln] 225bp reads: max_diff = 9\n[bwa_aln_core] calculate SA coordinate... 0.04 sec\n[bwa_aln_core] write to the disk... 0.00 sec\n[bwa_aln_core] 100 sequences have been processed.\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa aln -t 8 localref.fa /galaxy/server/database/objects/e/2/9/dataset_e29437f7-8a81-4bac-a8fa-dbd9d6a70c43.dat\n[main] Real time: 0.018 sec; CPU: 0.039 sec\n[bwa_aln] 17bp reads: max_diff = 2\n[bwa_aln] 38bp reads: max_diff = 3\n[bwa_aln] 64bp reads: max_diff = 4\n[bwa_aln] 93bp reads: max_diff = 5\n[bwa_aln] 124bp reads: max_diff = 6\n[bwa_aln] 157bp reads: max_diff = 7\n[bwa_aln] 190bp reads: max_diff = 8\n[bwa_aln] 225bp reads: max_diff = 9\n[bwa_aln_core] calculate SA coordinate... 0.03 sec\n[bwa_aln_core] write to the disk... 0.00 sec\n[bwa_aln_core] 100 sequences have been processed.\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa aln -t 8 localref.fa /galaxy/server/database/objects/e/7/a/dataset_e7aa1d48-72f5-469b-987a-cee73ae4ed9e.dat\n[main] Real time: 0.017 sec; CPU: 0.034 sec\n[bwa_sai2sam_pe_core] convert to sequence coordinate... \n[infer_isize] fail to infer insert size: too few good pairs\n[bwa_sai2sam_pe_core] time elapses: 0.00 sec\n[bwa_sai2sam_pe_core] changing coordinates of 0 alignments.\n[bwa_sai2sam_pe_core] align unmapped mate...\n[bwa_sai2sam_pe_core] time elapses: 0.00 sec\n[bwa_sai2sam_pe_core] refine gapped alignments... 0.00 sec\n[bwa_sai2sam_pe_core] print alignments... 0.00 sec\n[bwa_sai2sam_pe_core] 100 sequences have been processed.\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa sampe localref.fa first.sai second.sai /galaxy/server/database/objects/e/2/9/dataset_e29437f7-8a81-4bac-a8fa-dbd9d6a70c43.dat /galaxy/server/database/objects/e/7/a/dataset_e7aa1d48-72f5-469b-987a-cee73ae4ed9e.dat\n[main] Real time: 0.011 sec; CPU: 0.005 sec\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-12-30 01:23:47", "plugin": "core", "name": "end_epoch", "raw_value": "1735521827.0000000"}, {"title": "Job Start Time", "value": "2024-12-30 01:23:47", "plugin": "core", "name": "start_epoch", "raw_value": "1735521827.0000000"}, {"title": "Memory Allocated (MB)", "value": "21474", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "21474.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "bwa/0.7.18-2", "has_data": true, "data": {"tool_id": "bwa", "tool_version": "0.7.18", "test_index": 2, "time_seconds": 9.0396146774292, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "bwa/0.7.18-3", "has_data": true, "data": {"tool_id": "bwa", "tool_version": "0.7.18", "test_index": 3, "time_seconds": 28.245434045791626, "inputs": {"reference_source|ref_file": {"src": "hda", "id": "e09d38ac2ec8c55c"}, "reference_source|reference_source_selector": "history", "input_type|bam_input": {"src": "hda", "id": "00205c8c505c46b6"}, "input_type|input_type_selector": "paired_bam", "analysis_type|analysis_type_selector": "illumina"}, "job": {"model_class": "Job", "id": "4f97579405063640", "state": "ok", "exit_code": 0, "update_time": "2024-12-30T01:24:35.117005", "create_time": "2024-12-30T01:24:23.589560", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.18", "history_id": "1262154bdd2f9614", "external_id": "gxy-ft5qk", "command_line": "set -o | grep -q pipefail && set -o pipefail; ln -s '/galaxy/server/database/objects/8/6/a/dataset_86a852c0-322b-4204-ad4e-e305ea2cc15f.dat' 'localref.fa' && bwa index 'localref.fa' && bwa aln -t \"${GALAXY_SLOTS:-1}\" -b -1 'localref.fa' '/galaxy/server/database/objects/f/5/4/dataset_f544c714-2316-4665-af54-671b2dc53035.dat' > first.sai && bwa aln -t \"${GALAXY_SLOTS:-1}\" -b -2 'localref.fa' '/galaxy/server/database/objects/f/5/4/dataset_f544c714-2316-4665-af54-671b2dc53035.dat' > second.sai && bwa sampe 'localref.fa' first.sai second.sai '/galaxy/server/database/objects/f/5/4/dataset_f544c714-2316-4665-af54-671b2dc53035.dat' '/galaxy/server/database/objects/f/5/4/dataset_f544c714-2316-4665-af54-671b2dc53035.dat' | samtools sort -@${GALAXY_SLOTS:-2} -T \"${TMPDIR:-.}\" -O bam -o '/galaxy/server/database/objects/f/d/e/dataset_fdea253a-657d-4d0b-a14c-b948ecf98859.dat'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "analysis_type": "{\"__current_case__\": 0, \"analysis_type_selector\": \"illumina\"}", "rg": "{\"__current_case__\": 3, \"rg_selector\": \"do_not_set\"}", "input_type": "{\"__current_case__\": 3, \"adv_bam_pe_options\": {\"__current_case__\": 1, \"adv_pe_options_selector\": \"do_not_set\"}, \"bam_input\": {\"values\": [{\"id\": 154, \"src\": \"hda\"}]}, \"input_type_selector\": \"paired_bam\"}", "reference_source": "{\"__current_case__\": 1, \"index_a\": \"auto\", \"ref_file\": {\"values\": [{\"id\": 153, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}"}, "inputs": {"reference_source|ref_file": {"id": "e09d38ac2ec8c55c", "src": "hda", "uuid": "86a852c0-322b-4204-ad4e-e305ea2cc15f"}, "input_type|bam_input": {"id": "00205c8c505c46b6", "src": "hda", "uuid": "f544c714-2316-4665-af54-671b2dc53035"}}, "outputs": {"bam_output": {"id": "4f97579405063640", "src": "hda", "uuid": "fdea253a-657d-4d0b-a14c-b948ecf98859"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "[bwa_index] Pack FASTA... 0.00 sec\n[bwa_index] Construct BWT for the packed sequence...\n[bwa_index] 0.00 seconds elapse.\n[bwa_index] Update BWT... 0.00 sec\n[bwa_index] Pack forward-only FASTA... 0.00 sec\n[bwa_index] Construct SA from BWT and Occ... 0.00 sec\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa index localref.fa\n[main] Real time: 0.050 sec; CPU: 0.009 sec\n[bwa_aln] 17bp reads: max_diff = 2\n[bwa_aln] 38bp reads: max_diff = 3\n[bwa_aln] 64bp reads: max_diff = 4\n[bwa_aln] 93bp reads: max_diff = 5\n[bwa_aln] 124bp reads: max_diff = 6\n[bwa_aln] 157bp reads: max_diff = 7\n[bwa_aln] 190bp reads: max_diff = 8\n[bwa_aln] 225bp reads: max_diff = 9\n[bwa_aln_core] calculate SA coordinate... 0.03 sec\n[bwa_aln_core] write to the disk... 0.00 sec\n[bwa_aln_core] 100 sequences have been processed.\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa aln -t 8 -b -1 localref.fa /galaxy/server/database/objects/f/5/4/dataset_f544c714-2316-4665-af54-671b2dc53035.dat\n[main] Real time: 0.019 sec; CPU: 0.038 sec\n[bwa_aln] 17bp reads: max_diff = 2\n[bwa_aln] 38bp reads: max_diff = 3\n[bwa_aln] 64bp reads: max_diff = 4\n[bwa_aln] 93bp reads: max_diff = 5\n[bwa_aln] 124bp reads: max_diff = 6\n[bwa_aln] 157bp reads: max_diff = 7\n[bwa_aln] 190bp reads: max_diff = 8\n[bwa_aln] 225bp reads: max_diff = 9\n[bwa_aln_core] calculate SA coordinate... 0.03 sec\n[bwa_aln_core] write to the disk... 0.00 sec\n[bwa_aln_core] 100 sequences have been processed.\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa aln -t 8 -b -2 localref.fa /galaxy/server/database/objects/f/5/4/dataset_f544c714-2316-4665-af54-671b2dc53035.dat\n[main] Real time: 0.016 sec; CPU: 0.032 sec\n[bwa_sai2sam_pe_core] convert to sequence coordinate... \n[infer_isize] fail to infer insert size: too few good pairs\n[bwa_sai2sam_pe_core] time elapses: 0.00 sec\n[bwa_sai2sam_pe_core] changing coordinates of 0 alignments.\n[bwa_sai2sam_pe_core] align unmapped mate...\n[bwa_sai2sam_pe_core] time elapses: 0.00 sec\n[bwa_sai2sam_pe_core] refine gapped alignments... 0.00 sec\n[bwa_sai2sam_pe_core] print alignments... 0.00 sec\n[bwa_sai2sam_pe_core] 100 sequences have been processed.\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa sampe localref.fa first.sai second.sai /galaxy/server/database/objects/f/5/4/dataset_f544c714-2316-4665-af54-671b2dc53035.dat /galaxy/server/database/objects/f/5/4/dataset_f544c714-2316-4665-af54-671b2dc53035.dat\n[main] Real time: 0.013 sec; CPU: 0.006 sec\n", "job_stdout": "", "job_stderr": "", "stderr": "[bwa_index] Pack FASTA... 0.00 sec\n[bwa_index] Construct BWT for the packed sequence...\n[bwa_index] 0.00 seconds elapse.\n[bwa_index] Update BWT... 0.00 sec\n[bwa_index] Pack forward-only FASTA... 0.00 sec\n[bwa_index] Construct SA from BWT and Occ... 0.00 sec\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa index localref.fa\n[main] Real time: 0.050 sec; CPU: 0.009 sec\n[bwa_aln] 17bp reads: max_diff = 2\n[bwa_aln] 38bp reads: max_diff = 3\n[bwa_aln] 64bp reads: max_diff = 4\n[bwa_aln] 93bp reads: max_diff = 5\n[bwa_aln] 124bp reads: max_diff = 6\n[bwa_aln] 157bp reads: max_diff = 7\n[bwa_aln] 190bp reads: max_diff = 8\n[bwa_aln] 225bp reads: max_diff = 9\n[bwa_aln_core] calculate SA coordinate... 0.03 sec\n[bwa_aln_core] write to the disk... 0.00 sec\n[bwa_aln_core] 100 sequences have been processed.\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa aln -t 8 -b -1 localref.fa /galaxy/server/database/objects/f/5/4/dataset_f544c714-2316-4665-af54-671b2dc53035.dat\n[main] Real time: 0.019 sec; CPU: 0.038 sec\n[bwa_aln] 17bp reads: max_diff = 2\n[bwa_aln] 38bp reads: max_diff = 3\n[bwa_aln] 64bp reads: max_diff = 4\n[bwa_aln] 93bp reads: max_diff = 5\n[bwa_aln] 124bp reads: max_diff = 6\n[bwa_aln] 157bp reads: max_diff = 7\n[bwa_aln] 190bp reads: max_diff = 8\n[bwa_aln] 225bp reads: max_diff = 9\n[bwa_aln_core] calculate SA coordinate... 0.03 sec\n[bwa_aln_core] write to the disk... 0.00 sec\n[bwa_aln_core] 100 sequences have been processed.\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa aln -t 8 -b -2 localref.fa /galaxy/server/database/objects/f/5/4/dataset_f544c714-2316-4665-af54-671b2dc53035.dat\n[main] Real time: 0.016 sec; CPU: 0.032 sec\n[bwa_sai2sam_pe_core] convert to sequence coordinate... \n[infer_isize] fail to infer insert size: too few good pairs\n[bwa_sai2sam_pe_core] time elapses: 0.00 sec\n[bwa_sai2sam_pe_core] changing coordinates of 0 alignments.\n[bwa_sai2sam_pe_core] align unmapped mate...\n[bwa_sai2sam_pe_core] time elapses: 0.00 sec\n[bwa_sai2sam_pe_core] refine gapped alignments... 0.00 sec\n[bwa_sai2sam_pe_core] print alignments... 0.00 sec\n[bwa_sai2sam_pe_core] 100 sequences have been processed.\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa sampe localref.fa first.sai second.sai /galaxy/server/database/objects/f/5/4/dataset_f544c714-2316-4665-af54-671b2dc53035.dat /galaxy/server/database/objects/f/5/4/dataset_f544c714-2316-4665-af54-671b2dc53035.dat\n[main] Real time: 0.013 sec; CPU: 0.006 sec\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-12-30 01:24:25", "plugin": "core", "name": "end_epoch", "raw_value": "1735521865.0000000"}, {"title": "Job Start Time", "value": "2024-12-30 01:24:25", "plugin": "core", "name": "start_epoch", "raw_value": "1735521865.0000000"}, {"title": "Memory Allocated (MB)", "value": "21474", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "21474.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "bwa/0.7.18-4", "has_data": true, "data": {"tool_id": "bwa", "tool_version": "0.7.18", "test_index": 4, "time_seconds": 31.149874210357666, "inputs": {"reference_source|ref_file": {"src": "hda", "id": "acb31e04834d1552"}, "reference_source|reference_source_selector": "history", "input_type|fastq_input1": {"src": "hda", "id": "1a46ae39a1533e33"}, "input_type|fastq_input2": {"src": "hda", "id": "ef0423079d291afd"}, "input_type|input_type_selector": "paired", "rg|read_group_id_conditional|ID": "rg1", "rg|PL": "CAPILLARY", "rg|rg_selector": "set", "analysis_type|analysis_type_selector": "illumina"}, "job": {"model_class": "Job", "id": "5e0a58b814e449e7", "state": "ok", "exit_code": 0, "update_time": "2024-12-30T01:25:06.301297", "create_time": "2024-12-30T01:24:54.316615", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.18", "history_id": "1262154bdd2f9614", "external_id": "gxy-kgvn6", "command_line": "set -o | grep -q pipefail && set -o pipefail; ln -s '/galaxy/server/database/objects/a/f/5/dataset_af532a71-8f4f-4540-903d-9f85c201a615.dat' 'localref.fa' && bwa index 'localref.fa' && bwa aln -t \"${GALAXY_SLOTS:-1}\" 'localref.fa' '/galaxy/server/database/objects/6/2/2/dataset_6220af1a-6be9-4252-9598-5c85c3625797.dat' > first.sai && bwa aln -t \"${GALAXY_SLOTS:-1}\" 'localref.fa' '/galaxy/server/database/objects/c/b/f/dataset_cbfa711d-b371-43d3-9dc1-3d279ecde592.dat' > second.sai && bwa sampe -r '@RG\\tID:rg1\\tPL:CAPILLARY' 'localref.fa' first.sai second.sai '/galaxy/server/database/objects/6/2/2/dataset_6220af1a-6be9-4252-9598-5c85c3625797.dat' '/galaxy/server/database/objects/c/b/f/dataset_cbfa711d-b371-43d3-9dc1-3d279ecde592.dat' | samtools sort -@${GALAXY_SLOTS:-2} -T \"${TMPDIR:-.}\" -O bam -o '/galaxy/server/database/objects/7/a/8/dataset_7a8f6c70-5e53-4249-938b-34405b3fd34a.dat'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "analysis_type": "{\"__current_case__\": 0, \"analysis_type_selector\": \"illumina\"}", "rg": "{\"CN\": null, \"DS\": null, \"DT\": null, \"FO\": null, \"KS\": null, \"PG\": null, \"PI\": \"\", \"PL\": \"CAPILLARY\", \"PU\": null, \"__current_case__\": 1, \"read_group_id_conditional\": {\"ID\": \"rg1\", \"__current_case__\": 1, \"do_auto_name\": false}, \"read_group_lb_conditional\": {\"LB\": null, \"__current_case__\": 1, \"do_auto_name\": false}, \"read_group_sm_conditional\": {\"SM\": \"\", \"__current_case__\": 1, \"do_auto_name\": false}, \"rg_selector\": \"set\"}", "input_type": "{\"__current_case__\": 0, \"adv_pe_options\": {\"__current_case__\": 1, \"adv_pe_options_selector\": \"do_not_set\"}, \"fastq_input1\": {\"values\": [{\"id\": 157, \"src\": \"hda\"}]}, \"fastq_input2\": {\"values\": [{\"id\": 158, \"src\": \"hda\"}]}, \"input_type_selector\": \"paired\"}", "reference_source": "{\"__current_case__\": 1, \"index_a\": \"auto\", \"ref_file\": {\"values\": [{\"id\": 156, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}"}, "inputs": {"reference_source|ref_file": {"id": "acb31e04834d1552", "src": "hda", "uuid": "af532a71-8f4f-4540-903d-9f85c201a615"}, "input_type|fastq_input1": {"id": "1a46ae39a1533e33", "src": "hda", "uuid": "6220af1a-6be9-4252-9598-5c85c3625797"}, "input_type|fastq_input2": {"id": "ef0423079d291afd", "src": "hda", "uuid": "cbfa711d-b371-43d3-9dc1-3d279ecde592"}}, "outputs": {"bam_output": {"id": "5e0a58b814e449e7", "src": "hda", "uuid": "7a8f6c70-5e53-4249-938b-34405b3fd34a"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "[bwa_index] Pack FASTA... 0.00 sec\n[bwa_index] Construct BWT for the packed sequence...\n[bwa_index] 0.00 seconds elapse.\n[bwa_index] Update BWT... 0.00 sec\n[bwa_index] Pack forward-only FASTA... 0.00 sec\n[bwa_index] Construct SA from BWT and Occ... 0.00 sec\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa index localref.fa\n[main] Real time: 0.051 sec; CPU: 0.009 sec\n[bwa_aln] 17bp reads: max_diff = 2\n[bwa_aln] 38bp reads: max_diff = 3\n[bwa_aln] 64bp reads: max_diff = 4\n[bwa_aln] 93bp reads: max_diff = 5\n[bwa_aln] 124bp reads: max_diff = 6\n[bwa_aln] 157bp reads: max_diff = 7\n[bwa_aln] 190bp reads: max_diff = 8\n[bwa_aln] 225bp reads: max_diff = 9\n[bwa_aln_core] calculate SA coordinate... 0.04 sec\n[bwa_aln_core] write to the disk... 0.00 sec\n[bwa_aln_core] 100 sequences have been processed.\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa aln -t 8 localref.fa /galaxy/server/database/objects/6/2/2/dataset_6220af1a-6be9-4252-9598-5c85c3625797.dat\n[main] Real time: 0.019 sec; CPU: 0.043 sec\n[bwa_aln] 17bp reads: max_diff = 2\n[bwa_aln] 38bp reads: max_diff = 3\n[bwa_aln] 64bp reads: max_diff = 4\n[bwa_aln] 93bp reads: max_diff = 5\n[bwa_aln] 124bp reads: max_diff = 6\n[bwa_aln] 157bp reads: max_diff = 7\n[bwa_aln] 190bp reads: max_diff = 8\n[bwa_aln] 225bp reads: max_diff = 9\n[bwa_aln_core] calculate SA coordinate... 0.03 sec\n[bwa_aln_core] write to the disk... 0.00 sec\n[bwa_aln_core] 100 sequences have been processed.\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa aln -t 8 localref.fa /galaxy/server/database/objects/c/b/f/dataset_cbfa711d-b371-43d3-9dc1-3d279ecde592.dat\n[main] Real time: 0.018 sec; CPU: 0.033 sec\n[bwa_sai2sam_pe_core] convert to sequence coordinate... \n[infer_isize] fail to infer insert size: too few good pairs\n[bwa_sai2sam_pe_core] time elapses: 0.00 sec\n[bwa_sai2sam_pe_core] changing coordinates of 0 alignments.\n[bwa_sai2sam_pe_core] align unmapped mate...\n[bwa_sai2sam_pe_core] time elapses: 0.00 sec\n[bwa_sai2sam_pe_core] refine gapped alignments... 0.00 sec\n[bwa_sai2sam_pe_core] print alignments... 0.00 sec\n[bwa_sai2sam_pe_core] 100 sequences have been processed.\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa sampe -r @RG\\tID:rg1\\tPL:CAPILLARY localref.fa first.sai second.sai /galaxy/server/database/objects/6/2/2/dataset_6220af1a-6be9-4252-9598-5c85c3625797.dat /galaxy/server/database/objects/c/b/f/dataset_cbfa711d-b371-43d3-9dc1-3d279ecde592.dat\n[main] Real time: 0.010 sec; CPU: 0.004 sec\n", "job_stdout": "", "job_stderr": "", "stderr": "[bwa_index] Pack FASTA... 0.00 sec\n[bwa_index] Construct BWT for the packed sequence...\n[bwa_index] 0.00 seconds elapse.\n[bwa_index] Update BWT... 0.00 sec\n[bwa_index] Pack forward-only FASTA... 0.00 sec\n[bwa_index] Construct SA from BWT and Occ... 0.00 sec\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa index localref.fa\n[main] Real time: 0.051 sec; CPU: 0.009 sec\n[bwa_aln] 17bp reads: max_diff = 2\n[bwa_aln] 38bp reads: max_diff = 3\n[bwa_aln] 64bp reads: max_diff = 4\n[bwa_aln] 93bp reads: max_diff = 5\n[bwa_aln] 124bp reads: max_diff = 6\n[bwa_aln] 157bp reads: max_diff = 7\n[bwa_aln] 190bp reads: max_diff = 8\n[bwa_aln] 225bp reads: max_diff = 9\n[bwa_aln_core] calculate SA coordinate... 0.04 sec\n[bwa_aln_core] write to the disk... 0.00 sec\n[bwa_aln_core] 100 sequences have been processed.\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa aln -t 8 localref.fa /galaxy/server/database/objects/6/2/2/dataset_6220af1a-6be9-4252-9598-5c85c3625797.dat\n[main] Real time: 0.019 sec; CPU: 0.043 sec\n[bwa_aln] 17bp reads: max_diff = 2\n[bwa_aln] 38bp reads: max_diff = 3\n[bwa_aln] 64bp reads: max_diff = 4\n[bwa_aln] 93bp reads: max_diff = 5\n[bwa_aln] 124bp reads: max_diff = 6\n[bwa_aln] 157bp reads: max_diff = 7\n[bwa_aln] 190bp reads: max_diff = 8\n[bwa_aln] 225bp reads: max_diff = 9\n[bwa_aln_core] calculate SA coordinate... 0.03 sec\n[bwa_aln_core] write to the disk... 0.00 sec\n[bwa_aln_core] 100 sequences have been processed.\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa aln -t 8 localref.fa /galaxy/server/database/objects/c/b/f/dataset_cbfa711d-b371-43d3-9dc1-3d279ecde592.dat\n[main] Real time: 0.018 sec; CPU: 0.033 sec\n[bwa_sai2sam_pe_core] convert to sequence coordinate... \n[infer_isize] fail to infer insert size: too few good pairs\n[bwa_sai2sam_pe_core] time elapses: 0.00 sec\n[bwa_sai2sam_pe_core] changing coordinates of 0 alignments.\n[bwa_sai2sam_pe_core] align unmapped mate...\n[bwa_sai2sam_pe_core] time elapses: 0.00 sec\n[bwa_sai2sam_pe_core] refine gapped alignments... 0.00 sec\n[bwa_sai2sam_pe_core] print alignments... 0.00 sec\n[bwa_sai2sam_pe_core] 100 sequences have been processed.\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa sampe -r @RG\\tID:rg1\\tPL:CAPILLARY localref.fa first.sai second.sai /galaxy/server/database/objects/6/2/2/dataset_6220af1a-6be9-4252-9598-5c85c3625797.dat /galaxy/server/database/objects/c/b/f/dataset_cbfa711d-b371-43d3-9dc1-3d279ecde592.dat\n[main] Real time: 0.010 sec; CPU: 0.004 sec\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-12-30 01:24:56", "plugin": "core", "name": "end_epoch", "raw_value": "1735521896.0000000"}, {"title": "Job Start Time", "value": "2024-12-30 01:24:56", "plugin": "core", "name": "start_epoch", "raw_value": "1735521896.0000000"}, {"title": "Memory Allocated (MB)", "value": "21474", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "21474.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "deeptools_compute_gc_bias/3.5.4+galaxy0-0", "has_data": true, "data": {"tool_id": "deeptools_compute_gc_bias", "tool_version": "3.5.4+galaxy0", "test_index": 0, "time_seconds": 47.069599628448486, "inputs": {"bamInput": {"src": "hda", "id": "c82bbc66a620ae76"}, "source|input1": {"src": "hda", "id": "0e19f8b845668869"}, "source|ref_source": "history", "effectiveGenomeSize|effectiveGenomeSize": "10050", "effectiveGenomeSize|effectiveGenomeSize_opt": "specific", "fragmentLength": "300", "region": "chr2L", "advancedOpt|sampleSize": "10", "advancedOpt|regionSize": "1", "advancedOpt|showAdvancedOpt": "yes", "image_format": "none"}, "job": {"model_class": "Job", "id": "0f2a57d83e08c260", "state": "ok", "exit_code": 0, "update_time": "2024-12-30T01:22:50.158897", "create_time": "2024-12-30T01:22:21.409193", "galaxy_version": "23.1", "command_version": "computeGCBias 3.5.4", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/3.5.4+galaxy0", "history_id": "1262154bdd2f9614", "external_id": "gxy-lg4qn", "command_line": "ln -s '/galaxy/server/database/objects/3/7/3/dataset_3734d46b-308d-4777-9bb3-b8d6b5e76153.dat' local_bamInput.bam && ln -s '/galaxy/server/database/objects/_metadata_files/5/e/3/metadata_5e37ba68-658e-4309-84aa-125bffdbb7ab.dat' local_bamInput.bam.bai && computeGCBias --numberOfProcessors \"${GALAXY_SLOTS:-4}\" --bamfile local_bamInput.bam --GCbiasFrequenciesFile /galaxy/server/database/objects/d/8/4/dataset_d84da292-0cee-4866-8d65-82ce35ed2a96.dat --fragmentLength 300 --genome /galaxy/server/database/objects/5/8/d/dataset_58d1c012-f6f0-4dc5-ac52-6a247ec0862f.dat --effectiveGenomeSize 10050 --region 'chr2L' --sampleSize '10' --regionSize '1'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "image_format": "\"none\"", "advancedOpt": "{\"__current_case__\": 1, \"blackListFileName\": null, \"extraSampling\": null, \"regionSize\": \"1\", \"sampleSize\": \"10\", \"showAdvancedOpt\": \"yes\"}", "region": "\"chr2L\"", "fragmentLength": "\"300\"", "effectiveGenomeSize": "{\"__current_case__\": 0, \"effectiveGenomeSize\": \"10050\", \"effectiveGenomeSize_opt\": \"specific\"}", "source": "{\"__current_case__\": 1, \"input1\": {\"values\": [{\"id\": 141, \"src\": \"hda\"}]}, \"ref_source\": \"history\"}"}, "inputs": {"bamInput": {"id": "c82bbc66a620ae76", "src": "hda", "uuid": "3734d46b-308d-4777-9bb3-b8d6b5e76153"}, "source|input1": {"id": "0e19f8b845668869", "src": "hda", "uuid": "58d1c012-f6f0-4dc5-ac52-6a247ec0862f"}}, "outputs": {"outFileName": {"id": "0f2a57d83e08c260", "src": "hda", "uuid": "d84da292-0cee-4866-8d65-82ce35ed2a96"}}, "output_collections": {}, "tool_stdout": "2bit: /galaxy/server/database/objects/5/8/d/dataset_58d1c012-f6f0-4dc5-ac52-6a247ec0862f.dat\nbam: local_bamInput.bam\nfilter_out: None\nextra_sampling_file: None\ngenome_size: 10050\ntotal_reads: 12589\nreads_per_bp: 1.252636815920398\nmax_reads: 1553.0\nmin_reads: 82.0\ncomputing frequencies\nstepSize: 1005\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "2bit: /galaxy/server/database/objects/5/8/d/dataset_58d1c012-f6f0-4dc5-ac52-6a247ec0862f.dat\nbam: local_bamInput.bam\nfilter_out: None\nextra_sampling_file: None\ngenome_size: 10050\ntotal_reads: 12589\nreads_per_bp: 1.252636815920398\nmax_reads: 1553.0\nmin_reads: 82.0\ncomputing frequencies\nstepSize: 1005\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-12-30 01:22:38", "plugin": "core", "name": "end_epoch", "raw_value": "1735521758.0000000"}, {"title": "Job Start Time", "value": "2024-12-30 01:22:37", "plugin": "core", "name": "start_epoch", "raw_value": "1735521757.0000000"}, {"title": "Memory Allocated (MB)", "value": "25769", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "25769.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "fastq_filter/1.1.5+galaxy2-0", "has_data": true, "data": {"tool_id": "fastq_filter", "tool_version": "1.1.5+galaxy2", "test_index": 0, "time_seconds": 73.46885204315186, "inputs": {"input_file": {"src": "hda", "id": "1262154bdd2f9614"}, "min_size": "0", "max_size": "0", "min_quality": "0", "max_quality": "0", "max_num_deviants": "0", "paired_end": false, "fastq_filters_0|offset_type|left_column_offset": "0", "fastq_filters_0|offset_type|right_column_offset": "0", "fastq_filters_0|offset_type|base_offset_type": "offsets_absolute", "fastq_filters_0|score_operation": "min", "fastq_filters_0|score_comparison": ">=", "fastq_filters_0|score": "0"}, "job": {"model_class": "Job", "id": "2120c8b44284dbd0", "state": "ok", "exit_code": 0, "update_time": "2024-12-30T00:54:38.568645", "create_time": "2024-12-30T00:53:52.280384", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5+galaxy2", "history_id": "1262154bdd2f9614", "external_id": "gxy-qj8xc", "command_line": "gx-fastq-filter '/galaxy/server/database/objects/f/8/d/dataset_f8d2e3ae-0730-4f57-8e66-88b71398734c.dat' '/galaxy/server/database/jobs_directory/000/2/configs/tmpgn3htfkj' '/galaxy/server/database/objects/e/b/6/dataset_eb67a9a0-727d-4723-9f99-2f4e42a6a3ef.dat' '/galaxy/server/database/objects/e/b/6/dataset_eb67a9a0-727d-4723-9f99-2f4e42a6a3ef_files' 'sanger'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "fastq_filters": 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'Genotype::Mut,Mut,Mut,WT,WT,WT|Batch::b1,b2,b3,b1,b2,b3' -D 'Mut-WT' -P i -l '0.0' -p '0.05' -d 'BH' -G '6' -n 'TMM' -b && mkdir ./output_dir && cp '/galaxy/server/database/objects/f/9/3/dataset_f93a51db-78ad-4c8d-b9b1-4c3c48aaf706_files'/*tsv output_dir/ && cp -r ./glimma* '/galaxy/server/database/objects/f/9/3/dataset_f93a51db-78ad-4c8d-b9b1-4c3c48aaf706_files'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"lfc\": \"0.0\", \"normalisationOption\": \"TMM\", \"pAdjust\": \"BH\", \"pVal\": \"0.05\", \"robOption\": true, \"topgenes\": \"6\", \"treat\": false}", "out": "{\"filtCounts\": false, \"libinfo\": false, \"normCounts\": false, \"plots\": \"i\", \"rdaOption\": false, \"rscript\": false}", "f": "{\"filt\": {\"__current_case__\": 1, \"filt_select\": \"no\"}}", "cont": "{\"__current_case__\": 1, \"cfile\": \"no\", \"rep_contrast\": [{\"__index__\": 0, \"contrast\": 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"tool_stdout": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n[1] \"Extracting counts\"\n[1] \"Generating DGEList object\"\n[1] \"Generating Design\"\n[1] \"Calculating Normalisation Factors\"\n[1] \"Generating Contrasts\"\n[1] \"Generating MDS plot\"\n[1] \"Generating DE results\"\n", "tool_stderr": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n", "job_stdout": "", "job_stderr": "", "stderr": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n", "stdout": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n[1] \"Extracting counts\"\n[1] \"Generating DGEList object\"\n[1] \"Generating Design\"\n[1] \"Calculating Normalisation Factors\"\n[1] \"Generating Contrasts\"\n[1] \"Generating MDS plot\"\n[1] \"Generating DE results\"\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "19 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "19.0000000"}, {"title": "Job End Time", "value": "2024-12-30 01:28:35", "plugin": "core", "name": "end_epoch", "raw_value": "1735522115.0000000"}, {"title": "Job Start Time", "value": "2024-12-30 01:28:16", "plugin": "core", "name": "start_epoch", "raw_value": "1735522096.0000000"}, {"title": "Memory Allocated (MB)", "value": "4294", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4294.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "limma_voom/3.58.1+galaxy0-4", "has_data": true, "data": {"tool_id": "limma_voom", "tool_version": 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"command_line": "Rscript '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/119b069fc845/limma_voom/limma_voom.R' -R '/galaxy/server/database/objects/1/a/6/dataset_1a6ee646-65d3-4f29-b438-e30b6a4d5638.dat' -o '/galaxy/server/database/objects/1/a/6/dataset_1a6ee646-65d3-4f29-b438-e30b6a4d5638_files' -m '/galaxy/server/database/objects/5/0/7/dataset_5079b547-6f62-440f-b6be-37cee67a2794.dat' -f '/galaxy/server/database/objects/5/9/6/dataset_59637351-43db-440d-baf0-7eae2ce85afc.dat' -D 'Mut-WT' -P i -l '0.0' -p '0.05' -d 'BH' -G '6' -n 'TMM' -b && mkdir ./output_dir && cp '/galaxy/server/database/objects/1/a/6/dataset_1a6ee646-65d3-4f29-b438-e30b6a4d5638_files'/*tsv output_dir/ && cp -r ./glimma* '/galaxy/server/database/objects/1/a/6/dataset_1a6ee646-65d3-4f29-b438-e30b6a4d5638_files'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"lfc\": \"0.0\", \"normalisationOption\": \"TMM\", \"pAdjust\": \"BH\", \"pVal\": \"0.05\", \"robOption\": true, \"topgenes\": \"6\", \"treat\": false}", "out": "{\"filtCounts\": false, \"libinfo\": false, \"normCounts\": false, \"plots\": \"i\", \"rdaOption\": false, \"rscript\": false}", "f": "{\"filt\": {\"__current_case__\": 1, \"filt_select\": \"no\"}}", "cont": "{\"__current_case__\": 1, \"cfile\": \"no\", \"rep_contrast\": [{\"__index__\": 0, \"contrast\": \"Mut-WT\"}]}", "anno": "{\"__current_case__\": 1, \"annoOpt\": \"no\"}", "input": "{\"__current_case__\": 1, \"counts\": {\"values\": [{\"id\": 175, \"src\": \"hda\"}]}, \"fact\": {\"__current_case__\": 0, \"ffile\": \"yes\", \"finfo\": {\"values\": [{\"id\": 176, \"src\": \"hda\"}]}}, \"format\": \"matrix\"}", "deMethod": "{\"__current_case__\": 0, \"de_select\": \"voom\", \"weightOption\": false}"}, "inputs": {"input|counts": {"id": "0b4b4d92232ad17f", "src": "hda", "uuid": "5079b547-6f62-440f-b6be-37cee67a2794"}, "input|fact|finfo": {"id": "d4289a12a4802052", "src": "hda", "uuid": "59637351-43db-440d-baf0-7eae2ce85afc"}}, "outputs": {"outReport": {"id": "bf46a3337c78fbae", "src": "hda", "uuid": "1a6ee646-65d3-4f29-b438-e30b6a4d5638"}, "__new_primary_file_outTables|limma-voom_Mut-WT__": {"id": "d88e8580f2de0ee6", "src": "hda", "uuid": "bb86160c-1d2f-4a65-8431-8c770d623482"}}, "output_collections": {"outTables": {"id": "724c2bda50d999de", "src": "hdca"}}, "tool_stdout": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n[1] \"Extracting counts\"\n[1] \"Generating DGEList object\"\n[1] \"Generating Design\"\n[1] \"Calculating Normalisation Factors\"\n[1] \"Generating Contrasts\"\n[1] \"Generating MDS plot\"\n[1] \"Generating DE results\"\n", "tool_stderr": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n", "job_stdout": "", "job_stderr": "", "stderr": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n", "stdout": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n[1] \"Extracting counts\"\n[1] \"Generating DGEList object\"\n[1] \"Generating Design\"\n[1] \"Calculating Normalisation Factors\"\n[1] \"Generating Contrasts\"\n[1] \"Generating MDS plot\"\n[1] \"Generating DE results\"\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "19 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "19.0000000"}, {"title": "Job End Time", "value": "2024-12-30 01:29:21", "plugin": "core", "name": "end_epoch", "raw_value": "1735522161.0000000"}, {"title": "Job Start Time", "value": "2024-12-30 01:29:02", "plugin": 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'/galaxy/server/database/objects/d/7/1/dataset_d7181054-7395-454b-9487-57739a522b9c_files' -m '/galaxy/server/database/objects/5/9/b/dataset_59bd7131-9a57-498f-bc95-2fd0fb0c0269.dat' -i 'Genotype::Mut,Mut,Mut,WT,WT,WT' -D 'Mut-WT' -z '10' -s '3' -P i -F -x -l '0.0' -p '0.05' -d 'BH' -G '6' -n 'TMM' -b && mkdir ./output_dir && cp '/galaxy/server/database/objects/d/7/1/dataset_d7181054-7395-454b-9487-57739a522b9c_files'/*tsv output_dir/ && cp -r ./glimma* '/galaxy/server/database/objects/d/7/1/dataset_d7181054-7395-454b-9487-57739a522b9c_files' && cp '/galaxy/server/database/objects/d/7/1/dataset_d7181054-7395-454b-9487-57739a522b9c_files'/*counts output_dir/", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"lfc\": \"0.0\", \"normalisationOption\": \"TMM\", \"pAdjust\": \"BH\", \"pVal\": \"0.05\", \"robOption\": true, \"topgenes\": \"6\", \"treat\": false}", "out": "{\"filtCounts\": true, \"libinfo\": false, \"normCounts\": true, \"plots\": \"i\", \"rdaOption\": false, \"rscript\": false}", "f": "{\"filt\": {\"__current_case__\": 0, \"cformat\": {\"__current_case__\": 1, \"cntReq\": \"10\", \"format_select\": \"counts\", \"samples\": {\"__current_case__\": 1, \"cntSampleReq\": \"3\", \"count_select\": \"sample\"}}, \"filt_select\": \"yes\"}}", "cont": "{\"__current_case__\": 1, \"cfile\": \"no\", \"rep_contrast\": [{\"__index__\": 0, \"contrast\": \"Mut-WT\"}]}", "anno": "{\"__current_case__\": 1, \"annoOpt\": \"no\"}", "input": "{\"__current_case__\": 1, \"counts\": {\"values\": [{\"id\": 179, \"src\": \"hda\"}]}, \"fact\": {\"__current_case__\": 1, \"ffile\": \"no\", \"rep_factor\": [{\"__index__\": 0, \"factorName\": \"Genotype\", \"groupNames\": \"Mut,Mut,Mut,WT,WT,WT\"}]}, \"format\": \"matrix\"}", "deMethod": "{\"__current_case__\": 0, \"de_select\": \"voom\", \"weightOption\": false}"}, "inputs": {"input|counts": {"id": "fe862782b9d94df9", "src": "hda", "uuid": "59bd7131-9a57-498f-bc95-2fd0fb0c0269"}}, "outputs": {"outReport": {"id": "6dfd83583e16855b", "src": "hda", "uuid": "d7181054-7395-454b-9487-57739a522b9c"}, "outFilt": {"id": "c81c340ac1b1db4a", "src": "hda", "uuid": "8fa91a89-bcaf-48d3-b414-fbc033ee16e4"}, "outNorm": {"id": "de5fe91328addd71", "src": "hda", "uuid": "ea9951b0-4ec7-4388-bf71-36b41c927e62"}, "__new_primary_file_outTables|limma-voom_Mut-WT__": {"id": "e644d97e8e35fce2", "src": "hda", "uuid": "f474e88e-0b64-4fdf-aed5-a18124712ae6"}}, "output_collections": {"outTables": {"id": "0f853f868e941b7d", "src": "hdca"}}, "tool_stdout": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n[1] \"Extracting counts\"\n[1] \"Outputting filtered counts\"\n[1] \"Generating DGEList object\"\n[1] \"Generating Design\"\n[1] \"Calculating Normalisation Factors\"\n[1] \"Generating Contrasts\"\n[1] \"Generating MDS plot\"\n[1] \"Generating DE results\"\n", "tool_stderr": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n", "job_stdout": "", "job_stderr": "", "stderr": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n", "stdout": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n[1] \"Extracting counts\"\n[1] \"Outputting filtered counts\"\n[1] \"Generating DGEList object\"\n[1] \"Generating Design\"\n[1] \"Calculating Normalisation Factors\"\n[1] \"Generating Contrasts\"\n[1] \"Generating MDS plot\"\n[1] \"Generating DE results\"\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "19 seconds", "plugin": "core", "name": "runtime_seconds", 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"test_index": 7, "time_seconds": 68.23780393600464, "inputs": {"deMethod|de_select": "trend", "input|counts": {"src": "hda", "id": "935606a73f55d869"}, "input|fact|rep_factor_0|factorName": "Genotype", "input|fact|rep_factor_0|groupNames": "Mut,Mut,Mut,WT,WT,WT", "input|format": "matrix", "cont|rep_contrast_0|contrast": "Mut-WT", "cont|cfile": "no", "adv|topgenes": "6", "adv|normalisationOption": "TMM"}, "job": {"model_class": "Job", "id": "1e92894b0aa06402", "state": "ok", "exit_code": 0, "update_time": "2024-12-30T01:31:50.672234", "create_time": "2024-12-30T01:31:19.439202", "galaxy_version": "23.1", "command_version": "R version 4.3.2 (2023-10-31) -- \"Eye Holes\", limma version 3.58.1, edgeR version 4.0.2, statmod version 1.5.0, scales version 1.3.0, rjson version 0.2.21, getopt version 1.20.4, gplots version 3.1.3.1, Glimma version 2.12.0", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.58.1+galaxy0", "history_id": "1262154bdd2f9614", "external_id": "gxy-wl97r", "command_line": "Rscript '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/119b069fc845/limma_voom/limma_voom.R' -R '/galaxy/server/database/objects/5/f/b/dataset_5fb6d6c2-6094-482a-b760-4ea34f11fc75.dat' -o '/galaxy/server/database/objects/5/f/b/dataset_5fb6d6c2-6094-482a-b760-4ea34f11fc75_files' -m '/galaxy/server/database/objects/d/9/0/dataset_d903e634-7047-45ab-9df8-5eb22cad9f4a.dat' -i 'Genotype::Mut,Mut,Mut,WT,WT,WT' -D 'Mut-WT' -P i -l '0.0' -p '0.05' -d 'BH' -G '6' -t 3.0 -n 'TMM' -b && mkdir ./output_dir && cp '/galaxy/server/database/objects/5/f/b/dataset_5fb6d6c2-6094-482a-b760-4ea34f11fc75_files'/*tsv output_dir/ && cp -r ./glimma* '/galaxy/server/database/objects/5/f/b/dataset_5fb6d6c2-6094-482a-b760-4ea34f11fc75_files'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"lfc\": \"0.0\", 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--min_trim_size '4' --extra_end_trim '2' --end_threshold '75.0' --middle_threshold '85.0' --extra_middle_trim_good_side '10' --extra_middle_trim_bad_side '100' --min_split_read_size '1000' -o 'out.fasta'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "middle_adapter_settings": "{\"discard_middle\": false, \"extra_middle_trim_bad_side\": \"100\", \"extra_middle_trim_good_side\": \"10\", \"middle_threshold\": \"85.0\", \"min_split_read_size\": \"1000\", \"no_split\": false}", "end_adapter_settings": "{\"end_size\": \"150\", \"end_threshold\": \"75.0\", \"extra_end_trim\": \"2\", \"min_trim_size\": \"4\"}", "adapter_search_settings": "{\"adapter_threshold\": \"90.0\", \"check_reads\": \"10000\", \"scoring_scheme\": \"3,-6,-5,-2\"}", "barcode_binning_settings": "{\"barcode_diff\": \"5.0\", \"barcode_threshold\": \"75.0\", \"discard_unassigned\": false, \"require_two_barcodes\": false}", "format": "\"fasta\""}, "inputs": {"input_file": {"id": "9efbec2a30985c3f", "src": "hda", "uuid": "8eded40f-a858-4405-966f-216e8dfed63d"}}, "outputs": {"outfile": {"id": "7b54e7fe9b136d43", "src": "hda", "uuid": "840b2760-7376-4b6e-8295-8795d4d3abb6"}}, "output_collections": {}, "tool_stdout": "\n\u001b[1m\u001b[4mLoading reads\u001b[0m\n/galaxy/server/database/objects/8/e/d/dataset_8eded40f-a858-4405-966f-216e8dfed63d.dat\n9 reads loaded\n\n\n\u001b[1m\u001b[4mLooking for known adapter sets\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n Best \u001b[0m\n read Best \u001b[0m\n start read end\u001b[0m\n \u001b[4mSet %ID %ID \u001b[0m\n \u001b[32mSQK-NSK007 96.4 95.5\u001b[0m\n Rapid 62.5 0.0\n RBK004_upstream 72.7 0.0\n SQK-MAP006 62.2 63.6\n SQK-MAP006 short 60.7 60.0\n PCR adapters 1 66.7 73.9\n PCR adapters 2 66.7 63.6\n PCR adapters 3 68.0 72.0\n 1D^2 part 1 62.1 58.8\n 1D^2 part 2 79.4 68.8\n cDNA SSP 57.1 61.4\n Barcode 1 (reverse) 59.4 66.7\n Barcode 2 (reverse) 66.7 63.0\n Barcode 3 (reverse) 69.2 72.0\n Barcode 4 (reverse) 66.7 63.3\n Barcode 5 (reverse) 62.5 66.7\n Barcode 6 (reverse) 73.1 62.5\n Barcode 7 (reverse) 65.4 65.5\n Barcode 8 (reverse) 69.2 58.3\n Barcode 9 (reverse) 75.0 66.7\n Barcode 10 (reverse) 62.5 60.0\n Barcode 11 (reverse) 69.2 60.5\n Barcode 12 (reverse) 65.6 64.0\n Barcode 1 (forward) 65.4 61.5\n Barcode 2 (forward) 69.2 70.4\n Barcode 3 (forward) 73.1 68.0\n Barcode 4 (forward) 73.1 64.3\n Barcode 5 (forward) 62.5 66.7\n Barcode 6 (forward) 65.5 65.6\n Barcode 7 (forward) 73.1 66.7\n Barcode 8 (forward) 62.1 60.7\n Barcode 9 (forward) 68.0 70.8\n Barcode 10 (forward) 69.2 66.7\n Barcode 11 (forward) 65.4 60.7\n Barcode 12 (forward) 64.3 66.7\n Barcode 13 (forward) 64.3 69.2\n Barcode 14 (forward) 63.3 66.7\n Barcode 15 (forward) 66.7 66.7\n Barcode 16 (forward) 70.8 65.5\n Barcode 17 (forward) 69.2 66.7\n Barcode 18 (forward) 70.4 70.4\n Barcode 19 (forward) 65.5 64.0\n Barcode 20 (forward) 65.5 64.0\n Barcode 21 (forward) 64.3 66.7\n Barcode 22 (forward) 69.2 68.0\n Barcode 23 (forward) 61.5 66.7\n Barcode 24 (forward) 66.7 65.4\n Barcode 25 (forward) 64.0 65.5\n Barcode 26 (forward) 72.0 72.0\n Barcode 27 (forward) 77.8 60.7\n Barcode 28 (forward) 65.5 66.7\n Barcode 29 (forward) 62.5 66.7\n Barcode 30 (forward) 68.0 65.4\n Barcode 31 (forward) 62.5 69.2\n Barcode 32 (forward) 68.0 70.8\n Barcode 33 (forward) 62.5 70.4\n Barcode 34 (forward) 64.0 62.5\n Barcode 35 (forward) 65.5 65.4\n Barcode 36 (forward) 63.0 63.0\n Barcode 37 (forward) 67.9 64.3\n Barcode 38 (forward) 64.0 62.1\n Barcode 39 (forward) 64.0 69.2\n Barcode 40 (forward) 62.5 64.0\n Barcode 41 (forward) 68.0 65.5\n Barcode 42 (forward) 70.4 69.2\n Barcode 43 (forward) 63.3 63.3\n Barcode 44 (forward) 60.0 66.7\n Barcode 45 (forward) 73.1 65.4\n Barcode 46 (forward) 65.4 60.7\n Barcode 47 (forward) 65.5 64.0\n Barcode 48 (forward) 71.4 62.1\n Barcode 49 (forward) 69.2 62.1\n Barcode 50 (forward) 66.7 63.0\n Barcode 51 (forward) 69.2 64.3\n Barcode 52 (forward) 66.7 64.0\n Barcode 53 (forward) 67.9 69.0\n Barcode 54 (forward) 69.2 64.0\n Barcode 55 (forward) 66.7 73.1\n Barcode 56 (forward) 66.7 72.0\n Barcode 57 (forward) 69.0 60.0\n Barcode 58 (forward) 70.4 72.0\n Barcode 59 (forward) 56.7 66.7\n Barcode 60 (forward) 66.7 66.7\n Barcode 61 (forward) 70.8 65.5\n Barcode 62 (forward) 66.7 68.0\n Barcode 63 (forward) 66.7 60.7\n Barcode 64 (forward) 69.2 66.7\n Barcode 65 (forward) 61.5 69.0\n Barcode 66 (forward) 64.3 63.0\n Barcode 67 (forward) 66.7 67.9\n Barcode 68 (forward) 67.9 69.2\n Barcode 69 (forward) 69.2 75.0\n Barcode 70 (forward) 64.3 73.1\n Barcode 71 (forward) 64.0 71.4\n Barcode 72 (forward) 66.7 62.1\n Barcode 73 (forward) 67.7 64.0\n Barcode 74 (forward) 64.5 68.0\n Barcode 75 (forward) 65.4 65.5\n Barcode 76 (forward) 70.4 70.8\n Barcode 77 (forward) 65.4 64.3\n Barcode 78 (forward) 67.7 63.0\n Barcode 79 (forward) 70.8 69.2\n Barcode 80 (forward) 71.4 72.0\n Barcode 81 (forward) 68.0 66.7\n Barcode 82 (forward) 64.7 66.7\n Barcode 83 (forward) 69.2 68.0\n Barcode 84 (forward) 70.8 67.9\n Barcode 85 (forward) 61.5 60.0\n Barcode 86 (forward) 64.3 65.4\n Barcode 87 (forward) 66.7 65.4\n Barcode 88 (forward) 63.3 60.7\n Barcode 89 (forward) 69.2 66.7\n Barcode 90 (forward) 66.7 64.0\n Barcode 91 (forward) 68.0 64.3\n Barcode 92 (forward) 65.5 68.0\n Barcode 93 (forward) 69.2 73.1\n Barcode 94 (forward) 63.0 68.0\n Barcode 95 (forward) 64.0 63.3\n Barcode 96 (forward) 69.0 68.0\n\n\n\u001b[1m\u001b[4mTrimming adapters from read ends\u001b[0m\n SQK-NSK007_Y_Top: \u001b[31mAATGTACTTCGTTCAGTTACGTATTGCT\u001b[0m\n SQK-NSK007_Y_Bottom: \u001b[31mGCAATACGTAACTGAACGAAGT\u001b[0m\n\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n\n4 / 9 reads had adapters trimmed from their start (74 bp removed)\n3 / 9 reads had adapters trimmed from their end (49 bp removed)\n\n\n\u001b[1m\u001b[4mSplitting reads containing middle adapters\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r10 / 9 (111.1%)\r9 / 9 (100.0%)\n\n4 / 9 reads were split based on middle adapters\n\n\n\u001b[1m\u001b[4mSaving trimmed reads to file\u001b[0m\n\nSaved result to /galaxy/server/database/jobs_directory/000/129/working/out.fasta\n\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "\n\u001b[1m\u001b[4mLoading reads\u001b[0m\n/galaxy/server/database/objects/8/e/d/dataset_8eded40f-a858-4405-966f-216e8dfed63d.dat\n9 reads loaded\n\n\n\u001b[1m\u001b[4mLooking for known adapter sets\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n Best \u001b[0m\n read Best \u001b[0m\n start read end\u001b[0m\n \u001b[4mSet %ID %ID \u001b[0m\n \u001b[32mSQK-NSK007 96.4 95.5\u001b[0m\n Rapid 62.5 0.0\n RBK004_upstream 72.7 0.0\n SQK-MAP006 62.2 63.6\n SQK-MAP006 short 60.7 60.0\n PCR adapters 1 66.7 73.9\n PCR adapters 2 66.7 63.6\n PCR adapters 3 68.0 72.0\n 1D^2 part 1 62.1 58.8\n 1D^2 part 2 79.4 68.8\n cDNA SSP 57.1 61.4\n Barcode 1 (reverse) 59.4 66.7\n Barcode 2 (reverse) 66.7 63.0\n Barcode 3 (reverse) 69.2 72.0\n Barcode 4 (reverse) 66.7 63.3\n Barcode 5 (reverse) 62.5 66.7\n Barcode 6 (reverse) 73.1 62.5\n Barcode 7 (reverse) 65.4 65.5\n Barcode 8 (reverse) 69.2 58.3\n Barcode 9 (reverse) 75.0 66.7\n Barcode 10 (reverse) 62.5 60.0\n Barcode 11 (reverse) 69.2 60.5\n Barcode 12 (reverse) 65.6 64.0\n Barcode 1 (forward) 65.4 61.5\n Barcode 2 (forward) 69.2 70.4\n Barcode 3 (forward) 73.1 68.0\n Barcode 4 (forward) 73.1 64.3\n Barcode 5 (forward) 62.5 66.7\n Barcode 6 (forward) 65.5 65.6\n Barcode 7 (forward) 73.1 66.7\n Barcode 8 (forward) 62.1 60.7\n Barcode 9 (forward) 68.0 70.8\n Barcode 10 (forward) 69.2 66.7\n Barcode 11 (forward) 65.4 60.7\n Barcode 12 (forward) 64.3 66.7\n Barcode 13 (forward) 64.3 69.2\n Barcode 14 (forward) 63.3 66.7\n Barcode 15 (forward) 66.7 66.7\n Barcode 16 (forward) 70.8 65.5\n Barcode 17 (forward) 69.2 66.7\n Barcode 18 (forward) 70.4 70.4\n Barcode 19 (forward) 65.5 64.0\n Barcode 20 (forward) 65.5 64.0\n Barcode 21 (forward) 64.3 66.7\n Barcode 22 (forward) 69.2 68.0\n Barcode 23 (forward) 61.5 66.7\n Barcode 24 (forward) 66.7 65.4\n Barcode 25 (forward) 64.0 65.5\n Barcode 26 (forward) 72.0 72.0\n Barcode 27 (forward) 77.8 60.7\n Barcode 28 (forward) 65.5 66.7\n Barcode 29 (forward) 62.5 66.7\n Barcode 30 (forward) 68.0 65.4\n Barcode 31 (forward) 62.5 69.2\n Barcode 32 (forward) 68.0 70.8\n Barcode 33 (forward) 62.5 70.4\n Barcode 34 (forward) 64.0 62.5\n Barcode 35 (forward) 65.5 65.4\n Barcode 36 (forward) 63.0 63.0\n Barcode 37 (forward) 67.9 64.3\n Barcode 38 (forward) 64.0 62.1\n Barcode 39 (forward) 64.0 69.2\n Barcode 40 (forward) 62.5 64.0\n Barcode 41 (forward) 68.0 65.5\n Barcode 42 (forward) 70.4 69.2\n Barcode 43 (forward) 63.3 63.3\n Barcode 44 (forward) 60.0 66.7\n Barcode 45 (forward) 73.1 65.4\n Barcode 46 (forward) 65.4 60.7\n Barcode 47 (forward) 65.5 64.0\n Barcode 48 (forward) 71.4 62.1\n Barcode 49 (forward) 69.2 62.1\n Barcode 50 (forward) 66.7 63.0\n Barcode 51 (forward) 69.2 64.3\n Barcode 52 (forward) 66.7 64.0\n Barcode 53 (forward) 67.9 69.0\n Barcode 54 (forward) 69.2 64.0\n Barcode 55 (forward) 66.7 73.1\n Barcode 56 (forward) 66.7 72.0\n Barcode 57 (forward) 69.0 60.0\n Barcode 58 (forward) 70.4 72.0\n Barcode 59 (forward) 56.7 66.7\n Barcode 60 (forward) 66.7 66.7\n Barcode 61 (forward) 70.8 65.5\n Barcode 62 (forward) 66.7 68.0\n Barcode 63 (forward) 66.7 60.7\n Barcode 64 (forward) 69.2 66.7\n Barcode 65 (forward) 61.5 69.0\n Barcode 66 (forward) 64.3 63.0\n Barcode 67 (forward) 66.7 67.9\n Barcode 68 (forward) 67.9 69.2\n Barcode 69 (forward) 69.2 75.0\n Barcode 70 (forward) 64.3 73.1\n Barcode 71 (forward) 64.0 71.4\n Barcode 72 (forward) 66.7 62.1\n Barcode 73 (forward) 67.7 64.0\n Barcode 74 (forward) 64.5 68.0\n Barcode 75 (forward) 65.4 65.5\n Barcode 76 (forward) 70.4 70.8\n Barcode 77 (forward) 65.4 64.3\n Barcode 78 (forward) 67.7 63.0\n Barcode 79 (forward) 70.8 69.2\n Barcode 80 (forward) 71.4 72.0\n Barcode 81 (forward) 68.0 66.7\n Barcode 82 (forward) 64.7 66.7\n Barcode 83 (forward) 69.2 68.0\n Barcode 84 (forward) 70.8 67.9\n Barcode 85 (forward) 61.5 60.0\n Barcode 86 (forward) 64.3 65.4\n Barcode 87 (forward) 66.7 65.4\n Barcode 88 (forward) 63.3 60.7\n Barcode 89 (forward) 69.2 66.7\n Barcode 90 (forward) 66.7 64.0\n Barcode 91 (forward) 68.0 64.3\n Barcode 92 (forward) 65.5 68.0\n Barcode 93 (forward) 69.2 73.1\n Barcode 94 (forward) 63.0 68.0\n Barcode 95 (forward) 64.0 63.3\n Barcode 96 (forward) 69.0 68.0\n\n\n\u001b[1m\u001b[4mTrimming adapters from read ends\u001b[0m\n SQK-NSK007_Y_Top: \u001b[31mAATGTACTTCGTTCAGTTACGTATTGCT\u001b[0m\n SQK-NSK007_Y_Bottom: \u001b[31mGCAATACGTAACTGAACGAAGT\u001b[0m\n\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n\n4 / 9 reads had adapters trimmed from their start (74 bp removed)\n3 / 9 reads had adapters trimmed from their end (49 bp removed)\n\n\n\u001b[1m\u001b[4mSplitting reads containing middle adapters\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r10 / 9 (111.1%)\r9 / 9 (100.0%)\n\n4 / 9 reads were split based on middle adapters\n\n\n\u001b[1m\u001b[4mSaving trimmed reads to file\u001b[0m\n\nSaved result to /galaxy/server/database/jobs_directory/000/129/working/out.fasta\n\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-12-30 01:19:32", "plugin": "core", "name": "end_epoch", "raw_value": "1735521572.0000000"}, {"title": "Job Start Time", "value": "2024-12-30 01:19:31", "plugin": "core", "name": "start_epoch", "raw_value": "1735521571.0000000"}, {"title": "Memory Allocated (MB)", "value": "42949", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "42949.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "porechop/0.2.4+galaxy0-1", "has_data": true, "data": {"tool_id": "porechop", "tool_version": "0.2.4+galaxy0", "test_index": 1, "time_seconds": 27.4476957321167, "inputs": {"input_file": {"src": "hda", "id": "a6742216c12826b8"}, "format": "fastq"}, "job": {"model_class": "Job", "id": "254e9a522d7e7a58", "state": "ok", "exit_code": 0, "update_time": "2024-12-30T01:20:09.945744", "create_time": "2024-12-30T01:19:58.068321", "galaxy_version": "23.1", "command_version": "0.2.4", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0", "history_id": "1262154bdd2f9614", "external_id": "gxy-dhtmc", "command_line": "porechop -i '/galaxy/server/database/objects/a/6/0/dataset_a60e903a-1dc8-4c7b-ad77-2427e659d5d2.dat' --format 'fastq' --barcode_threshold '75.0' --barcode_diff '5.0' --adapter_threshold '90.0' --check_reads '10000' --scoring_scheme '3,-6,-5,-2' --end_size '150' --min_trim_size '4' --extra_end_trim '2' --end_threshold '75.0' --middle_threshold '85.0' --extra_middle_trim_good_side '10' --extra_middle_trim_bad_side '100' --min_split_read_size '1000' -o 'out.fastq'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "middle_adapter_settings": "{\"discard_middle\": false, \"extra_middle_trim_bad_side\": \"100\", \"extra_middle_trim_good_side\": \"10\", \"middle_threshold\": \"85.0\", \"min_split_read_size\": \"1000\", \"no_split\": false}", "end_adapter_settings": "{\"end_size\": \"150\", \"end_threshold\": \"75.0\", \"extra_end_trim\": \"2\", \"min_trim_size\": \"4\"}", "adapter_search_settings": "{\"adapter_threshold\": \"90.0\", \"check_reads\": \"10000\", \"scoring_scheme\": \"3,-6,-5,-2\"}", "barcode_binning_settings": "{\"barcode_diff\": \"5.0\", \"barcode_threshold\": \"75.0\", \"discard_unassigned\": false, \"require_two_barcodes\": false}", "format": "\"fastq\""}, "inputs": {"input_file": {"id": "a6742216c12826b8", "src": "hda", "uuid": "a60e903a-1dc8-4c7b-ad77-2427e659d5d2"}}, "outputs": {"outfile": {"id": "254e9a522d7e7a58", "src": "hda", "uuid": "61814dd4-91ee-43de-9163-0fdcb42e5007"}}, "output_collections": {}, "tool_stdout": "\n\u001b[1m\u001b[4mLoading reads\u001b[0m\n/galaxy/server/database/objects/a/6/0/dataset_a60e903a-1dc8-4c7b-ad77-2427e659d5d2.dat\n9 reads loaded\n\n\n\u001b[1m\u001b[4mLooking for known adapter sets\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n Best \u001b[0m\n read Best \u001b[0m\n start read end\u001b[0m\n \u001b[4mSet %ID %ID \u001b[0m\n \u001b[32mSQK-NSK007 96.4 95.5\u001b[0m\n Rapid 62.5 0.0\n RBK004_upstream 72.7 0.0\n SQK-MAP006 62.2 63.6\n SQK-MAP006 short 60.7 60.0\n PCR adapters 1 66.7 73.9\n PCR adapters 2 66.7 63.6\n PCR adapters 3 68.0 72.0\n 1D^2 part 1 62.1 58.8\n 1D^2 part 2 79.4 68.8\n cDNA SSP 57.1 61.4\n Barcode 1 (reverse) 59.4 66.7\n Barcode 2 (reverse) 66.7 63.0\n Barcode 3 (reverse) 69.2 72.0\n Barcode 4 (reverse) 66.7 63.3\n Barcode 5 (reverse) 62.5 66.7\n Barcode 6 (reverse) 73.1 62.5\n Barcode 7 (reverse) 65.4 65.5\n Barcode 8 (reverse) 69.2 58.3\n Barcode 9 (reverse) 75.0 66.7\n Barcode 10 (reverse) 62.5 60.0\n Barcode 11 (reverse) 69.2 60.5\n Barcode 12 (reverse) 65.6 64.0\n Barcode 1 (forward) 65.4 61.5\n Barcode 2 (forward) 69.2 70.4\n Barcode 3 (forward) 73.1 68.0\n Barcode 4 (forward) 73.1 64.3\n Barcode 5 (forward) 62.5 66.7\n Barcode 6 (forward) 65.5 65.6\n Barcode 7 (forward) 73.1 66.7\n Barcode 8 (forward) 62.1 60.7\n Barcode 9 (forward) 68.0 70.8\n Barcode 10 (forward) 69.2 66.7\n Barcode 11 (forward) 65.4 60.7\n Barcode 12 (forward) 64.3 66.7\n Barcode 13 (forward) 64.3 69.2\n Barcode 14 (forward) 63.3 66.7\n Barcode 15 (forward) 66.7 66.7\n Barcode 16 (forward) 70.8 65.5\n Barcode 17 (forward) 69.2 66.7\n Barcode 18 (forward) 70.4 70.4\n Barcode 19 (forward) 65.5 64.0\n Barcode 20 (forward) 65.5 64.0\n Barcode 21 (forward) 64.3 66.7\n Barcode 22 (forward) 69.2 68.0\n Barcode 23 (forward) 61.5 66.7\n Barcode 24 (forward) 66.7 65.4\n Barcode 25 (forward) 64.0 65.5\n Barcode 26 (forward) 72.0 72.0\n Barcode 27 (forward) 77.8 60.7\n Barcode 28 (forward) 65.5 66.7\n Barcode 29 (forward) 62.5 66.7\n Barcode 30 (forward) 68.0 65.4\n Barcode 31 (forward) 62.5 69.2\n Barcode 32 (forward) 68.0 70.8\n Barcode 33 (forward) 62.5 70.4\n Barcode 34 (forward) 64.0 62.5\n Barcode 35 (forward) 65.5 65.4\n Barcode 36 (forward) 63.0 63.0\n Barcode 37 (forward) 67.9 64.3\n Barcode 38 (forward) 64.0 62.1\n Barcode 39 (forward) 64.0 69.2\n Barcode 40 (forward) 62.5 64.0\n Barcode 41 (forward) 68.0 65.5\n Barcode 42 (forward) 70.4 69.2\n Barcode 43 (forward) 63.3 63.3\n Barcode 44 (forward) 60.0 66.7\n Barcode 45 (forward) 73.1 65.4\n Barcode 46 (forward) 65.4 60.7\n Barcode 47 (forward) 65.5 64.0\n Barcode 48 (forward) 71.4 62.1\n Barcode 49 (forward) 69.2 62.1\n Barcode 50 (forward) 66.7 63.0\n Barcode 51 (forward) 69.2 64.3\n Barcode 52 (forward) 66.7 64.0\n Barcode 53 (forward) 67.9 69.0\n Barcode 54 (forward) 69.2 64.0\n Barcode 55 (forward) 66.7 73.1\n Barcode 56 (forward) 66.7 72.0\n Barcode 57 (forward) 69.0 60.0\n Barcode 58 (forward) 70.4 72.0\n Barcode 59 (forward) 56.7 66.7\n Barcode 60 (forward) 66.7 66.7\n Barcode 61 (forward) 70.8 65.5\n Barcode 62 (forward) 66.7 68.0\n Barcode 63 (forward) 66.7 60.7\n Barcode 64 (forward) 69.2 66.7\n Barcode 65 (forward) 61.5 69.0\n Barcode 66 (forward) 64.3 63.0\n Barcode 67 (forward) 66.7 67.9\n Barcode 68 (forward) 67.9 69.2\n Barcode 69 (forward) 69.2 75.0\n Barcode 70 (forward) 64.3 73.1\n Barcode 71 (forward) 64.0 71.4\n Barcode 72 (forward) 66.7 62.1\n Barcode 73 (forward) 67.7 64.0\n Barcode 74 (forward) 64.5 68.0\n Barcode 75 (forward) 65.4 65.5\n Barcode 76 (forward) 70.4 70.8\n Barcode 77 (forward) 65.4 64.3\n Barcode 78 (forward) 67.7 63.0\n Barcode 79 (forward) 70.8 69.2\n Barcode 80 (forward) 71.4 72.0\n Barcode 81 (forward) 68.0 66.7\n Barcode 82 (forward) 64.7 66.7\n Barcode 83 (forward) 69.2 68.0\n Barcode 84 (forward) 70.8 67.9\n Barcode 85 (forward) 61.5 60.0\n Barcode 86 (forward) 64.3 65.4\n Barcode 87 (forward) 66.7 65.4\n Barcode 88 (forward) 63.3 60.7\n Barcode 89 (forward) 69.2 66.7\n Barcode 90 (forward) 66.7 64.0\n Barcode 91 (forward) 68.0 64.3\n Barcode 92 (forward) 65.5 68.0\n Barcode 93 (forward) 69.2 73.1\n Barcode 94 (forward) 63.0 68.0\n Barcode 95 (forward) 64.0 63.3\n Barcode 96 (forward) 69.0 68.0\n\n\n\u001b[1m\u001b[4mTrimming adapters from read ends\u001b[0m\n SQK-NSK007_Y_Top: \u001b[31mAATGTACTTCGTTCAGTTACGTATTGCT\u001b[0m\n SQK-NSK007_Y_Bottom: \u001b[31mGCAATACGTAACTGAACGAAGT\u001b[0m\n\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n\n4 / 9 reads had adapters trimmed from their start (74 bp removed)\n3 / 9 reads had adapters trimmed from their end (49 bp removed)\n\n\n\u001b[1m\u001b[4mSplitting reads containing middle adapters\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r10 / 9 (111.1%)\r9 / 9 (100.0%)\n\n4 / 9 reads were split based on middle adapters\n\n\n\u001b[1m\u001b[4mSaving trimmed reads to file\u001b[0m\n\nSaved result to /galaxy/server/database/jobs_directory/000/131/working/out.fastq\n\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "\n\u001b[1m\u001b[4mLoading reads\u001b[0m\n/galaxy/server/database/objects/a/6/0/dataset_a60e903a-1dc8-4c7b-ad77-2427e659d5d2.dat\n9 reads loaded\n\n\n\u001b[1m\u001b[4mLooking for known adapter sets\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n Best \u001b[0m\n read Best \u001b[0m\n start read end\u001b[0m\n \u001b[4mSet %ID %ID \u001b[0m\n \u001b[32mSQK-NSK007 96.4 95.5\u001b[0m\n Rapid 62.5 0.0\n RBK004_upstream 72.7 0.0\n SQK-MAP006 62.2 63.6\n SQK-MAP006 short 60.7 60.0\n PCR adapters 1 66.7 73.9\n PCR adapters 2 66.7 63.6\n PCR adapters 3 68.0 72.0\n 1D^2 part 1 62.1 58.8\n 1D^2 part 2 79.4 68.8\n cDNA SSP 57.1 61.4\n Barcode 1 (reverse) 59.4 66.7\n Barcode 2 (reverse) 66.7 63.0\n Barcode 3 (reverse) 69.2 72.0\n Barcode 4 (reverse) 66.7 63.3\n Barcode 5 (reverse) 62.5 66.7\n Barcode 6 (reverse) 73.1 62.5\n Barcode 7 (reverse) 65.4 65.5\n Barcode 8 (reverse) 69.2 58.3\n Barcode 9 (reverse) 75.0 66.7\n Barcode 10 (reverse) 62.5 60.0\n Barcode 11 (reverse) 69.2 60.5\n Barcode 12 (reverse) 65.6 64.0\n Barcode 1 (forward) 65.4 61.5\n Barcode 2 (forward) 69.2 70.4\n Barcode 3 (forward) 73.1 68.0\n Barcode 4 (forward) 73.1 64.3\n Barcode 5 (forward) 62.5 66.7\n Barcode 6 (forward) 65.5 65.6\n Barcode 7 (forward) 73.1 66.7\n Barcode 8 (forward) 62.1 60.7\n Barcode 9 (forward) 68.0 70.8\n Barcode 10 (forward) 69.2 66.7\n Barcode 11 (forward) 65.4 60.7\n Barcode 12 (forward) 64.3 66.7\n Barcode 13 (forward) 64.3 69.2\n Barcode 14 (forward) 63.3 66.7\n Barcode 15 (forward) 66.7 66.7\n Barcode 16 (forward) 70.8 65.5\n Barcode 17 (forward) 69.2 66.7\n Barcode 18 (forward) 70.4 70.4\n Barcode 19 (forward) 65.5 64.0\n Barcode 20 (forward) 65.5 64.0\n Barcode 21 (forward) 64.3 66.7\n Barcode 22 (forward) 69.2 68.0\n Barcode 23 (forward) 61.5 66.7\n Barcode 24 (forward) 66.7 65.4\n Barcode 25 (forward) 64.0 65.5\n Barcode 26 (forward) 72.0 72.0\n Barcode 27 (forward) 77.8 60.7\n Barcode 28 (forward) 65.5 66.7\n Barcode 29 (forward) 62.5 66.7\n Barcode 30 (forward) 68.0 65.4\n Barcode 31 (forward) 62.5 69.2\n Barcode 32 (forward) 68.0 70.8\n Barcode 33 (forward) 62.5 70.4\n Barcode 34 (forward) 64.0 62.5\n Barcode 35 (forward) 65.5 65.4\n Barcode 36 (forward) 63.0 63.0\n Barcode 37 (forward) 67.9 64.3\n Barcode 38 (forward) 64.0 62.1\n Barcode 39 (forward) 64.0 69.2\n Barcode 40 (forward) 62.5 64.0\n Barcode 41 (forward) 68.0 65.5\n Barcode 42 (forward) 70.4 69.2\n Barcode 43 (forward) 63.3 63.3\n Barcode 44 (forward) 60.0 66.7\n Barcode 45 (forward) 73.1 65.4\n Barcode 46 (forward) 65.4 60.7\n Barcode 47 (forward) 65.5 64.0\n Barcode 48 (forward) 71.4 62.1\n Barcode 49 (forward) 69.2 62.1\n Barcode 50 (forward) 66.7 63.0\n Barcode 51 (forward) 69.2 64.3\n Barcode 52 (forward) 66.7 64.0\n Barcode 53 (forward) 67.9 69.0\n Barcode 54 (forward) 69.2 64.0\n Barcode 55 (forward) 66.7 73.1\n Barcode 56 (forward) 66.7 72.0\n Barcode 57 (forward) 69.0 60.0\n Barcode 58 (forward) 70.4 72.0\n Barcode 59 (forward) 56.7 66.7\n Barcode 60 (forward) 66.7 66.7\n Barcode 61 (forward) 70.8 65.5\n Barcode 62 (forward) 66.7 68.0\n Barcode 63 (forward) 66.7 60.7\n Barcode 64 (forward) 69.2 66.7\n Barcode 65 (forward) 61.5 69.0\n Barcode 66 (forward) 64.3 63.0\n Barcode 67 (forward) 66.7 67.9\n Barcode 68 (forward) 67.9 69.2\n Barcode 69 (forward) 69.2 75.0\n Barcode 70 (forward) 64.3 73.1\n Barcode 71 (forward) 64.0 71.4\n Barcode 72 (forward) 66.7 62.1\n Barcode 73 (forward) 67.7 64.0\n Barcode 74 (forward) 64.5 68.0\n Barcode 75 (forward) 65.4 65.5\n Barcode 76 (forward) 70.4 70.8\n Barcode 77 (forward) 65.4 64.3\n Barcode 78 (forward) 67.7 63.0\n Barcode 79 (forward) 70.8 69.2\n Barcode 80 (forward) 71.4 72.0\n Barcode 81 (forward) 68.0 66.7\n Barcode 82 (forward) 64.7 66.7\n Barcode 83 (forward) 69.2 68.0\n Barcode 84 (forward) 70.8 67.9\n Barcode 85 (forward) 61.5 60.0\n Barcode 86 (forward) 64.3 65.4\n Barcode 87 (forward) 66.7 65.4\n Barcode 88 (forward) 63.3 60.7\n Barcode 89 (forward) 69.2 66.7\n Barcode 90 (forward) 66.7 64.0\n Barcode 91 (forward) 68.0 64.3\n Barcode 92 (forward) 65.5 68.0\n Barcode 93 (forward) 69.2 73.1\n Barcode 94 (forward) 63.0 68.0\n Barcode 95 (forward) 64.0 63.3\n Barcode 96 (forward) 69.0 68.0\n\n\n\u001b[1m\u001b[4mTrimming adapters from read ends\u001b[0m\n SQK-NSK007_Y_Top: \u001b[31mAATGTACTTCGTTCAGTTACGTATTGCT\u001b[0m\n SQK-NSK007_Y_Bottom: \u001b[31mGCAATACGTAACTGAACGAAGT\u001b[0m\n\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n\n4 / 9 reads had adapters trimmed from their start (74 bp removed)\n3 / 9 reads had adapters trimmed from their end (49 bp removed)\n\n\n\u001b[1m\u001b[4mSplitting reads containing middle adapters\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r10 / 9 (111.1%)\r9 / 9 (100.0%)\n\n4 / 9 reads were split based on middle adapters\n\n\n\u001b[1m\u001b[4mSaving trimmed reads to file\u001b[0m\n\nSaved result to /galaxy/server/database/jobs_directory/000/131/working/out.fastq\n\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-12-30 01:20:01", "plugin": "core", "name": "end_epoch", "raw_value": "1735521601.0000000"}, {"title": "Job Start Time", "value": "2024-12-30 01:20:00", "plugin": "core", "name": "start_epoch", "raw_value": "1735521600.0000000"}, {"title": "Memory Allocated (MB)", "value": "42949", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "42949.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "porechop/0.2.4+galaxy0-2", "has_data": true, "data": {"tool_id": "porechop", "tool_version": "0.2.4+galaxy0", "test_index": 2, "time_seconds": 27.26868438720703, "inputs": {"input_file": {"src": "hda", "id": "92d6b7f9fa68a9ec"}, "format": "fastq"}, "job": {"model_class": "Job", "id": "5eec17c7711e2db5", "state": "ok", "exit_code": 0, "update_time": "2024-12-30T01:20:37.090202", "create_time": "2024-12-30T01:20:25.088207", "galaxy_version": "23.1", "command_version": "0.2.4", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0", "history_id": "1262154bdd2f9614", "external_id": "gxy-lz7z7", "command_line": "porechop -i '/galaxy/server/database/objects/2/6/0/dataset_26086907-339b-4ad4-9f75-5e65d05ab0cc.dat' --format 'fastq' --barcode_threshold '75.0' --barcode_diff '5.0' --adapter_threshold '90.0' --check_reads '10000' --scoring_scheme '3,-6,-5,-2' --end_size '150' --min_trim_size '4' --extra_end_trim '2' --end_threshold '75.0' --middle_threshold '85.0' --extra_middle_trim_good_side '10' --extra_middle_trim_bad_side '100' --min_split_read_size '1000' -o 'out.fastq'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "middle_adapter_settings": "{\"discard_middle\": false, \"extra_middle_trim_bad_side\": \"100\", \"extra_middle_trim_good_side\": \"10\", \"middle_threshold\": \"85.0\", \"min_split_read_size\": \"1000\", \"no_split\": false}", "end_adapter_settings": "{\"end_size\": \"150\", \"end_threshold\": \"75.0\", \"extra_end_trim\": \"2\", \"min_trim_size\": \"4\"}", "adapter_search_settings": "{\"adapter_threshold\": \"90.0\", \"check_reads\": \"10000\", \"scoring_scheme\": \"3,-6,-5,-2\"}", "barcode_binning_settings": "{\"barcode_diff\": \"5.0\", \"barcode_threshold\": \"75.0\", \"discard_unassigned\": false, \"require_two_barcodes\": false}", "format": "\"fastq\""}, "inputs": {"input_file": {"id": "92d6b7f9fa68a9ec", "src": "hda", "uuid": "26086907-339b-4ad4-9f75-5e65d05ab0cc"}}, "outputs": {"outfile": {"id": "5eec17c7711e2db5", "src": "hda", "uuid": "ae2ce737-6b1b-4296-aac5-b2f0e08f277b"}}, "output_collections": {}, "tool_stdout": "\n\u001b[1m\u001b[4mLoading reads\u001b[0m\n/galaxy/server/database/objects/2/6/0/dataset_26086907-339b-4ad4-9f75-5e65d05ab0cc.dat\n9 reads loaded\n\n\n\u001b[1m\u001b[4mLooking for known adapter sets\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n Best \u001b[0m\n read Best \u001b[0m\n start read end\u001b[0m\n \u001b[4mSet %ID %ID \u001b[0m\n \u001b[32mSQK-NSK007 96.4 95.5\u001b[0m\n Rapid 62.5 0.0\n RBK004_upstream 72.7 0.0\n SQK-MAP006 62.2 63.6\n SQK-MAP006 short 60.7 60.0\n PCR adapters 1 66.7 73.9\n PCR adapters 2 66.7 63.6\n PCR adapters 3 68.0 72.0\n 1D^2 part 1 62.1 58.8\n 1D^2 part 2 79.4 68.8\n cDNA SSP 57.1 61.4\n Barcode 1 (reverse) 59.4 66.7\n Barcode 2 (reverse) 66.7 63.0\n Barcode 3 (reverse) 69.2 72.0\n Barcode 4 (reverse) 66.7 63.3\n Barcode 5 (reverse) 62.5 66.7\n Barcode 6 (reverse) 73.1 62.5\n Barcode 7 (reverse) 65.4 65.5\n Barcode 8 (reverse) 69.2 58.3\n Barcode 9 (reverse) 75.0 66.7\n Barcode 10 (reverse) 62.5 60.0\n Barcode 11 (reverse) 69.2 60.5\n Barcode 12 (reverse) 65.6 64.0\n Barcode 1 (forward) 65.4 61.5\n Barcode 2 (forward) 69.2 70.4\n Barcode 3 (forward) 73.1 68.0\n Barcode 4 (forward) 73.1 64.3\n Barcode 5 (forward) 62.5 66.7\n Barcode 6 (forward) 65.5 65.6\n Barcode 7 (forward) 73.1 66.7\n Barcode 8 (forward) 62.1 60.7\n Barcode 9 (forward) 68.0 70.8\n Barcode 10 (forward) 69.2 66.7\n Barcode 11 (forward) 65.4 60.7\n Barcode 12 (forward) 64.3 66.7\n Barcode 13 (forward) 64.3 69.2\n Barcode 14 (forward) 63.3 66.7\n Barcode 15 (forward) 66.7 66.7\n Barcode 16 (forward) 70.8 65.5\n Barcode 17 (forward) 69.2 66.7\n Barcode 18 (forward) 70.4 70.4\n Barcode 19 (forward) 65.5 64.0\n Barcode 20 (forward) 65.5 64.0\n Barcode 21 (forward) 64.3 66.7\n Barcode 22 (forward) 69.2 68.0\n Barcode 23 (forward) 61.5 66.7\n Barcode 24 (forward) 66.7 65.4\n Barcode 25 (forward) 64.0 65.5\n Barcode 26 (forward) 72.0 72.0\n Barcode 27 (forward) 77.8 60.7\n Barcode 28 (forward) 65.5 66.7\n Barcode 29 (forward) 62.5 66.7\n Barcode 30 (forward) 68.0 65.4\n Barcode 31 (forward) 62.5 69.2\n Barcode 32 (forward) 68.0 70.8\n Barcode 33 (forward) 62.5 70.4\n Barcode 34 (forward) 64.0 62.5\n Barcode 35 (forward) 65.5 65.4\n Barcode 36 (forward) 63.0 63.0\n Barcode 37 (forward) 67.9 64.3\n Barcode 38 (forward) 64.0 62.1\n Barcode 39 (forward) 64.0 69.2\n Barcode 40 (forward) 62.5 64.0\n Barcode 41 (forward) 68.0 65.5\n Barcode 42 (forward) 70.4 69.2\n Barcode 43 (forward) 63.3 63.3\n Barcode 44 (forward) 60.0 66.7\n Barcode 45 (forward) 73.1 65.4\n Barcode 46 (forward) 65.4 60.7\n Barcode 47 (forward) 65.5 64.0\n Barcode 48 (forward) 71.4 62.1\n Barcode 49 (forward) 69.2 62.1\n Barcode 50 (forward) 66.7 63.0\n Barcode 51 (forward) 69.2 64.3\n Barcode 52 (forward) 66.7 64.0\n Barcode 53 (forward) 67.9 69.0\n Barcode 54 (forward) 69.2 64.0\n Barcode 55 (forward) 66.7 73.1\n Barcode 56 (forward) 66.7 72.0\n Barcode 57 (forward) 69.0 60.0\n Barcode 58 (forward) 70.4 72.0\n Barcode 59 (forward) 56.7 66.7\n Barcode 60 (forward) 66.7 66.7\n Barcode 61 (forward) 70.8 65.5\n Barcode 62 (forward) 66.7 68.0\n Barcode 63 (forward) 66.7 60.7\n Barcode 64 (forward) 69.2 66.7\n Barcode 65 (forward) 61.5 69.0\n Barcode 66 (forward) 64.3 63.0\n Barcode 67 (forward) 66.7 67.9\n Barcode 68 (forward) 67.9 69.2\n Barcode 69 (forward) 69.2 75.0\n Barcode 70 (forward) 64.3 73.1\n Barcode 71 (forward) 64.0 71.4\n Barcode 72 (forward) 66.7 62.1\n Barcode 73 (forward) 67.7 64.0\n Barcode 74 (forward) 64.5 68.0\n Barcode 75 (forward) 65.4 65.5\n Barcode 76 (forward) 70.4 70.8\n Barcode 77 (forward) 65.4 64.3\n Barcode 78 (forward) 67.7 63.0\n Barcode 79 (forward) 70.8 69.2\n Barcode 80 (forward) 71.4 72.0\n Barcode 81 (forward) 68.0 66.7\n Barcode 82 (forward) 64.7 66.7\n Barcode 83 (forward) 69.2 68.0\n Barcode 84 (forward) 70.8 67.9\n Barcode 85 (forward) 61.5 60.0\n Barcode 86 (forward) 64.3 65.4\n Barcode 87 (forward) 66.7 65.4\n Barcode 88 (forward) 63.3 60.7\n Barcode 89 (forward) 69.2 66.7\n Barcode 90 (forward) 66.7 64.0\n Barcode 91 (forward) 68.0 64.3\n Barcode 92 (forward) 65.5 68.0\n Barcode 93 (forward) 69.2 73.1\n Barcode 94 (forward) 63.0 68.0\n Barcode 95 (forward) 64.0 63.3\n Barcode 96 (forward) 69.0 68.0\n\n\n\u001b[1m\u001b[4mTrimming adapters from read ends\u001b[0m\n SQK-NSK007_Y_Top: \u001b[31mAATGTACTTCGTTCAGTTACGTATTGCT\u001b[0m\n SQK-NSK007_Y_Bottom: \u001b[31mGCAATACGTAACTGAACGAAGT\u001b[0m\n\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n\n4 / 9 reads had adapters trimmed from their start (74 bp removed)\n3 / 9 reads had adapters trimmed from their end (49 bp removed)\n\n\n\u001b[1m\u001b[4mSplitting reads containing middle adapters\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r10 / 9 (111.1%)\r9 / 9 (100.0%)\n\n4 / 9 reads were split based on middle adapters\n\n\n\u001b[1m\u001b[4mSaving trimmed reads to file\u001b[0m\n\nSaved result to /galaxy/server/database/jobs_directory/000/133/working/out.fastq\n\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "\n\u001b[1m\u001b[4mLoading reads\u001b[0m\n/galaxy/server/database/objects/2/6/0/dataset_26086907-339b-4ad4-9f75-5e65d05ab0cc.dat\n9 reads loaded\n\n\n\u001b[1m\u001b[4mLooking for known adapter sets\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n Best \u001b[0m\n read Best \u001b[0m\n start read end\u001b[0m\n \u001b[4mSet %ID %ID \u001b[0m\n \u001b[32mSQK-NSK007 96.4 95.5\u001b[0m\n Rapid 62.5 0.0\n RBK004_upstream 72.7 0.0\n SQK-MAP006 62.2 63.6\n SQK-MAP006 short 60.7 60.0\n PCR adapters 1 66.7 73.9\n PCR adapters 2 66.7 63.6\n PCR adapters 3 68.0 72.0\n 1D^2 part 1 62.1 58.8\n 1D^2 part 2 79.4 68.8\n cDNA SSP 57.1 61.4\n Barcode 1 (reverse) 59.4 66.7\n Barcode 2 (reverse) 66.7 63.0\n Barcode 3 (reverse) 69.2 72.0\n Barcode 4 (reverse) 66.7 63.3\n Barcode 5 (reverse) 62.5 66.7\n Barcode 6 (reverse) 73.1 62.5\n Barcode 7 (reverse) 65.4 65.5\n Barcode 8 (reverse) 69.2 58.3\n Barcode 9 (reverse) 75.0 66.7\n Barcode 10 (reverse) 62.5 60.0\n Barcode 11 (reverse) 69.2 60.5\n Barcode 12 (reverse) 65.6 64.0\n Barcode 1 (forward) 65.4 61.5\n Barcode 2 (forward) 69.2 70.4\n Barcode 3 (forward) 73.1 68.0\n Barcode 4 (forward) 73.1 64.3\n Barcode 5 (forward) 62.5 66.7\n Barcode 6 (forward) 65.5 65.6\n Barcode 7 (forward) 73.1 66.7\n Barcode 8 (forward) 62.1 60.7\n Barcode 9 (forward) 68.0 70.8\n Barcode 10 (forward) 69.2 66.7\n Barcode 11 (forward) 65.4 60.7\n Barcode 12 (forward) 64.3 66.7\n Barcode 13 (forward) 64.3 69.2\n Barcode 14 (forward) 63.3 66.7\n Barcode 15 (forward) 66.7 66.7\n Barcode 16 (forward) 70.8 65.5\n Barcode 17 (forward) 69.2 66.7\n Barcode 18 (forward) 70.4 70.4\n Barcode 19 (forward) 65.5 64.0\n Barcode 20 (forward) 65.5 64.0\n Barcode 21 (forward) 64.3 66.7\n Barcode 22 (forward) 69.2 68.0\n Barcode 23 (forward) 61.5 66.7\n Barcode 24 (forward) 66.7 65.4\n Barcode 25 (forward) 64.0 65.5\n Barcode 26 (forward) 72.0 72.0\n Barcode 27 (forward) 77.8 60.7\n Barcode 28 (forward) 65.5 66.7\n Barcode 29 (forward) 62.5 66.7\n Barcode 30 (forward) 68.0 65.4\n Barcode 31 (forward) 62.5 69.2\n Barcode 32 (forward) 68.0 70.8\n Barcode 33 (forward) 62.5 70.4\n Barcode 34 (forward) 64.0 62.5\n Barcode 35 (forward) 65.5 65.4\n Barcode 36 (forward) 63.0 63.0\n Barcode 37 (forward) 67.9 64.3\n Barcode 38 (forward) 64.0 62.1\n Barcode 39 (forward) 64.0 69.2\n Barcode 40 (forward) 62.5 64.0\n Barcode 41 (forward) 68.0 65.5\n Barcode 42 (forward) 70.4 69.2\n Barcode 43 (forward) 63.3 63.3\n Barcode 44 (forward) 60.0 66.7\n Barcode 45 (forward) 73.1 65.4\n Barcode 46 (forward) 65.4 60.7\n Barcode 47 (forward) 65.5 64.0\n Barcode 48 (forward) 71.4 62.1\n Barcode 49 (forward) 69.2 62.1\n Barcode 50 (forward) 66.7 63.0\n Barcode 51 (forward) 69.2 64.3\n Barcode 52 (forward) 66.7 64.0\n Barcode 53 (forward) 67.9 69.0\n Barcode 54 (forward) 69.2 64.0\n Barcode 55 (forward) 66.7 73.1\n Barcode 56 (forward) 66.7 72.0\n Barcode 57 (forward) 69.0 60.0\n Barcode 58 (forward) 70.4 72.0\n Barcode 59 (forward) 56.7 66.7\n Barcode 60 (forward) 66.7 66.7\n Barcode 61 (forward) 70.8 65.5\n Barcode 62 (forward) 66.7 68.0\n Barcode 63 (forward) 66.7 60.7\n Barcode 64 (forward) 69.2 66.7\n Barcode 65 (forward) 61.5 69.0\n Barcode 66 (forward) 64.3 63.0\n Barcode 67 (forward) 66.7 67.9\n Barcode 68 (forward) 67.9 69.2\n Barcode 69 (forward) 69.2 75.0\n Barcode 70 (forward) 64.3 73.1\n Barcode 71 (forward) 64.0 71.4\n Barcode 72 (forward) 66.7 62.1\n Barcode 73 (forward) 67.7 64.0\n Barcode 74 (forward) 64.5 68.0\n Barcode 75 (forward) 65.4 65.5\n Barcode 76 (forward) 70.4 70.8\n Barcode 77 (forward) 65.4 64.3\n Barcode 78 (forward) 67.7 63.0\n Barcode 79 (forward) 70.8 69.2\n Barcode 80 (forward) 71.4 72.0\n Barcode 81 (forward) 68.0 66.7\n Barcode 82 (forward) 64.7 66.7\n Barcode 83 (forward) 69.2 68.0\n Barcode 84 (forward) 70.8 67.9\n Barcode 85 (forward) 61.5 60.0\n Barcode 86 (forward) 64.3 65.4\n Barcode 87 (forward) 66.7 65.4\n Barcode 88 (forward) 63.3 60.7\n Barcode 89 (forward) 69.2 66.7\n Barcode 90 (forward) 66.7 64.0\n Barcode 91 (forward) 68.0 64.3\n Barcode 92 (forward) 65.5 68.0\n Barcode 93 (forward) 69.2 73.1\n Barcode 94 (forward) 63.0 68.0\n Barcode 95 (forward) 64.0 63.3\n Barcode 96 (forward) 69.0 68.0\n\n\n\u001b[1m\u001b[4mTrimming adapters from read ends\u001b[0m\n SQK-NSK007_Y_Top: \u001b[31mAATGTACTTCGTTCAGTTACGTATTGCT\u001b[0m\n SQK-NSK007_Y_Bottom: \u001b[31mGCAATACGTAACTGAACGAAGT\u001b[0m\n\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n\n4 / 9 reads had adapters trimmed from their start (74 bp removed)\n3 / 9 reads had adapters trimmed from their end (49 bp removed)\n\n\n\u001b[1m\u001b[4mSplitting reads containing middle adapters\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r10 / 9 (111.1%)\r9 / 9 (100.0%)\n\n4 / 9 reads were split based on middle adapters\n\n\n\u001b[1m\u001b[4mSaving trimmed reads to file\u001b[0m\n\nSaved result to /galaxy/server/database/jobs_directory/000/133/working/out.fastq\n\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-12-30 01:20:28", "plugin": "core", "name": "end_epoch", "raw_value": "1735521628.0000000"}, {"title": "Job Start Time", "value": "2024-12-30 01:20:27", "plugin": "core", "name": "start_epoch", "raw_value": "1735521627.0000000"}, {"title": "Memory Allocated (MB)", "value": "42949", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "42949.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "porechop/0.2.4+galaxy0-3", "has_data": true, "data": {"tool_id": "porechop", "tool_version": "0.2.4+galaxy0", "test_index": 3, "time_seconds": 26.903056621551514, "inputs": {"input_file": {"src": "hda", "id": "65776e38c288081b"}, "format": "fasta.gz"}, "job": {"model_class": "Job", "id": "98ba3f43b2ec1f79", "state": "ok", "exit_code": 0, "update_time": "2024-12-30T01:21:04.273182", "create_time": "2024-12-30T01:20:52.496086", "galaxy_version": "23.1", "command_version": "0.2.4", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0", "history_id": "1262154bdd2f9614", "external_id": "gxy-46j8x", "command_line": "porechop -i '/galaxy/server/database/objects/2/6/1/dataset_261587ba-6f35-4919-99ac-dd8495488eab.dat' --format 'fasta.gz' --barcode_threshold '75.0' --barcode_diff '5.0' --adapter_threshold '90.0' --check_reads '10000' --scoring_scheme '3,-6,-5,-2' --end_size '150' --min_trim_size '4' --extra_end_trim '2' --end_threshold '75.0' --middle_threshold '85.0' --extra_middle_trim_good_side '10' --extra_middle_trim_bad_side '100' --min_split_read_size '1000' -o 'out.fasta.gz'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "middle_adapter_settings": "{\"discard_middle\": false, \"extra_middle_trim_bad_side\": \"100\", \"extra_middle_trim_good_side\": \"10\", \"middle_threshold\": \"85.0\", \"min_split_read_size\": \"1000\", \"no_split\": false}", "end_adapter_settings": "{\"end_size\": \"150\", \"end_threshold\": \"75.0\", \"extra_end_trim\": \"2\", \"min_trim_size\": \"4\"}", "adapter_search_settings": "{\"adapter_threshold\": \"90.0\", \"check_reads\": \"10000\", \"scoring_scheme\": \"3,-6,-5,-2\"}", "barcode_binning_settings": "{\"barcode_diff\": \"5.0\", \"barcode_threshold\": \"75.0\", \"discard_unassigned\": false, \"require_two_barcodes\": false}", "format": "\"fasta.gz\""}, "inputs": {"input_file": {"id": "65776e38c288081b", "src": "hda", "uuid": "261587ba-6f35-4919-99ac-dd8495488eab"}}, "outputs": {"outfile": {"id": "98ba3f43b2ec1f79", "src": "hda", "uuid": "62a0d775-cab4-4fce-b293-c8a81f22373f"}}, "output_collections": {}, "tool_stdout": "\n\u001b[1m\u001b[4mLoading reads\u001b[0m\n/galaxy/server/database/objects/2/6/1/dataset_261587ba-6f35-4919-99ac-dd8495488eab.dat\n9 reads loaded\n\n\n\u001b[1m\u001b[4mLooking for known adapter sets\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n Best \u001b[0m\n read Best \u001b[0m\n start read end\u001b[0m\n \u001b[4mSet %ID %ID \u001b[0m\n \u001b[32mSQK-NSK007 96.4 95.5\u001b[0m\n Rapid 62.5 0.0\n RBK004_upstream 72.7 0.0\n SQK-MAP006 62.2 63.6\n SQK-MAP006 short 60.7 60.0\n PCR adapters 1 66.7 73.9\n PCR adapters 2 66.7 63.6\n PCR adapters 3 68.0 72.0\n 1D^2 part 1 62.1 58.8\n 1D^2 part 2 79.4 68.8\n cDNA SSP 57.1 61.4\n Barcode 1 (reverse) 59.4 66.7\n Barcode 2 (reverse) 66.7 63.0\n Barcode 3 (reverse) 69.2 72.0\n Barcode 4 (reverse) 66.7 63.3\n Barcode 5 (reverse) 62.5 66.7\n Barcode 6 (reverse) 73.1 62.5\n Barcode 7 (reverse) 65.4 65.5\n Barcode 8 (reverse) 69.2 58.3\n Barcode 9 (reverse) 75.0 66.7\n Barcode 10 (reverse) 62.5 60.0\n Barcode 11 (reverse) 69.2 60.5\n Barcode 12 (reverse) 65.6 64.0\n Barcode 1 (forward) 65.4 61.5\n Barcode 2 (forward) 69.2 70.4\n Barcode 3 (forward) 73.1 68.0\n Barcode 4 (forward) 73.1 64.3\n Barcode 5 (forward) 62.5 66.7\n Barcode 6 (forward) 65.5 65.6\n Barcode 7 (forward) 73.1 66.7\n Barcode 8 (forward) 62.1 60.7\n Barcode 9 (forward) 68.0 70.8\n Barcode 10 (forward) 69.2 66.7\n Barcode 11 (forward) 65.4 60.7\n Barcode 12 (forward) 64.3 66.7\n Barcode 13 (forward) 64.3 69.2\n Barcode 14 (forward) 63.3 66.7\n Barcode 15 (forward) 66.7 66.7\n Barcode 16 (forward) 70.8 65.5\n Barcode 17 (forward) 69.2 66.7\n Barcode 18 (forward) 70.4 70.4\n Barcode 19 (forward) 65.5 64.0\n Barcode 20 (forward) 65.5 64.0\n Barcode 21 (forward) 64.3 66.7\n Barcode 22 (forward) 69.2 68.0\n Barcode 23 (forward) 61.5 66.7\n Barcode 24 (forward) 66.7 65.4\n Barcode 25 (forward) 64.0 65.5\n Barcode 26 (forward) 72.0 72.0\n Barcode 27 (forward) 77.8 60.7\n Barcode 28 (forward) 65.5 66.7\n Barcode 29 (forward) 62.5 66.7\n Barcode 30 (forward) 68.0 65.4\n Barcode 31 (forward) 62.5 69.2\n Barcode 32 (forward) 68.0 70.8\n Barcode 33 (forward) 62.5 70.4\n Barcode 34 (forward) 64.0 62.5\n Barcode 35 (forward) 65.5 65.4\n Barcode 36 (forward) 63.0 63.0\n Barcode 37 (forward) 67.9 64.3\n Barcode 38 (forward) 64.0 62.1\n Barcode 39 (forward) 64.0 69.2\n Barcode 40 (forward) 62.5 64.0\n Barcode 41 (forward) 68.0 65.5\n Barcode 42 (forward) 70.4 69.2\n Barcode 43 (forward) 63.3 63.3\n Barcode 44 (forward) 60.0 66.7\n Barcode 45 (forward) 73.1 65.4\n Barcode 46 (forward) 65.4 60.7\n Barcode 47 (forward) 65.5 64.0\n Barcode 48 (forward) 71.4 62.1\n Barcode 49 (forward) 69.2 62.1\n Barcode 50 (forward) 66.7 63.0\n Barcode 51 (forward) 69.2 64.3\n Barcode 52 (forward) 66.7 64.0\n Barcode 53 (forward) 67.9 69.0\n Barcode 54 (forward) 69.2 64.0\n Barcode 55 (forward) 66.7 73.1\n Barcode 56 (forward) 66.7 72.0\n Barcode 57 (forward) 69.0 60.0\n Barcode 58 (forward) 70.4 72.0\n Barcode 59 (forward) 56.7 66.7\n Barcode 60 (forward) 66.7 66.7\n Barcode 61 (forward) 70.8 65.5\n Barcode 62 (forward) 66.7 68.0\n Barcode 63 (forward) 66.7 60.7\n Barcode 64 (forward) 69.2 66.7\n Barcode 65 (forward) 61.5 69.0\n Barcode 66 (forward) 64.3 63.0\n Barcode 67 (forward) 66.7 67.9\n Barcode 68 (forward) 67.9 69.2\n Barcode 69 (forward) 69.2 75.0\n Barcode 70 (forward) 64.3 73.1\n Barcode 71 (forward) 64.0 71.4\n Barcode 72 (forward) 66.7 62.1\n Barcode 73 (forward) 67.7 64.0\n Barcode 74 (forward) 64.5 68.0\n Barcode 75 (forward) 65.4 65.5\n Barcode 76 (forward) 70.4 70.8\n Barcode 77 (forward) 65.4 64.3\n Barcode 78 (forward) 67.7 63.0\n Barcode 79 (forward) 70.8 69.2\n Barcode 80 (forward) 71.4 72.0\n Barcode 81 (forward) 68.0 66.7\n Barcode 82 (forward) 64.7 66.7\n Barcode 83 (forward) 69.2 68.0\n Barcode 84 (forward) 70.8 67.9\n Barcode 85 (forward) 61.5 60.0\n Barcode 86 (forward) 64.3 65.4\n Barcode 87 (forward) 66.7 65.4\n Barcode 88 (forward) 63.3 60.7\n Barcode 89 (forward) 69.2 66.7\n Barcode 90 (forward) 66.7 64.0\n Barcode 91 (forward) 68.0 64.3\n Barcode 92 (forward) 65.5 68.0\n Barcode 93 (forward) 69.2 73.1\n Barcode 94 (forward) 63.0 68.0\n Barcode 95 (forward) 64.0 63.3\n Barcode 96 (forward) 69.0 68.0\n\n\n\u001b[1m\u001b[4mTrimming adapters from read ends\u001b[0m\n SQK-NSK007_Y_Top: \u001b[31mAATGTACTTCGTTCAGTTACGTATTGCT\u001b[0m\n SQK-NSK007_Y_Bottom: \u001b[31mGCAATACGTAACTGAACGAAGT\u001b[0m\n\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n\n4 / 9 reads had adapters trimmed from their start (74 bp removed)\n3 / 9 reads had adapters trimmed from their end (49 bp removed)\n\n\n\u001b[1m\u001b[4mSplitting reads containing middle adapters\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r10 / 9 (111.1%)\r9 / 9 (100.0%)\n\n4 / 9 reads were split based on middle adapters\n\n\n\u001b[1m\u001b[4mSaving trimmed reads to file\u001b[0m\npigz not found - using gzip to compress\n\nSaved result to /galaxy/server/database/jobs_directory/000/135/working/out.fasta.gz\n\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "\n\u001b[1m\u001b[4mLoading reads\u001b[0m\n/galaxy/server/database/objects/2/6/1/dataset_261587ba-6f35-4919-99ac-dd8495488eab.dat\n9 reads loaded\n\n\n\u001b[1m\u001b[4mLooking for known adapter sets\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n Best \u001b[0m\n read Best \u001b[0m\n start read end\u001b[0m\n \u001b[4mSet %ID %ID \u001b[0m\n \u001b[32mSQK-NSK007 96.4 95.5\u001b[0m\n Rapid 62.5 0.0\n RBK004_upstream 72.7 0.0\n SQK-MAP006 62.2 63.6\n SQK-MAP006 short 60.7 60.0\n PCR adapters 1 66.7 73.9\n PCR adapters 2 66.7 63.6\n PCR adapters 3 68.0 72.0\n 1D^2 part 1 62.1 58.8\n 1D^2 part 2 79.4 68.8\n cDNA SSP 57.1 61.4\n Barcode 1 (reverse) 59.4 66.7\n Barcode 2 (reverse) 66.7 63.0\n Barcode 3 (reverse) 69.2 72.0\n Barcode 4 (reverse) 66.7 63.3\n Barcode 5 (reverse) 62.5 66.7\n Barcode 6 (reverse) 73.1 62.5\n Barcode 7 (reverse) 65.4 65.5\n Barcode 8 (reverse) 69.2 58.3\n Barcode 9 (reverse) 75.0 66.7\n Barcode 10 (reverse) 62.5 60.0\n Barcode 11 (reverse) 69.2 60.5\n Barcode 12 (reverse) 65.6 64.0\n Barcode 1 (forward) 65.4 61.5\n Barcode 2 (forward) 69.2 70.4\n Barcode 3 (forward) 73.1 68.0\n Barcode 4 (forward) 73.1 64.3\n Barcode 5 (forward) 62.5 66.7\n Barcode 6 (forward) 65.5 65.6\n Barcode 7 (forward) 73.1 66.7\n Barcode 8 (forward) 62.1 60.7\n Barcode 9 (forward) 68.0 70.8\n Barcode 10 (forward) 69.2 66.7\n Barcode 11 (forward) 65.4 60.7\n Barcode 12 (forward) 64.3 66.7\n Barcode 13 (forward) 64.3 69.2\n Barcode 14 (forward) 63.3 66.7\n Barcode 15 (forward) 66.7 66.7\n Barcode 16 (forward) 70.8 65.5\n Barcode 17 (forward) 69.2 66.7\n Barcode 18 (forward) 70.4 70.4\n Barcode 19 (forward) 65.5 64.0\n Barcode 20 (forward) 65.5 64.0\n Barcode 21 (forward) 64.3 66.7\n Barcode 22 (forward) 69.2 68.0\n Barcode 23 (forward) 61.5 66.7\n Barcode 24 (forward) 66.7 65.4\n Barcode 25 (forward) 64.0 65.5\n Barcode 26 (forward) 72.0 72.0\n Barcode 27 (forward) 77.8 60.7\n Barcode 28 (forward) 65.5 66.7\n Barcode 29 (forward) 62.5 66.7\n Barcode 30 (forward) 68.0 65.4\n Barcode 31 (forward) 62.5 69.2\n Barcode 32 (forward) 68.0 70.8\n Barcode 33 (forward) 62.5 70.4\n Barcode 34 (forward) 64.0 62.5\n Barcode 35 (forward) 65.5 65.4\n Barcode 36 (forward) 63.0 63.0\n Barcode 37 (forward) 67.9 64.3\n Barcode 38 (forward) 64.0 62.1\n Barcode 39 (forward) 64.0 69.2\n Barcode 40 (forward) 62.5 64.0\n Barcode 41 (forward) 68.0 65.5\n Barcode 42 (forward) 70.4 69.2\n Barcode 43 (forward) 63.3 63.3\n Barcode 44 (forward) 60.0 66.7\n Barcode 45 (forward) 73.1 65.4\n Barcode 46 (forward) 65.4 60.7\n Barcode 47 (forward) 65.5 64.0\n Barcode 48 (forward) 71.4 62.1\n Barcode 49 (forward) 69.2 62.1\n Barcode 50 (forward) 66.7 63.0\n Barcode 51 (forward) 69.2 64.3\n Barcode 52 (forward) 66.7 64.0\n Barcode 53 (forward) 67.9 69.0\n Barcode 54 (forward) 69.2 64.0\n Barcode 55 (forward) 66.7 73.1\n Barcode 56 (forward) 66.7 72.0\n Barcode 57 (forward) 69.0 60.0\n Barcode 58 (forward) 70.4 72.0\n Barcode 59 (forward) 56.7 66.7\n Barcode 60 (forward) 66.7 66.7\n Barcode 61 (forward) 70.8 65.5\n Barcode 62 (forward) 66.7 68.0\n Barcode 63 (forward) 66.7 60.7\n Barcode 64 (forward) 69.2 66.7\n Barcode 65 (forward) 61.5 69.0\n Barcode 66 (forward) 64.3 63.0\n Barcode 67 (forward) 66.7 67.9\n Barcode 68 (forward) 67.9 69.2\n Barcode 69 (forward) 69.2 75.0\n Barcode 70 (forward) 64.3 73.1\n Barcode 71 (forward) 64.0 71.4\n Barcode 72 (forward) 66.7 62.1\n Barcode 73 (forward) 67.7 64.0\n Barcode 74 (forward) 64.5 68.0\n Barcode 75 (forward) 65.4 65.5\n Barcode 76 (forward) 70.4 70.8\n Barcode 77 (forward) 65.4 64.3\n Barcode 78 (forward) 67.7 63.0\n Barcode 79 (forward) 70.8 69.2\n Barcode 80 (forward) 71.4 72.0\n Barcode 81 (forward) 68.0 66.7\n Barcode 82 (forward) 64.7 66.7\n Barcode 83 (forward) 69.2 68.0\n Barcode 84 (forward) 70.8 67.9\n Barcode 85 (forward) 61.5 60.0\n Barcode 86 (forward) 64.3 65.4\n Barcode 87 (forward) 66.7 65.4\n Barcode 88 (forward) 63.3 60.7\n Barcode 89 (forward) 69.2 66.7\n Barcode 90 (forward) 66.7 64.0\n Barcode 91 (forward) 68.0 64.3\n Barcode 92 (forward) 65.5 68.0\n Barcode 93 (forward) 69.2 73.1\n Barcode 94 (forward) 63.0 68.0\n Barcode 95 (forward) 64.0 63.3\n Barcode 96 (forward) 69.0 68.0\n\n\n\u001b[1m\u001b[4mTrimming adapters from read ends\u001b[0m\n SQK-NSK007_Y_Top: \u001b[31mAATGTACTTCGTTCAGTTACGTATTGCT\u001b[0m\n SQK-NSK007_Y_Bottom: \u001b[31mGCAATACGTAACTGAACGAAGT\u001b[0m\n\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n\n4 / 9 reads had adapters trimmed from their start (74 bp removed)\n3 / 9 reads had adapters trimmed from their end (49 bp removed)\n\n\n\u001b[1m\u001b[4mSplitting reads containing middle adapters\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r10 / 9 (111.1%)\r9 / 9 (100.0%)\n\n4 / 9 reads were split based on middle adapters\n\n\n\u001b[1m\u001b[4mSaving trimmed reads to file\u001b[0m\npigz not found - using gzip to compress\n\nSaved result to /galaxy/server/database/jobs_directory/000/135/working/out.fasta.gz\n\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-12-30 01:20:54", "plugin": "core", "name": "end_epoch", "raw_value": "1735521654.0000000"}, {"title": "Job Start Time", "value": "2024-12-30 01:20:54", "plugin": "core", "name": "start_epoch", "raw_value": "1735521654.0000000"}, {"title": "Memory Allocated (MB)", "value": "42949", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "42949.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "porechop/0.2.4+galaxy0-4", "has_data": true, "data": {"tool_id": "porechop", "tool_version": "0.2.4+galaxy0", "test_index": 4, "time_seconds": 28.63512921333313, "inputs": {"input_file": {"src": "hda", "id": "599abfd6fe8206a3"}, "format": "fastq.gz"}, "job": {"model_class": "Job", "id": "30849d827d0b87e9", "state": "ok", "exit_code": 0, "update_time": "2024-12-30T01:21:32.849325", "create_time": "2024-12-30T01:21:21.133877", "galaxy_version": "23.1", "command_version": "0.2.4", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0", "history_id": "1262154bdd2f9614", "external_id": "gxy-xch9r", "command_line": "porechop -i '/galaxy/server/database/objects/6/4/b/dataset_64b22bcd-c800-4207-9736-15d61ef12e06.dat' --format 'fastq.gz' --barcode_threshold '75.0' --barcode_diff '5.0' --adapter_threshold '90.0' --check_reads '10000' --scoring_scheme '3,-6,-5,-2' --end_size '150' --min_trim_size '4' --extra_end_trim '2' --end_threshold '75.0' --middle_threshold '85.0' --extra_middle_trim_good_side '10' --extra_middle_trim_bad_side '100' --min_split_read_size '1000' -o 'out.fastq.gz'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "middle_adapter_settings": "{\"discard_middle\": false, \"extra_middle_trim_bad_side\": \"100\", \"extra_middle_trim_good_side\": \"10\", \"middle_threshold\": \"85.0\", \"min_split_read_size\": \"1000\", \"no_split\": false}", "end_adapter_settings": "{\"end_size\": \"150\", \"end_threshold\": \"75.0\", \"extra_end_trim\": \"2\", \"min_trim_size\": \"4\"}", "adapter_search_settings": "{\"adapter_threshold\": \"90.0\", \"check_reads\": \"10000\", \"scoring_scheme\": \"3,-6,-5,-2\"}", "barcode_binning_settings": "{\"barcode_diff\": \"5.0\", \"barcode_threshold\": \"75.0\", \"discard_unassigned\": false, \"require_two_barcodes\": false}", "format": "\"fastq.gz\""}, "inputs": {"input_file": {"id": "599abfd6fe8206a3", "src": "hda", "uuid": "64b22bcd-c800-4207-9736-15d61ef12e06"}}, "outputs": {"outfile": {"id": "30849d827d0b87e9", "src": "hda", "uuid": "a146f0b5-37ca-48b5-8f8d-3ea59cf047e9"}}, "output_collections": {}, "tool_stdout": "\n\u001b[1m\u001b[4mLoading reads\u001b[0m\n/galaxy/server/database/objects/6/4/b/dataset_64b22bcd-c800-4207-9736-15d61ef12e06.dat\n9 reads loaded\n\n\n\u001b[1m\u001b[4mLooking for known adapter sets\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n Best \u001b[0m\n read Best \u001b[0m\n start read end\u001b[0m\n \u001b[4mSet %ID %ID \u001b[0m\n \u001b[32mSQK-NSK007 96.4 95.5\u001b[0m\n Rapid 62.5 0.0\n RBK004_upstream 72.7 0.0\n SQK-MAP006 62.2 63.6\n SQK-MAP006 short 60.7 60.0\n PCR adapters 1 66.7 73.9\n PCR adapters 2 66.7 63.6\n PCR adapters 3 68.0 72.0\n 1D^2 part 1 62.1 58.8\n 1D^2 part 2 79.4 68.8\n cDNA SSP 57.1 61.4\n Barcode 1 (reverse) 59.4 66.7\n Barcode 2 (reverse) 66.7 63.0\n Barcode 3 (reverse) 69.2 72.0\n Barcode 4 (reverse) 66.7 63.3\n Barcode 5 (reverse) 62.5 66.7\n Barcode 6 (reverse) 73.1 62.5\n Barcode 7 (reverse) 65.4 65.5\n Barcode 8 (reverse) 69.2 58.3\n Barcode 9 (reverse) 75.0 66.7\n Barcode 10 (reverse) 62.5 60.0\n Barcode 11 (reverse) 69.2 60.5\n Barcode 12 (reverse) 65.6 64.0\n Barcode 1 (forward) 65.4 61.5\n Barcode 2 (forward) 69.2 70.4\n Barcode 3 (forward) 73.1 68.0\n Barcode 4 (forward) 73.1 64.3\n Barcode 5 (forward) 62.5 66.7\n Barcode 6 (forward) 65.5 65.6\n Barcode 7 (forward) 73.1 66.7\n Barcode 8 (forward) 62.1 60.7\n Barcode 9 (forward) 68.0 70.8\n Barcode 10 (forward) 69.2 66.7\n Barcode 11 (forward) 65.4 60.7\n Barcode 12 (forward) 64.3 66.7\n Barcode 13 (forward) 64.3 69.2\n Barcode 14 (forward) 63.3 66.7\n Barcode 15 (forward) 66.7 66.7\n Barcode 16 (forward) 70.8 65.5\n Barcode 17 (forward) 69.2 66.7\n Barcode 18 (forward) 70.4 70.4\n Barcode 19 (forward) 65.5 64.0\n Barcode 20 (forward) 65.5 64.0\n Barcode 21 (forward) 64.3 66.7\n Barcode 22 (forward) 69.2 68.0\n Barcode 23 (forward) 61.5 66.7\n Barcode 24 (forward) 66.7 65.4\n Barcode 25 (forward) 64.0 65.5\n Barcode 26 (forward) 72.0 72.0\n Barcode 27 (forward) 77.8 60.7\n Barcode 28 (forward) 65.5 66.7\n Barcode 29 (forward) 62.5 66.7\n Barcode 30 (forward) 68.0 65.4\n Barcode 31 (forward) 62.5 69.2\n Barcode 32 (forward) 68.0 70.8\n Barcode 33 (forward) 62.5 70.4\n Barcode 34 (forward) 64.0 62.5\n Barcode 35 (forward) 65.5 65.4\n Barcode 36 (forward) 63.0 63.0\n Barcode 37 (forward) 67.9 64.3\n Barcode 38 (forward) 64.0 62.1\n Barcode 39 (forward) 64.0 69.2\n Barcode 40 (forward) 62.5 64.0\n Barcode 41 (forward) 68.0 65.5\n Barcode 42 (forward) 70.4 69.2\n Barcode 43 (forward) 63.3 63.3\n Barcode 44 (forward) 60.0 66.7\n Barcode 45 (forward) 73.1 65.4\n Barcode 46 (forward) 65.4 60.7\n Barcode 47 (forward) 65.5 64.0\n Barcode 48 (forward) 71.4 62.1\n Barcode 49 (forward) 69.2 62.1\n Barcode 50 (forward) 66.7 63.0\n Barcode 51 (forward) 69.2 64.3\n Barcode 52 (forward) 66.7 64.0\n Barcode 53 (forward) 67.9 69.0\n Barcode 54 (forward) 69.2 64.0\n Barcode 55 (forward) 66.7 73.1\n Barcode 56 (forward) 66.7 72.0\n Barcode 57 (forward) 69.0 60.0\n Barcode 58 (forward) 70.4 72.0\n Barcode 59 (forward) 56.7 66.7\n Barcode 60 (forward) 66.7 66.7\n Barcode 61 (forward) 70.8 65.5\n Barcode 62 (forward) 66.7 68.0\n Barcode 63 (forward) 66.7 60.7\n Barcode 64 (forward) 69.2 66.7\n Barcode 65 (forward) 61.5 69.0\n Barcode 66 (forward) 64.3 63.0\n Barcode 67 (forward) 66.7 67.9\n Barcode 68 (forward) 67.9 69.2\n Barcode 69 (forward) 69.2 75.0\n Barcode 70 (forward) 64.3 73.1\n Barcode 71 (forward) 64.0 71.4\n Barcode 72 (forward) 66.7 62.1\n Barcode 73 (forward) 67.7 64.0\n Barcode 74 (forward) 64.5 68.0\n Barcode 75 (forward) 65.4 65.5\n Barcode 76 (forward) 70.4 70.8\n Barcode 77 (forward) 65.4 64.3\n Barcode 78 (forward) 67.7 63.0\n Barcode 79 (forward) 70.8 69.2\n Barcode 80 (forward) 71.4 72.0\n Barcode 81 (forward) 68.0 66.7\n Barcode 82 (forward) 64.7 66.7\n Barcode 83 (forward) 69.2 68.0\n Barcode 84 (forward) 70.8 67.9\n Barcode 85 (forward) 61.5 60.0\n Barcode 86 (forward) 64.3 65.4\n Barcode 87 (forward) 66.7 65.4\n Barcode 88 (forward) 63.3 60.7\n Barcode 89 (forward) 69.2 66.7\n Barcode 90 (forward) 66.7 64.0\n Barcode 91 (forward) 68.0 64.3\n Barcode 92 (forward) 65.5 68.0\n Barcode 93 (forward) 69.2 73.1\n Barcode 94 (forward) 63.0 68.0\n Barcode 95 (forward) 64.0 63.3\n Barcode 96 (forward) 69.0 68.0\n\n\n\u001b[1m\u001b[4mTrimming adapters from read ends\u001b[0m\n SQK-NSK007_Y_Top: \u001b[31mAATGTACTTCGTTCAGTTACGTATTGCT\u001b[0m\n SQK-NSK007_Y_Bottom: \u001b[31mGCAATACGTAACTGAACGAAGT\u001b[0m\n\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n\n4 / 9 reads had adapters trimmed from their start (74 bp removed)\n3 / 9 reads had adapters trimmed from their end (49 bp removed)\n\n\n\u001b[1m\u001b[4mSplitting reads containing middle adapters\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r10 / 9 (111.1%)\r9 / 9 (100.0%)\n\n4 / 9 reads were split based on middle adapters\n\n\n\u001b[1m\u001b[4mSaving trimmed reads to file\u001b[0m\npigz not found - using gzip to compress\n\nSaved result to /galaxy/server/database/jobs_directory/000/137/working/out.fastq.gz\n\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "\n\u001b[1m\u001b[4mLoading reads\u001b[0m\n/galaxy/server/database/objects/6/4/b/dataset_64b22bcd-c800-4207-9736-15d61ef12e06.dat\n9 reads loaded\n\n\n\u001b[1m\u001b[4mLooking for known adapter sets\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n Best \u001b[0m\n read Best \u001b[0m\n start read end\u001b[0m\n \u001b[4mSet %ID %ID \u001b[0m\n \u001b[32mSQK-NSK007 96.4 95.5\u001b[0m\n Rapid 62.5 0.0\n RBK004_upstream 72.7 0.0\n SQK-MAP006 62.2 63.6\n SQK-MAP006 short 60.7 60.0\n PCR adapters 1 66.7 73.9\n PCR adapters 2 66.7 63.6\n PCR adapters 3 68.0 72.0\n 1D^2 part 1 62.1 58.8\n 1D^2 part 2 79.4 68.8\n cDNA SSP 57.1 61.4\n Barcode 1 (reverse) 59.4 66.7\n Barcode 2 (reverse) 66.7 63.0\n Barcode 3 (reverse) 69.2 72.0\n Barcode 4 (reverse) 66.7 63.3\n Barcode 5 (reverse) 62.5 66.7\n Barcode 6 (reverse) 73.1 62.5\n Barcode 7 (reverse) 65.4 65.5\n Barcode 8 (reverse) 69.2 58.3\n Barcode 9 (reverse) 75.0 66.7\n Barcode 10 (reverse) 62.5 60.0\n Barcode 11 (reverse) 69.2 60.5\n Barcode 12 (reverse) 65.6 64.0\n Barcode 1 (forward) 65.4 61.5\n Barcode 2 (forward) 69.2 70.4\n Barcode 3 (forward) 73.1 68.0\n Barcode 4 (forward) 73.1 64.3\n Barcode 5 (forward) 62.5 66.7\n Barcode 6 (forward) 65.5 65.6\n Barcode 7 (forward) 73.1 66.7\n Barcode 8 (forward) 62.1 60.7\n Barcode 9 (forward) 68.0 70.8\n Barcode 10 (forward) 69.2 66.7\n Barcode 11 (forward) 65.4 60.7\n Barcode 12 (forward) 64.3 66.7\n Barcode 13 (forward) 64.3 69.2\n Barcode 14 (forward) 63.3 66.7\n Barcode 15 (forward) 66.7 66.7\n Barcode 16 (forward) 70.8 65.5\n Barcode 17 (forward) 69.2 66.7\n Barcode 18 (forward) 70.4 70.4\n Barcode 19 (forward) 65.5 64.0\n Barcode 20 (forward) 65.5 64.0\n Barcode 21 (forward) 64.3 66.7\n Barcode 22 (forward) 69.2 68.0\n Barcode 23 (forward) 61.5 66.7\n Barcode 24 (forward) 66.7 65.4\n Barcode 25 (forward) 64.0 65.5\n Barcode 26 (forward) 72.0 72.0\n Barcode 27 (forward) 77.8 60.7\n Barcode 28 (forward) 65.5 66.7\n Barcode 29 (forward) 62.5 66.7\n Barcode 30 (forward) 68.0 65.4\n Barcode 31 (forward) 62.5 69.2\n Barcode 32 (forward) 68.0 70.8\n Barcode 33 (forward) 62.5 70.4\n Barcode 34 (forward) 64.0 62.5\n Barcode 35 (forward) 65.5 65.4\n Barcode 36 (forward) 63.0 63.0\n Barcode 37 (forward) 67.9 64.3\n Barcode 38 (forward) 64.0 62.1\n Barcode 39 (forward) 64.0 69.2\n Barcode 40 (forward) 62.5 64.0\n Barcode 41 (forward) 68.0 65.5\n Barcode 42 (forward) 70.4 69.2\n Barcode 43 (forward) 63.3 63.3\n Barcode 44 (forward) 60.0 66.7\n Barcode 45 (forward) 73.1 65.4\n Barcode 46 (forward) 65.4 60.7\n Barcode 47 (forward) 65.5 64.0\n Barcode 48 (forward) 71.4 62.1\n Barcode 49 (forward) 69.2 62.1\n Barcode 50 (forward) 66.7 63.0\n Barcode 51 (forward) 69.2 64.3\n Barcode 52 (forward) 66.7 64.0\n Barcode 53 (forward) 67.9 69.0\n Barcode 54 (forward) 69.2 64.0\n Barcode 55 (forward) 66.7 73.1\n Barcode 56 (forward) 66.7 72.0\n Barcode 57 (forward) 69.0 60.0\n Barcode 58 (forward) 70.4 72.0\n Barcode 59 (forward) 56.7 66.7\n Barcode 60 (forward) 66.7 66.7\n Barcode 61 (forward) 70.8 65.5\n Barcode 62 (forward) 66.7 68.0\n Barcode 63 (forward) 66.7 60.7\n Barcode 64 (forward) 69.2 66.7\n Barcode 65 (forward) 61.5 69.0\n Barcode 66 (forward) 64.3 63.0\n Barcode 67 (forward) 66.7 67.9\n Barcode 68 (forward) 67.9 69.2\n Barcode 69 (forward) 69.2 75.0\n Barcode 70 (forward) 64.3 73.1\n Barcode 71 (forward) 64.0 71.4\n Barcode 72 (forward) 66.7 62.1\n Barcode 73 (forward) 67.7 64.0\n Barcode 74 (forward) 64.5 68.0\n Barcode 75 (forward) 65.4 65.5\n Barcode 76 (forward) 70.4 70.8\n Barcode 77 (forward) 65.4 64.3\n Barcode 78 (forward) 67.7 63.0\n Barcode 79 (forward) 70.8 69.2\n Barcode 80 (forward) 71.4 72.0\n Barcode 81 (forward) 68.0 66.7\n Barcode 82 (forward) 64.7 66.7\n Barcode 83 (forward) 69.2 68.0\n Barcode 84 (forward) 70.8 67.9\n Barcode 85 (forward) 61.5 60.0\n Barcode 86 (forward) 64.3 65.4\n Barcode 87 (forward) 66.7 65.4\n Barcode 88 (forward) 63.3 60.7\n Barcode 89 (forward) 69.2 66.7\n Barcode 90 (forward) 66.7 64.0\n Barcode 91 (forward) 68.0 64.3\n Barcode 92 (forward) 65.5 68.0\n Barcode 93 (forward) 69.2 73.1\n Barcode 94 (forward) 63.0 68.0\n Barcode 95 (forward) 64.0 63.3\n Barcode 96 (forward) 69.0 68.0\n\n\n\u001b[1m\u001b[4mTrimming adapters from read ends\u001b[0m\n SQK-NSK007_Y_Top: \u001b[31mAATGTACTTCGTTCAGTTACGTATTGCT\u001b[0m\n SQK-NSK007_Y_Bottom: \u001b[31mGCAATACGTAACTGAACGAAGT\u001b[0m\n\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n\n4 / 9 reads had adapters trimmed from their start (74 bp removed)\n3 / 9 reads had adapters trimmed from their end (49 bp removed)\n\n\n\u001b[1m\u001b[4mSplitting reads containing middle adapters\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r10 / 9 (111.1%)\r9 / 9 (100.0%)\n\n4 / 9 reads were split based on middle adapters\n\n\n\u001b[1m\u001b[4mSaving trimmed reads to file\u001b[0m\npigz not found - using gzip to compress\n\nSaved result to /galaxy/server/database/jobs_directory/000/137/working/out.fastq.gz\n\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-12-30 01:21:23", "plugin": "core", "name": "end_epoch", "raw_value": "1735521683.0000000"}, {"title": "Job Start Time", "value": "2024-12-30 01:21:22", "plugin": "core", "name": "start_epoch", "raw_value": "1735521682.0000000"}, {"title": "Memory Allocated (MB)", "value": "42949", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "42949.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "porechop/0.2.4+galaxy0-5", "has_data": true, "data": {"tool_id": "porechop", "tool_version": "0.2.4+galaxy0", "test_index": 5, "time_seconds": 29.119664430618286, "inputs": {"input_file": {"src": "hda", "id": "2549e2abd59b5ab2"}, "format": "fasta", "barcode_binning_settings|barcode_threshold": "70", "barcode_binning_settings|barcode_diff": "4", "barcode_binning_settings|require_two_barcodes": true, "barcode_binning_settings|discard_unassigned": true, "end_adapter_settings|end_size": "100", "end_adapter_settings|min_trim_size": "2", "end_adapter_settings|extra_end_trim": "1", "end_adapter_settings|end_threshold": "80", "middle_adapter_settings|discard_middle": true, "middle_adapter_settings|middle_threshold": "90", "middle_adapter_settings|min_split_read_size": "1500"}, "job": {"model_class": "Job", "id": "9fbbcd7e53eeecb6", "state": "ok", "exit_code": 0, "update_time": "2024-12-30T01:22:02.222451", "create_time": "2024-12-30T01:21:49.476152", "galaxy_version": "23.1", "command_version": "0.2.4", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0", "history_id": "1262154bdd2f9614", "external_id": "gxy-c722g", "command_line": "porechop -i '/galaxy/server/database/objects/7/7/8/dataset_778ce91e-3e64-4bc8-9084-c99006669b2d.dat' --format 'fasta' --barcode_threshold '70.0' --barcode_diff '4.0' --require_two_barcodes --discard_unassigned --adapter_threshold '90.0' --check_reads '10000' --scoring_scheme '3,-6,-5,-2' --end_size '100' --min_trim_size '2' --extra_end_trim '1' --end_threshold '80.0' --discard_middle --middle_threshold '90.0' --extra_middle_trim_good_side '10' --extra_middle_trim_bad_side '100' --min_split_read_size '1500' -o 'out.fasta'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "middle_adapter_settings": "{\"discard_middle\": true, \"extra_middle_trim_bad_side\": \"100\", \"extra_middle_trim_good_side\": \"10\", \"middle_threshold\": \"90.0\", \"min_split_read_size\": \"1500\", \"no_split\": false}", "end_adapter_settings": "{\"end_size\": \"100\", \"end_threshold\": \"80.0\", \"extra_end_trim\": \"1\", \"min_trim_size\": \"2\"}", "adapter_search_settings": "{\"adapter_threshold\": \"90.0\", \"check_reads\": \"10000\", \"scoring_scheme\": \"3,-6,-5,-2\"}", "barcode_binning_settings": "{\"barcode_diff\": \"4.0\", \"barcode_threshold\": \"70.0\", \"discard_unassigned\": true, \"require_two_barcodes\": true}", "format": "\"fasta\""}, "inputs": {"input_file": {"id": "2549e2abd59b5ab2", "src": "hda", "uuid": "778ce91e-3e64-4bc8-9084-c99006669b2d"}}, "outputs": {"outfile": {"id": "9fbbcd7e53eeecb6", "src": "hda", "uuid": "98af874d-a463-43f2-8a49-1bd38b8fb0aa"}}, "output_collections": {}, "tool_stdout": "\n\u001b[1m\u001b[4mLoading reads\u001b[0m\n/galaxy/server/database/objects/7/7/8/dataset_778ce91e-3e64-4bc8-9084-c99006669b2d.dat\n9 reads loaded\n\n\n\u001b[1m\u001b[4mLooking for known adapter sets\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n Best \u001b[0m\n read Best \u001b[0m\n start read end\u001b[0m\n \u001b[4mSet %ID %ID \u001b[0m\n \u001b[32mSQK-NSK007 96.4 95.5\u001b[0m\n Rapid 62.5 0.0\n RBK004_upstream 72.7 0.0\n SQK-MAP006 58.8 63.6\n SQK-MAP006 short 58.6 57.7\n PCR adapters 1 66.7 73.9\n PCR adapters 2 65.4 63.6\n PCR adapters 3 68.0 70.4\n 1D^2 part 1 66.7 58.6\n 1D^2 part 2 79.4 68.8\n cDNA SSP 58.7 61.4\n Barcode 1 (reverse) 58.3 66.7\n Barcode 2 (reverse) 66.7 50.0\n Barcode 3 (reverse) 69.2 69.2\n Barcode 4 (reverse) 66.7 61.5\n Barcode 5 (reverse) 62.5 69.2\n Barcode 6 (reverse) 65.4 62.5\n Barcode 7 (reverse) 62.5 65.5\n Barcode 8 (reverse) 59.3 58.3\n Barcode 9 (reverse) 75.0 66.7\n Barcode 10 (reverse) 57.7 60.0\n Barcode 11 (reverse) 69.2 60.5\n Barcode 12 (reverse) 65.6 55.2\n Barcode 1 (forward) 65.4 62.1\n Barcode 2 (forward) 69.2 70.4\n Barcode 3 (forward) 65.4 68.0\n Barcode 4 (forward) 63.3 64.3\n Barcode 5 (forward) 57.1 56.0\n Barcode 6 (forward) 45.7 63.0\n Barcode 7 (forward) 73.1 62.1\n Barcode 8 (forward) 62.1 60.6\n Barcode 9 (forward) 64.3 66.7\n Barcode 10 (forward) 61.8 68.0\n Barcode 11 (forward) 65.4 60.7\n Barcode 12 (forward) 60.6 66.7\n Barcode 13 (forward) 64.5 69.2\n Barcode 14 (forward) 63.3 66.7\n Barcode 15 (forward) 66.7 66.7\n Barcode 16 (forward) 65.5 64.0\n Barcode 17 (forward) 69.2 66.7\n Barcode 18 (forward) 70.4 64.0\n Barcode 19 (forward) 64.5 63.0\n Barcode 20 (forward) 65.5 64.0\n Barcode 21 (forward) 64.3 66.7\n Barcode 22 (forward) 69.2 68.0\n Barcode 23 (forward) 57.9 65.5\n Barcode 24 (forward) 66.7 61.3\n Barcode 25 (forward) 59.4 68.0\n Barcode 26 (forward) 64.3 72.0\n Barcode 27 (forward) 61.3 59.4\n Barcode 28 (forward) 65.4 62.5\n Barcode 29 (forward) 57.7 62.5\n Barcode 30 (forward) 68.0 64.0\n Barcode 31 (forward) 62.1 61.5\n Barcode 32 (forward) 68.0 70.8\n Barcode 33 (forward) 46.2 70.4\n Barcode 34 (forward) 64.0 18.5\n Barcode 35 (forward) 64.3 65.4\n Barcode 36 (forward) 63.0 63.0\n Barcode 37 (forward) 67.9 64.3\n Barcode 38 (forward) 64.0 62.1\n Barcode 39 (forward) 61.5 62.5\n Barcode 40 (forward) 62.5 64.0\n Barcode 41 (forward) 68.0 65.5\n Barcode 42 (forward) 70.4 69.2\n Barcode 43 (forward) 63.3 62.5\n Barcode 44 (forward) 60.0 66.7\n Barcode 45 (forward) 73.1 65.4\n Barcode 46 (forward) 66.7 60.7\n Barcode 47 (forward) 64.3 61.5\n Barcode 48 (forward) 71.4 65.4\n Barcode 49 (forward) 69.2 62.1\n Barcode 50 (forward) 66.7 57.1\n Barcode 51 (forward) 69.2 59.3\n Barcode 52 (forward) 62.5 64.0\n Barcode 53 (forward) 65.4 69.0\n Barcode 54 (forward) 69.2 62.1\n Barcode 55 (forward) 66.7 73.1\n Barcode 56 (forward) 62.5 64.0\n Barcode 57 (forward) 66.7 55.6\n Barcode 58 (forward) 67.7 66.7\n Barcode 59 (forward) 56.7 59.4\n Barcode 60 (forward) 66.7 63.0\n Barcode 61 (forward) 70.8 65.5\n Barcode 62 (forward) 66.7 68.0\n Barcode 63 (forward) 66.7 62.5\n Barcode 64 (forward) 60.7 67.9\n Barcode 65 (forward) 61.5 62.5\n Barcode 66 (forward) 61.5 61.3\n Barcode 67 (forward) 66.7 60.0\n Barcode 68 (forward) 67.9 69.2\n Barcode 69 (forward) 65.5 66.7\n Barcode 70 (forward) 64.3 73.1\n Barcode 71 (forward) 60.7 71.4\n Barcode 72 (forward) 66.7 62.1\n Barcode 73 (forward) 67.7 63.6\n Barcode 74 (forward) 64.5 68.0\n Barcode 75 (forward) 65.4 65.5\n Barcode 76 (forward) 60.6 64.0\n Barcode 77 (forward) 65.4 62.1\n Barcode 78 (forward) 66.7 63.3\n Barcode 79 (forward) 70.8 66.7\n Barcode 80 (forward) 62.5 66.7\n Barcode 81 (forward) 68.0 66.7\n Barcode 82 (forward) 64.0 66.7\n Barcode 83 (forward) 64.0 68.0\n Barcode 84 (forward) 64.5 67.9\n Barcode 85 (forward) 61.5 58.3\n Barcode 86 (forward) 64.3 66.7\n Barcode 87 (forward) 66.7 65.5\n Barcode 88 (forward) 63.3 61.5\n Barcode 89 (forward) 69.0 66.7\n Barcode 90 (forward) 64.3 61.3\n Barcode 91 (forward) 53.3 64.0\n Barcode 92 (forward) 65.5 68.0\n Barcode 93 (forward) 63.3 71.4\n Barcode 94 (forward) 61.5 64.5\n Barcode 95 (forward) 62.1 63.3\n Barcode 96 (forward) 69.0 68.0\n\n\n\u001b[1m\u001b[4mTrimming adapters from read ends\u001b[0m\n SQK-NSK007_Y_Top: \u001b[31mAATGTACTTCGTTCAGTTACGTATTGCT\u001b[0m\n SQK-NSK007_Y_Bottom: \u001b[31mGCAATACGTAACTGAACGAAGT\u001b[0m\n\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n\n4 / 9 reads had adapters trimmed from their start (70 bp removed)\n3 / 9 reads had adapters trimmed from their end (46 bp removed)\n\n\n\u001b[1m\u001b[4mDiscarding reads containing middle adapters\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r10 / 9 (111.1%)\r9 / 9 (100.0%)\n\n4 / 9 reads were discarded based on middle adapters\n\n\n\u001b[1m\u001b[4mSaving trimmed reads to file\u001b[0m\n\nSaved result to /galaxy/server/database/jobs_directory/000/139/working/out.fasta\n\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "\n\u001b[1m\u001b[4mLoading reads\u001b[0m\n/galaxy/server/database/objects/7/7/8/dataset_778ce91e-3e64-4bc8-9084-c99006669b2d.dat\n9 reads loaded\n\n\n\u001b[1m\u001b[4mLooking for known adapter sets\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n Best \u001b[0m\n read Best \u001b[0m\n start read end\u001b[0m\n \u001b[4mSet %ID %ID \u001b[0m\n \u001b[32mSQK-NSK007 96.4 95.5\u001b[0m\n Rapid 62.5 0.0\n RBK004_upstream 72.7 0.0\n SQK-MAP006 58.8 63.6\n SQK-MAP006 short 58.6 57.7\n PCR adapters 1 66.7 73.9\n PCR adapters 2 65.4 63.6\n PCR adapters 3 68.0 70.4\n 1D^2 part 1 66.7 58.6\n 1D^2 part 2 79.4 68.8\n cDNA SSP 58.7 61.4\n Barcode 1 (reverse) 58.3 66.7\n Barcode 2 (reverse) 66.7 50.0\n Barcode 3 (reverse) 69.2 69.2\n Barcode 4 (reverse) 66.7 61.5\n Barcode 5 (reverse) 62.5 69.2\n Barcode 6 (reverse) 65.4 62.5\n Barcode 7 (reverse) 62.5 65.5\n Barcode 8 (reverse) 59.3 58.3\n Barcode 9 (reverse) 75.0 66.7\n Barcode 10 (reverse) 57.7 60.0\n Barcode 11 (reverse) 69.2 60.5\n Barcode 12 (reverse) 65.6 55.2\n Barcode 1 (forward) 65.4 62.1\n Barcode 2 (forward) 69.2 70.4\n Barcode 3 (forward) 65.4 68.0\n Barcode 4 (forward) 63.3 64.3\n Barcode 5 (forward) 57.1 56.0\n Barcode 6 (forward) 45.7 63.0\n Barcode 7 (forward) 73.1 62.1\n Barcode 8 (forward) 62.1 60.6\n Barcode 9 (forward) 64.3 66.7\n Barcode 10 (forward) 61.8 68.0\n Barcode 11 (forward) 65.4 60.7\n Barcode 12 (forward) 60.6 66.7\n Barcode 13 (forward) 64.5 69.2\n Barcode 14 (forward) 63.3 66.7\n Barcode 15 (forward) 66.7 66.7\n Barcode 16 (forward) 65.5 64.0\n Barcode 17 (forward) 69.2 66.7\n Barcode 18 (forward) 70.4 64.0\n Barcode 19 (forward) 64.5 63.0\n Barcode 20 (forward) 65.5 64.0\n Barcode 21 (forward) 64.3 66.7\n Barcode 22 (forward) 69.2 68.0\n Barcode 23 (forward) 57.9 65.5\n Barcode 24 (forward) 66.7 61.3\n Barcode 25 (forward) 59.4 68.0\n Barcode 26 (forward) 64.3 72.0\n Barcode 27 (forward) 61.3 59.4\n Barcode 28 (forward) 65.4 62.5\n Barcode 29 (forward) 57.7 62.5\n Barcode 30 (forward) 68.0 64.0\n Barcode 31 (forward) 62.1 61.5\n Barcode 32 (forward) 68.0 70.8\n Barcode 33 (forward) 46.2 70.4\n Barcode 34 (forward) 64.0 18.5\n Barcode 35 (forward) 64.3 65.4\n Barcode 36 (forward) 63.0 63.0\n Barcode 37 (forward) 67.9 64.3\n Barcode 38 (forward) 64.0 62.1\n Barcode 39 (forward) 61.5 62.5\n Barcode 40 (forward) 62.5 64.0\n Barcode 41 (forward) 68.0 65.5\n Barcode 42 (forward) 70.4 69.2\n Barcode 43 (forward) 63.3 62.5\n Barcode 44 (forward) 60.0 66.7\n Barcode 45 (forward) 73.1 65.4\n Barcode 46 (forward) 66.7 60.7\n Barcode 47 (forward) 64.3 61.5\n Barcode 48 (forward) 71.4 65.4\n Barcode 49 (forward) 69.2 62.1\n Barcode 50 (forward) 66.7 57.1\n Barcode 51 (forward) 69.2 59.3\n Barcode 52 (forward) 62.5 64.0\n Barcode 53 (forward) 65.4 69.0\n Barcode 54 (forward) 69.2 62.1\n Barcode 55 (forward) 66.7 73.1\n Barcode 56 (forward) 62.5 64.0\n Barcode 57 (forward) 66.7 55.6\n Barcode 58 (forward) 67.7 66.7\n Barcode 59 (forward) 56.7 59.4\n Barcode 60 (forward) 66.7 63.0\n Barcode 61 (forward) 70.8 65.5\n Barcode 62 (forward) 66.7 68.0\n Barcode 63 (forward) 66.7 62.5\n Barcode 64 (forward) 60.7 67.9\n Barcode 65 (forward) 61.5 62.5\n Barcode 66 (forward) 61.5 61.3\n Barcode 67 (forward) 66.7 60.0\n Barcode 68 (forward) 67.9 69.2\n Barcode 69 (forward) 65.5 66.7\n Barcode 70 (forward) 64.3 73.1\n Barcode 71 (forward) 60.7 71.4\n Barcode 72 (forward) 66.7 62.1\n Barcode 73 (forward) 67.7 63.6\n Barcode 74 (forward) 64.5 68.0\n Barcode 75 (forward) 65.4 65.5\n Barcode 76 (forward) 60.6 64.0\n Barcode 77 (forward) 65.4 62.1\n Barcode 78 (forward) 66.7 63.3\n Barcode 79 (forward) 70.8 66.7\n Barcode 80 (forward) 62.5 66.7\n Barcode 81 (forward) 68.0 66.7\n Barcode 82 (forward) 64.0 66.7\n Barcode 83 (forward) 64.0 68.0\n Barcode 84 (forward) 64.5 67.9\n Barcode 85 (forward) 61.5 58.3\n Barcode 86 (forward) 64.3 66.7\n Barcode 87 (forward) 66.7 65.5\n Barcode 88 (forward) 63.3 61.5\n Barcode 89 (forward) 69.0 66.7\n Barcode 90 (forward) 64.3 61.3\n Barcode 91 (forward) 53.3 64.0\n Barcode 92 (forward) 65.5 68.0\n Barcode 93 (forward) 63.3 71.4\n Barcode 94 (forward) 61.5 64.5\n Barcode 95 (forward) 62.1 63.3\n Barcode 96 (forward) 69.0 68.0\n\n\n\u001b[1m\u001b[4mTrimming adapters from read ends\u001b[0m\n SQK-NSK007_Y_Top: \u001b[31mAATGTACTTCGTTCAGTTACGTATTGCT\u001b[0m\n SQK-NSK007_Y_Bottom: \u001b[31mGCAATACGTAACTGAACGAAGT\u001b[0m\n\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n\n4 / 9 reads had adapters trimmed from their start (70 bp removed)\n3 / 9 reads had adapters trimmed from their end (46 bp removed)\n\n\n\u001b[1m\u001b[4mDiscarding reads containing middle adapters\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r10 / 9 (111.1%)\r9 / 9 (100.0%)\n\n4 / 9 reads were discarded based on middle adapters\n\n\n\u001b[1m\u001b[4mSaving trimmed reads to file\u001b[0m\n\nSaved result to /galaxy/server/database/jobs_directory/000/139/working/out.fasta\n\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-12-30 01:21:52", "plugin": "core", "name": "end_epoch", "raw_value": "1735521712.0000000"}, {"title": "Job Start Time", "value": "2024-12-30 01:21:51", "plugin": "core", "name": "start_epoch", "raw_value": "1735521711.0000000"}, {"title": "Memory Allocated (MB)", "value": "42949", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "42949.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "samtools_split/1.9-0", "has_data": true, "data": {"tool_id": "samtools_split", "tool_version": "1.9", "test_index": 0, "time_seconds": 26.20690417289734, "inputs": {"input_bam": {"src": "hda", "id": "274f511891181a00"}}, "job": {"model_class": "Job", "id": "196b84ddca54174e", "state": "error", "exit_code": null, "update_time": "2024-12-30T01:11:04.111061", "create_time": "2024-12-30T01:10:55.277916", "galaxy_version": "23.1", "command_version": null, "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.9", "history_id": "1262154bdd2f9614", "external_id": "gxy-6hvzc", "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && samtools split -f 'Read_Group_%!.bam' -u '/galaxy/server/database/objects/1/4/c/dataset_14cae4b9-035c-43dd-b791-7a371b5cb643.dat' -@ $addthreads '/galaxy/server/database/objects/1/6/c/dataset_16c65af2-71c6-444d-b73a-9dbe010b8b63.dat'", "traceback": null, "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "header": null}, "inputs": {"input_bam": {"id": "274f511891181a00", "src": "hda", "uuid": "16c65af2-71c6-444d-b73a-9dbe010b8b63"}}, "outputs": {"output": {"id": "196b84ddca54174e", "src": "hda", "uuid": "14cae4b9-035c-43dd-b791-7a371b5cb643"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": null, "job_stderr": null, "stderr": "", "stdout": "", "job_messages": null, "dependencies": [], "user_email": "tests@fake.org", "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.9, exit_code: None, stderr: .", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.9, exit_code: None, stderr: ."], "status": "failure"}}, {"id": "samtools_view/1.9+galaxy3-0", "has_data": true, "data": {"tool_id": "samtools_view", "tool_version": "1.9+galaxy3", "test_index": 0, "time_seconds": 34.40943241119385, "inputs": {"input": {"src": "hda", "id": "5033959ec363fc59"}}, "job": {"model_class": "Job", "id": "222157f9a6d65187", "state": "ok", "exit_code": 0, "update_time": "2024-12-30T00:58:50.972867", "create_time": "2024-12-30T00:58:31.706145", "galaxy_version": "23.1", "command_version": "Version: 1.9 (using htslib 1.9)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3", "history_id": "1262154bdd2f9614", "external_id": "gxy-mv5xd", "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/9/c/3/dataset_9c358bf5-6246-44f9-b451-9344843dd2df.dat' infile && samtools view -@ $addthreads -b -o outfile infile && samtools sort -@ $addthreads -m $addmemory\"M\" -T \"${TMPDIR:-.}\" -O bam -o tmpsam outfile && mv tmpsam outfile", "traceback": null, "params": {"__input_ext": "\"sam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addref_cond": "{\"__current_case__\": 0, \"addref_select\": \"no\"}", "mode": "{\"__current_case__\": 0, \"output_options\": {\"__current_case__\": 0, \"adv_output\": {\"collapsecigar\": false, \"readtags\": []}, \"output_format\": {\"__current_case__\": 2, \"oformat\": \"bam\"}, \"reads_report_type\": \"retained\"}, \"outtype\": \"all_reads\"}"}, "inputs": {"input": {"id": "5033959ec363fc59", "src": "hda", "uuid": "9c358bf5-6246-44f9-b451-9344843dd2df"}}, "outputs": {"outputsam": {"id": "222157f9a6d65187", "src": "hda", "uuid": "91316a40-ef40-41cf-b9f3-7f10c5d9601d"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Job Start Time", "value": "2024-12-30 00:58:40", "plugin": "core", "name": "start_epoch", "raw_value": "1735520320.0000000"}, {"title": "Job End Time", "value": "2024-12-30 00:58:40", "plugin": "core", "name": "end_epoch", "raw_value": "1735520320.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "output_problems": ["Output outputsam: Test output file (sam_to_bam_out1.bam) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "samtools_view/1.9+galaxy3-1", "has_data": true, "data": {"tool_id": "samtools_view", "tool_version": "1.9+galaxy3", "test_index": 1, "status": "skip"}}, {"id": "samtools_view/1.9+galaxy3-10", "has_data": true, "data": {"tool_id": "samtools_view", "tool_version": "1.9+galaxy3", "test_index": 10, "time_seconds": 28.19634771347046, "inputs": {"input": {"src": "hda", "id": "5b8b9eb8992c0fc5"}, "mode|output_options|output_format|with_header": true, "mode|output_options|output_format|oformat": "sam"}, "job": {"model_class": "Job", "id": "c6df0a97b5b7e3be", "state": "ok", "exit_code": 0, "update_time": "2024-12-30T01:02:52.772411", "create_time": "2024-12-30T01:02:42.172851", "galaxy_version": "23.1", "command_version": "Version: 1.9 (using htslib 1.9)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3", "history_id": "1262154bdd2f9614", "external_id": "gxy-q2p44", "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/6/5/8/dataset_65847279-3505-415f-acf6-d92d9038b5c4.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/6/2/0/metadata_62000f91-16f1-4941-a503-c9eddf4de206.dat' infile.bai && samtools view -@ $addthreads -h -o outfile infile", "traceback": null, "params": {"mode": "{\"__current_case__\": 0, \"output_options\": {\"__current_case__\": 0, \"adv_output\": {\"collapsecigar\": false, \"readtags\": []}, \"output_format\": {\"__current_case__\": 1, \"oformat\": \"sam\", \"with_header\": true}, \"reads_report_type\": \"retained\"}, \"outtype\": \"all_reads\"}", "addref_cond": "{\"__current_case__\": 0, \"addref_select\": \"no\"}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"bam\""}, "inputs": {"input": {"id": "5b8b9eb8992c0fc5", "src": "hda", "uuid": "65847279-3505-415f-acf6-d92d9038b5c4"}}, "outputs": {"outputsam": {"id": "c6df0a97b5b7e3be", "src": "hda", "uuid": "4b0623b9-1f49-4503-a66c-4b0592c5b92b"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-12-30 01:02:43", "plugin": "core", "name": "end_epoch", "raw_value": "1735520563.0000000"}, {"title": "Job Start Time", "value": "2024-12-30 01:02:43", "plugin": "core", "name": "start_epoch", "raw_value": "1735520563.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output outputsam: Test output file (bam_to_sam_out1.sam) is missing. 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If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "samtools_view/1.9+galaxy3-12", "has_data": true, "data": {"tool_id": "samtools_view", "tool_version": "1.9+galaxy3", "test_index": 12, "time_seconds": 9.909362554550171, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "samtools_view/1.9+galaxy3-13", "has_data": true, "data": {"tool_id": "samtools_view", "tool_version": "1.9+galaxy3", "test_index": 13, "time_seconds": 29.287654161453247, "inputs": {"input": {"src": "hda", "id": "1716993f2d8bea0f"}, "mode|output_options|reads_report_type": "count", "mode|outtype": "all_reads"}, "job": {"model_class": "Job", "id": "11d61bdc0121fdce", "state": "ok", "exit_code": 0, "update_time": "2024-12-30T01:04:00.497973", "create_time": "2024-12-30T01:03:48.128171", "galaxy_version": "23.1", "command_version": "Version: 1.9 (using htslib 1.9)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3", "history_id": "1262154bdd2f9614", "external_id": "gxy-rmprs", "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/b/7/5/dataset_b75648cc-5249-4304-8ace-91d5cc9ef736.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/9/5/f/metadata_95f71871-7671-4ce0-a133-901b41e93fef.dat' infile.bai && samtools view -@ $addthreads -c -o outfile infile", "traceback": null, "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addref_cond": "{\"__current_case__\": 0, \"addref_select\": \"no\"}", "mode": "{\"__current_case__\": 0, \"output_options\": {\"__current_case__\": 1, \"reads_report_type\": \"count\"}, \"outtype\": \"all_reads\"}"}, "inputs": {"input": {"id": "1716993f2d8bea0f", "src": "hda", "uuid": "b75648cc-5249-4304-8ace-91d5cc9ef736"}}, "outputs": {"outputcnt": {"id": "11d61bdc0121fdce", "src": "hda", "uuid": "42e0785c-a848-48fe-a08c-0b862e215d98"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-12-30 01:03:49", "plugin": "core", "name": "end_epoch", "raw_value": "1735520629.0000000"}, {"title": "Job Start Time", "value": "2024-12-30 01:03:49", "plugin": "core", "name": "start_epoch", "raw_value": "1735520629.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output outputcnt: Test output file (test_counts.tab) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "samtools_view/1.9+galaxy3-14", "has_data": true, "data": {"tool_id": "samtools_view", "tool_version": "1.9+galaxy3", "test_index": 14, "time_seconds": 30.16211986541748, "inputs": {"input": {"src": "hda", "id": "81557b37ce6f097c"}, "mode|filter_config|cond_region|select_region": "no", "mode|output_options|output_format|oformat": "cram", "mode|outtype": "selected_reads", "addref_cond|ref": {"src": "hda", "id": "a842bb8a80bc64df"}, "addref_cond|addref_select": "history"}, "job": {"model_class": "Job", "id": "627114804621566b", "state": "ok", "exit_code": 0, "update_time": "2024-12-30T01:04:30.734705", "create_time": "2024-12-30T01:04:18.237430", "galaxy_version": "23.1", "command_version": "Version: 1.9 (using htslib 1.9)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3", "history_id": "1262154bdd2f9614", "external_id": "gxy-x8tp2", "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/a/1/2/dataset_a12e5adb-c6f6-4c5c-b777-5253dc17e5c5.dat' reference.fa && samtools faidx reference.fa && ln -s '/galaxy/server/database/objects/1/8/3/dataset_183c37b0-bee7-4a73-a48e-30ab382a4229.dat' infile && samtools view -@ $addthreads -C -o outfile --output-fmt-option no_ref -T 'reference.fa' -t 'reference.fa.fai' infile", "traceback": null, "params": {"__input_ext": "\"sam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addref_cond": "{\"__current_case__\": 1, \"addref_select\": \"history\", \"ref\": {\"values\": [{\"id\": 46, \"src\": \"hda\"}]}}", "mode": "{\"__current_case__\": 1, \"filter_config\": {\"cigarcons\": \"\", \"cond_region\": {\"__current_case__\": 0, \"select_region\": \"no\"}, \"cond_rg\": {\"__current_case__\": 0, \"select_rg\": \"no\"}, \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"inclusive_filter\": null, \"library\": null, \"quality\": \"\"}, \"output_options\": {\"__current_case__\": 0, \"adv_output\": {\"collapsecigar\": false, \"readtags\": []}, \"complementary_output\": false, \"output_format\": {\"__current_case__\": 3, \"oformat\": \"cram\"}, \"reads_report_type\": \"retained\"}, \"outtype\": \"selected_reads\", \"subsample_config\": {\"subsampling_mode\": {\"__current_case__\": 0, \"factor\": \"1.0\", \"seed\": \"\", \"select_subsample\": \"fraction\"}}}"}, "inputs": {"input": {"id": "81557b37ce6f097c", "src": "hda", "uuid": "183c37b0-bee7-4a73-a48e-30ab382a4229"}, "addref_cond|ref": {"id": "a842bb8a80bc64df", "src": "hda", "uuid": "a12e5adb-c6f6-4c5c-b777-5253dc17e5c5"}}, "outputs": {"outputsam": {"id": "627114804621566b", "src": "hda", "uuid": "a9873827-fc02-4b4a-9cb2-b29b6072215a"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-12-30 01:04:20", "plugin": "core", "name": "end_epoch", "raw_value": "1735520660.0000000"}, {"title": "Job Start Time", "value": "2024-12-30 01:04:20", "plugin": "core", "name": "start_epoch", "raw_value": "1735520660.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output outputsam: Test output file (test.cram) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "samtools_view/1.9+galaxy3-15", "has_data": true, "data": {"tool_id": "samtools_view", "tool_version": "1.9+galaxy3", "test_index": 15, "time_seconds": 29.5900981426239, "inputs": {"input": {"src": "hda", "id": "afbc9e957401521f"}, "mode|filter_config|cond_region|select_region": "no", "mode|output_options|output_format|oformat": "cram", "mode|outtype": "selected_reads", "addref_cond|ref": {"src": "hda", "id": "9efb84aa16c06c86"}, "addref_cond|addref_select": "history"}, "job": {"model_class": "Job", "id": "8fb60f5115b6f92c", "state": "ok", "exit_code": 0, "update_time": "2024-12-30T01:05:00.344717", "create_time": "2024-12-30T01:04:48.134235", "galaxy_version": "23.1", "command_version": "Version: 1.9 (using htslib 1.9)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3", "history_id": "1262154bdd2f9614", "external_id": "gxy-49j8g", "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/9/d/d/dataset_9dd09f3c-6b61-4cf5-9b57-7f146d6f38a3.dat' reference.fa && samtools faidx reference.fa && ln -s '/galaxy/server/database/objects/f/9/4/dataset_f9405ae4-38bc-415f-bab2-c96fdb4e7e11.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/2/8/2/metadata_28276a21-5728-4dd1-90cf-15f56bbf1923.dat' infile.bai && samtools view -@ $addthreads -C -o outfile --output-fmt-option no_ref -T 'reference.fa' -t 'reference.fa.fai' infile", "traceback": null, "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addref_cond": "{\"__current_case__\": 1, \"addref_select\": \"history\", \"ref\": {\"values\": [{\"id\": 49, \"src\": \"hda\"}]}}", "mode": "{\"__current_case__\": 1, \"filter_config\": {\"cigarcons\": \"\", \"cond_region\": {\"__current_case__\": 0, \"select_region\": \"no\"}, \"cond_rg\": {\"__current_case__\": 0, \"select_rg\": \"no\"}, \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"inclusive_filter\": null, \"library\": null, \"quality\": \"\"}, \"output_options\": {\"__current_case__\": 0, \"adv_output\": {\"collapsecigar\": false, \"readtags\": []}, \"complementary_output\": false, \"output_format\": {\"__current_case__\": 3, \"oformat\": \"cram\"}, \"reads_report_type\": \"retained\"}, \"outtype\": \"selected_reads\", \"subsample_config\": {\"subsampling_mode\": {\"__current_case__\": 0, \"factor\": \"1.0\", \"seed\": \"\", \"select_subsample\": \"fraction\"}}}"}, "inputs": {"addref_cond|ref": {"id": "9efb84aa16c06c86", "src": "hda", "uuid": "9dd09f3c-6b61-4cf5-9b57-7f146d6f38a3"}, "input": {"id": "afbc9e957401521f", "src": "hda", "uuid": "f9405ae4-38bc-415f-bab2-c96fdb4e7e11"}}, "outputs": {"outputsam": {"id": "8fb60f5115b6f92c", "src": "hda", "uuid": "b64148af-5c88-4762-ad1d-81593f749c67"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-12-30 01:04:50", "plugin": "core", "name": "end_epoch", "raw_value": "1735520690.0000000"}, {"title": "Job Start Time", "value": "2024-12-30 01:04:50", "plugin": "core", "name": "start_epoch", "raw_value": "1735520690.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output outputsam: Test output file (test.cram) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "samtools_view/1.9+galaxy3-16", "has_data": true, "data": {"tool_id": "samtools_view", "tool_version": "1.9+galaxy3", "test_index": 16, "status": "skip"}}, {"id": "samtools_view/1.9+galaxy3-17", "has_data": true, "data": {"tool_id": "samtools_view", "tool_version": "1.9+galaxy3", "test_index": 17, "time_seconds": 30.39615273475647, "inputs": {"input": {"src": "hda", "id": "724900be56f9469b"}, "mode|filter_config|cond_region|regions": "CHROMOSOME_I", "mode|filter_config|cond_region|select_region": "text", "mode|output_options|output_format|oformat": "cram", "mode|outtype": "selected_reads", "addref_cond|ref": {"src": "hda", "id": "46173ea66ac5197a"}, "addref_cond|addref_select": "history"}, "job": {"model_class": "Job", "id": "3467a254fce916da", "state": "ok", "exit_code": 0, "update_time": "2024-12-30T01:05:30.936308", "create_time": "2024-12-30T01:05:18.460021", "galaxy_version": "23.1", "command_version": "Version: 1.9 (using htslib 1.9)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3", "history_id": "1262154bdd2f9614", "external_id": "gxy-hzvsg", "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/4/2/5/dataset_425bbfb2-986a-4fcb-98e6-07eaae34e0a7.dat' reference.fa && samtools faidx reference.fa && ln -s '/galaxy/server/database/objects/d/0/2/dataset_d027d03b-d98a-428c-b9b0-fb69149577f8.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/e/e/b/metadata_eebd7975-99dd-4822-91ab-d287b5a0a2fc.dat' infile.bai && samtools view -@ $addthreads -C -o outfile --output-fmt-option no_ref -T 'reference.fa' -t 'reference.fa.fai' infile 'CHROMOSOME_I'", "traceback": null, "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addref_cond": "{\"__current_case__\": 1, \"addref_select\": \"history\", \"ref\": {\"values\": [{\"id\": 52, \"src\": \"hda\"}]}}", "mode": "{\"__current_case__\": 1, \"filter_config\": {\"cigarcons\": \"\", \"cond_region\": {\"__current_case__\": 1, \"regions\": \"CHROMOSOME_I\", \"select_region\": \"text\"}, \"cond_rg\": {\"__current_case__\": 0, \"select_rg\": \"no\"}, \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"inclusive_filter\": null, \"library\": null, \"quality\": \"\"}, \"output_options\": {\"__current_case__\": 0, \"adv_output\": {\"collapsecigar\": false, \"readtags\": []}, \"complementary_output\": false, \"output_format\": {\"__current_case__\": 3, \"oformat\": \"cram\"}, \"reads_report_type\": \"retained\"}, \"outtype\": \"selected_reads\", \"subsample_config\": {\"subsampling_mode\": {\"__current_case__\": 0, \"factor\": \"1.0\", \"seed\": \"\", \"select_subsample\": \"fraction\"}}}"}, "inputs": {"input": {"id": "724900be56f9469b", "src": "hda", "uuid": "d027d03b-d98a-428c-b9b0-fb69149577f8"}, "addref_cond|ref": {"id": "46173ea66ac5197a", "src": "hda", "uuid": "425bbfb2-986a-4fcb-98e6-07eaae34e0a7"}}, "outputs": {"outputsam": {"id": "3467a254fce916da", "src": "hda", "uuid": "e3610e5b-0553-4f20-bebc-891c929483ea"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-12-30 01:05:20", "plugin": "core", "name": "end_epoch", "raw_value": "1735520720.0000000"}, {"title": "Job Start Time", "value": "2024-12-30 01:05:20", "plugin": "core", "name": "start_epoch", "raw_value": "1735520720.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output outputsam: Test output file (test.cram) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "samtools_view/1.9+galaxy3-18", "has_data": true, "data": {"tool_id": "samtools_view", "tool_version": "1.9+galaxy3", "test_index": 18, "time_seconds": 27.791242361068726, "inputs": {"input": {"src": "hda", "id": "a12eb6ea508f124b"}, "mode|filter_config|cond_region|regions": "CHROMOSOME_I", "mode|filter_config|cond_region|select_region": "text", "mode|output_options|output_format|oformat": "bam", "mode|outtype": "selected_reads", "addref_cond|ref": {"src": "hda", "id": "dd71cca156f1390f"}, "addref_cond|addref_select": "history"}, "job": {"model_class": "Job", "id": "d127a80372ea6698", "state": "ok", "exit_code": 0, "update_time": "2024-12-30T01:05:58.583185", "create_time": "2024-12-30T01:05:47.178031", "galaxy_version": "23.1", "command_version": "Version: 1.9 (using htslib 1.9)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3", "history_id": "1262154bdd2f9614", "external_id": "gxy-m56ks", "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/4/f/c/dataset_4fcc00dc-751e-4498-8317-f1cb142787bc.dat' reference.fa && samtools faidx reference.fa && ln -s '/galaxy/server/database/objects/4/6/d/dataset_46dd4fb2-6af8-4022-a912-e17351796ee0.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/1/1/6/metadata_116d9fab-db82-45f6-93df-576f1b775a6b.dat' infile.crai && samtools view -@ $addthreads -b -o outfile -T 'reference.fa' -t 'reference.fa.fai' infile 'CHROMOSOME_I' && samtools sort -@ $addthreads -m $addmemory\"M\" -T \"${TMPDIR:-.}\" -O bam -o tmpsam outfile && mv tmpsam outfile", "traceback": null, "params": {"__input_ext": "\"cram\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addref_cond": "{\"__current_case__\": 1, \"addref_select\": \"history\", \"ref\": {\"values\": [{\"id\": 55, \"src\": \"hda\"}]}}", "mode": "{\"__current_case__\": 1, \"filter_config\": {\"cigarcons\": \"\", \"cond_region\": {\"__current_case__\": 1, \"regions\": \"CHROMOSOME_I\", \"select_region\": \"text\"}, \"cond_rg\": {\"__current_case__\": 0, \"select_rg\": \"no\"}, \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"inclusive_filter\": null, \"library\": null, \"quality\": \"\"}, \"output_options\": {\"__current_case__\": 0, \"adv_output\": {\"collapsecigar\": false, \"readtags\": []}, \"complementary_output\": false, \"output_format\": {\"__current_case__\": 2, \"oformat\": \"bam\"}, \"reads_report_type\": \"retained\"}, \"outtype\": \"selected_reads\", \"subsample_config\": {\"subsampling_mode\": {\"__current_case__\": 0, \"factor\": \"1.0\", \"seed\": \"\", \"select_subsample\": \"fraction\"}}}"}, "inputs": {"input": {"id": "a12eb6ea508f124b", "src": "hda", "uuid": "46dd4fb2-6af8-4022-a912-e17351796ee0"}, "addref_cond|ref": {"id": "dd71cca156f1390f", "src": "hda", "uuid": "4fcc00dc-751e-4498-8317-f1cb142787bc"}}, "outputs": {"outputsam": {"id": "d127a80372ea6698", "src": "hda", "uuid": "304191dc-360c-4fbb-b4e9-2f6b31cbd005"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-12-30 01:05:49", "plugin": "core", "name": "end_epoch", "raw_value": "1735520749.0000000"}, {"title": "Job Start Time", "value": "2024-12-30 01:05:49", "plugin": "core", "name": "start_epoch", "raw_value": "1735520749.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output outputsam: Test output file (test.bam) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "samtools_view/1.9+galaxy3-19", "has_data": true, "data": {"tool_id": "samtools_view", "tool_version": "1.9+galaxy3", "test_index": 19, "time_seconds": 31.789435625076294, "inputs": {"input": {"src": "hda", "id": "7b986663b792e971"}, "mode|filter_config|cond_region|bedfile": {"src": "hda", "id": "6c57b686e8db6b8e"}, "mode|filter_config|cond_region|select_region": "bed", "mode|output_options|output_format|oformat": "bam", "mode|outtype": "selected_reads", "addref_cond|ref": {"src": "hda", "id": "7c12007f05f1af25"}, "addref_cond|addref_select": "history"}, "job": {"model_class": "Job", "id": "65e560fe91597247", "state": "ok", "exit_code": 0, "update_time": "2024-12-30T01:06:30.544421", "create_time": "2024-12-30T01:06:19.088077", "galaxy_version": "23.1", "command_version": "Version: 1.9 (using htslib 1.9)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3", "history_id": "1262154bdd2f9614", "external_id": "gxy-5v2h8", "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/0/b/e/dataset_0be8db0d-ed15-4d1b-bbd0-e48481d5ed7e.dat' reference.fa && samtools faidx reference.fa && ln -s '/galaxy/server/database/objects/f/7/3/dataset_f731860a-fd80-46b3-8a12-4efe5bf7de87.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/f/9/a/metadata_f9acfaec-d116-4b6b-b841-76ffece825e9.dat' infile.crai && samtools view -@ $addthreads -b -L '/galaxy/server/database/objects/7/6/5/dataset_765c02a8-6dc0-4307-9417-9468f73def3f.dat' -o outfile -T 'reference.fa' -t 'reference.fa.fai' infile && samtools sort -@ $addthreads -m $addmemory\"M\" -T \"${TMPDIR:-.}\" -O bam -o tmpsam outfile && mv tmpsam outfile", "traceback": null, "params": {"__input_ext": "\"cram\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addref_cond": "{\"__current_case__\": 1, \"addref_select\": \"history\", \"ref\": {\"values\": [{\"id\": 59, \"src\": \"hda\"}]}}", "mode": "{\"__current_case__\": 1, \"filter_config\": {\"cigarcons\": \"\", \"cond_region\": {\"__current_case__\": 2, \"bedfile\": {\"values\": [{\"id\": 58, \"src\": \"hda\"}]}, \"select_region\": \"bed\"}, \"cond_rg\": {\"__current_case__\": 0, \"select_rg\": \"no\"}, \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"inclusive_filter\": null, \"library\": null, \"quality\": \"\"}, \"output_options\": {\"__current_case__\": 0, \"adv_output\": {\"collapsecigar\": false, \"readtags\": []}, \"complementary_output\": false, \"output_format\": {\"__current_case__\": 2, \"oformat\": \"bam\"}, \"reads_report_type\": \"retained\"}, \"outtype\": \"selected_reads\", \"subsample_config\": {\"subsampling_mode\": {\"__current_case__\": 0, \"factor\": \"1.0\", \"seed\": \"\", \"select_subsample\": \"fraction\"}}}"}, "inputs": {"addref_cond|ref": {"id": "7c12007f05f1af25", "src": "hda", "uuid": "0be8db0d-ed15-4d1b-bbd0-e48481d5ed7e"}, "input": {"id": "7b986663b792e971", "src": "hda", "uuid": "f731860a-fd80-46b3-8a12-4efe5bf7de87"}, "mode|filter_config|cond_region|bedfile": {"id": "6c57b686e8db6b8e", "src": "hda", "uuid": "765c02a8-6dc0-4307-9417-9468f73def3f"}}, "outputs": {"outputsam": {"id": "65e560fe91597247", "src": "hda", "uuid": "cb012666-9787-44ea-b63d-1c0ec051aab5"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-12-30 01:06:20", "plugin": "core", "name": "end_epoch", "raw_value": "1735520780.0000000"}, {"title": "Job Start Time", "value": "2024-12-30 01:06:20", "plugin": "core", "name": "start_epoch", "raw_value": "1735520780.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output outputsam: Test output file (test.bam) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "samtools_view/1.9+galaxy3-2", "has_data": true, "data": {"tool_id": "samtools_view", "tool_version": "1.9+galaxy3", "test_index": 2, "time_seconds": 16.1102294921875, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "samtools_view/1.9+galaxy3-20", "has_data": true, "data": {"tool_id": "samtools_view", "tool_version": "1.9+galaxy3", "test_index": 20, "time_seconds": 27.01251196861267, "inputs": {"input": {"src": "hda", "id": "c74eab4166fbb65c"}, "mode|subsample_config|subsampling_mode|target": "2", "mode|subsample_config|subsampling_mode|select_subsample": "target", "mode|output_options|output_format|oformat": "input", "mode|outtype": "selected_reads"}, "job": {"model_class": "Job", "id": "55446d6113bb19bb", "state": "ok", "exit_code": 0, "update_time": "2024-12-30T01:06:57.718051", "create_time": "2024-12-30T01:06:46.852650", "galaxy_version": "23.1", "command_version": "Version: 1.9 (using htslib 1.9)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3", "history_id": "1262154bdd2f9614", "external_id": "gxy-khcsb", "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/d/b/d/dataset_dbdffe9f-c7bc-444e-bbae-300c74415e55.dat' infile && sample_fragment=`samtools view -c infile | awk '{s=$1} END {frac=s/2; print(frac > 1 ? 22814+1/frac : \".0\")}'` && samtools view -@ $addthreads -h -s ${sample_fragment} -o outfile infile", "traceback": null, "params": {"__input_ext": "\"sam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addref_cond": "{\"__current_case__\": 0, \"addref_select\": \"no\"}", "mode": "{\"__current_case__\": 1, \"filter_config\": {\"cigarcons\": \"\", \"cond_region\": {\"__current_case__\": 0, \"select_region\": \"no\"}, \"cond_rg\": {\"__current_case__\": 0, \"select_rg\": \"no\"}, \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"inclusive_filter\": null, \"library\": null, \"quality\": \"\"}, \"output_options\": {\"__current_case__\": 0, \"adv_output\": {\"collapsecigar\": false, \"readtags\": []}, \"complementary_output\": false, \"output_format\": {\"__current_case__\": 0, \"oformat\": \"input\"}, \"reads_report_type\": \"retained\"}, \"outtype\": \"selected_reads\", \"subsample_config\": {\"subsampling_mode\": {\"__current_case__\": 1, \"seed\": \"\", \"select_subsample\": \"target\", \"target\": \"2\"}}}"}, "inputs": {"input": {"id": "c74eab4166fbb65c", "src": "hda", "uuid": "dbdffe9f-c7bc-444e-bbae-300c74415e55"}}, "outputs": {"outputsam": {"id": "55446d6113bb19bb", "src": "hda", "uuid": "1faf36ab-d895-48a8-8713-be8ddda7cd2f"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-12-30 01:06:48", "plugin": "core", "name": "end_epoch", "raw_value": "1735520808.0000000"}, {"title": "Job Start Time", "value": "2024-12-30 01:06:48", "plugin": "core", "name": "start_epoch", "raw_value": "1735520808.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output outputsam: Test output file (test_ds.sam) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "samtools_view/1.9+galaxy3-21", "has_data": true, "data": {"tool_id": "samtools_view", "tool_version": "1.9+galaxy3", "test_index": 21, "time_seconds": 27.421420335769653, "inputs": {"input": {"src": "hda", "id": "e3a4941fedae6737"}, "mode|subsample_config|subsampling_mode|target": "20", "mode|subsample_config|subsampling_mode|select_subsample": "target", "mode|output_options|output_format|oformat": "input", "mode|outtype": "selected_reads"}, "job": {"model_class": "Job", "id": "3a4309e493a64a5f", "state": "ok", "exit_code": 0, "update_time": "2024-12-30T01:07:25.039006", "create_time": "2024-12-30T01:07:13.279332", "galaxy_version": "23.1", "command_version": "Version: 1.9 (using htslib 1.9)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3", "history_id": "1262154bdd2f9614", "external_id": "gxy-jcwj2", "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/7/8/6/dataset_7864d95e-a321-445b-90f0-df71307aacff.dat' infile && sample_fragment=`samtools view -c infile | awk '{s=$1} END {frac=s/20; print(frac > 1 ? 22282+1/frac : \".0\")}'` && samtools view -@ $addthreads -h -s ${sample_fragment} -o outfile infile", "traceback": null, "params": {"__input_ext": "\"sam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addref_cond": "{\"__current_case__\": 0, \"addref_select\": \"no\"}", "mode": "{\"__current_case__\": 1, \"filter_config\": {\"cigarcons\": \"\", \"cond_region\": {\"__current_case__\": 0, \"select_region\": \"no\"}, \"cond_rg\": {\"__current_case__\": 0, \"select_rg\": \"no\"}, \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"inclusive_filter\": null, \"library\": null, \"quality\": \"\"}, \"output_options\": {\"__current_case__\": 0, \"adv_output\": {\"collapsecigar\": false, \"readtags\": []}, \"complementary_output\": false, \"output_format\": {\"__current_case__\": 0, \"oformat\": \"input\"}, \"reads_report_type\": \"retained\"}, \"outtype\": \"selected_reads\", \"subsample_config\": {\"subsampling_mode\": {\"__current_case__\": 1, \"seed\": \"\", \"select_subsample\": \"target\", \"target\": \"20\"}}}"}, "inputs": {"input": {"id": "e3a4941fedae6737", "src": "hda", "uuid": "7864d95e-a321-445b-90f0-df71307aacff"}}, "outputs": {"outputsam": {"id": "3a4309e493a64a5f", "src": "hda", "uuid": "22d05080-35b5-4bb2-a81b-8b122acb85be"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-12-30 01:07:15", "plugin": "core", "name": "end_epoch", "raw_value": "1735520835.0000000"}, {"title": "Job Start Time", "value": "2024-12-30 01:07:15", "plugin": "core", "name": "start_epoch", "raw_value": "1735520835.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output outputsam: Test output file (test.sam) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "samtools_view/1.9+galaxy3-22", "has_data": true, "data": {"tool_id": "samtools_view", "tool_version": "1.9+galaxy3", "test_index": 22, "time_seconds": 28.16676163673401, "inputs": {"input": {"src": "hda", "id": "8764eb2d79202145"}, "mode|subsample_config|subsampling_mode|target": "20", "mode|subsample_config|subsampling_mode|select_subsample": "target", "mode|output_options|output_format|oformat": "input", "mode|outtype": "selected_reads"}, "job": {"model_class": "Job", "id": "aae1891d4b88b804", "state": "ok", "exit_code": 0, "update_time": "2024-12-30T01:07:53.201986", "create_time": "2024-12-30T01:07:41.511904", "galaxy_version": "23.1", "command_version": "Version: 1.9 (using htslib 1.9)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3", "history_id": "1262154bdd2f9614", "external_id": "gxy-psg9x", "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/0/c/8/dataset_0c830e5f-1034-4803-94bb-5a8039234634.dat' infile && sample_fragment=`samtools view -c infile | awk '{s=$1} END {frac=s/20; print(frac > 1 ? 1296+1/frac : \".0\")}'` && samtools view -@ $addthreads -h -s ${sample_fragment} -o outfile infile", "traceback": null, "params": {"__input_ext": "\"sam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addref_cond": "{\"__current_case__\": 0, \"addref_select\": \"no\"}", "mode": "{\"__current_case__\": 1, \"filter_config\": {\"cigarcons\": \"\", \"cond_region\": {\"__current_case__\": 0, \"select_region\": \"no\"}, \"cond_rg\": {\"__current_case__\": 0, \"select_rg\": \"no\"}, \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"inclusive_filter\": null, \"library\": null, \"quality\": \"\"}, \"output_options\": {\"__current_case__\": 0, \"adv_output\": {\"collapsecigar\": false, \"readtags\": []}, \"complementary_output\": false, \"output_format\": {\"__current_case__\": 0, \"oformat\": \"input\"}, \"reads_report_type\": \"retained\"}, \"outtype\": \"selected_reads\", \"subsample_config\": {\"subsampling_mode\": {\"__current_case__\": 1, \"seed\": \"\", \"select_subsample\": \"target\", \"target\": \"20\"}}}"}, "inputs": {"input": {"id": "8764eb2d79202145", "src": "hda", "uuid": "0c830e5f-1034-4803-94bb-5a8039234634"}}, "outputs": {"outputsam": {"id": "aae1891d4b88b804", "src": "hda", "uuid": "430803ef-01ca-4df5-ba06-88fa7d40363b"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-12-30 01:07:43", "plugin": "core", "name": "end_epoch", "raw_value": "1735520863.0000000"}, {"title": "Job Start Time", "value": "2024-12-30 01:07:43", "plugin": "core", "name": "start_epoch", "raw_value": "1735520863.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output outputsam: Test output file (no_reads.sam) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "samtools_view/1.9+galaxy3-23", "has_data": true, "data": {"tool_id": "samtools_view", "tool_version": "1.9+galaxy3", "test_index": 23, "time_seconds": 27.74349308013916, "inputs": {"input": {"src": "hda", "id": "87d7d1c2fb9d83f3"}, "mode|subsample_config|subsampling_mode|target": "20", "mode|subsample_config|subsampling_mode|select_subsample": "target", "mode|output_options|output_format|oformat": "input", "mode|outtype": "selected_reads"}, "job": {"model_class": "Job", "id": "7411613e1a6fc733", "state": "ok", "exit_code": 0, "update_time": "2024-12-30T01:08:21.046622", "create_time": "2024-12-30T01:08:10.260225", "galaxy_version": "23.1", "command_version": "Version: 1.9 (using htslib 1.9)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3", "history_id": "1262154bdd2f9614", "external_id": "gxy-lthl6", "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/7/2/8/dataset_7284bea3-7c90-4bcc-82ae-d861509bd241.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/8/c/5/metadata_8c58fb01-7778-4431-95af-4bf00b8bb188.dat' infile.bai && sample_fragment=`samtools idxstats infile | awk '{s+=$4+$3} END {frac=s/20; print(frac > 1 ? 25744+1/frac : \".0\")}'` && samtools view -@ $addthreads -b -s ${sample_fragment} -o outfile infile", "traceback": null, "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addref_cond": "{\"__current_case__\": 0, \"addref_select\": \"no\"}", "mode": "{\"__current_case__\": 1, \"filter_config\": {\"cigarcons\": \"\", \"cond_region\": {\"__current_case__\": 0, \"select_region\": \"no\"}, \"cond_rg\": {\"__current_case__\": 0, \"select_rg\": \"no\"}, \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"inclusive_filter\": null, \"library\": null, \"quality\": \"\"}, \"output_options\": {\"__current_case__\": 0, \"adv_output\": {\"collapsecigar\": false, \"readtags\": []}, \"complementary_output\": false, \"output_format\": {\"__current_case__\": 0, \"oformat\": \"input\"}, \"reads_report_type\": \"retained\"}, \"outtype\": \"selected_reads\", \"subsample_config\": {\"subsampling_mode\": {\"__current_case__\": 1, \"seed\": \"\", \"select_subsample\": \"target\", \"target\": \"20\"}}}"}, "inputs": {"input": {"id": "87d7d1c2fb9d83f3", "src": "hda", "uuid": "7284bea3-7c90-4bcc-82ae-d861509bd241"}}, "outputs": {"outputsam": {"id": "7411613e1a6fc733", "src": "hda", "uuid": "fb959da4-cc90-42ce-9055-72ea445bf993"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-12-30 01:08:12", "plugin": "core", "name": "end_epoch", "raw_value": "1735520892.0000000"}, {"title": "Job Start Time", "value": "2024-12-30 01:08:11", "plugin": "core", "name": "start_epoch", "raw_value": "1735520891.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output outputsam: Test output file (no_reads.bam) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "samtools_view/1.9+galaxy3-24", "has_data": true, "data": {"tool_id": "samtools_view", "tool_version": "1.9+galaxy3", "test_index": 24, "time_seconds": 25.93255853652954, "inputs": {"input": {"src": "hda", "id": "9b0aace47f069df0"}, "mode|subsample_config|subsampling_mode|target": "2", "mode|subsample_config|subsampling_mode|seed": "7", "mode|subsample_config|subsampling_mode|select_subsample": "target", "mode|output_options|output_format|oformat": "input", "mode|outtype": "selected_reads"}, "job": {"model_class": "Job", "id": "844808caf7756563", "state": "ok", "exit_code": 0, "update_time": "2024-12-30T01:08:47.149690", "create_time": "2024-12-30T01:08:36.357441", "galaxy_version": "23.1", "command_version": "Version: 1.9 (using htslib 1.9)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3", "history_id": "1262154bdd2f9614", "external_id": "gxy-cnbfl", "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/3/6/6/dataset_366a2c7e-195e-47f4-a18e-8be36dbd1e09.dat' infile && sample_fragment=`samtools view -c infile | awk '{s=$1} END {frac=s/2; print(frac > 1 ? 7+1/frac : \".0\")}'` && samtools view -@ $addthreads -h -s ${sample_fragment} -o outfile infile", "traceback": null, "params": {"__input_ext": "\"sam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addref_cond": "{\"__current_case__\": 0, \"addref_select\": \"no\"}", "mode": "{\"__current_case__\": 1, \"filter_config\": {\"cigarcons\": \"\", \"cond_region\": {\"__current_case__\": 0, \"select_region\": \"no\"}, \"cond_rg\": {\"__current_case__\": 0, \"select_rg\": \"no\"}, \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"inclusive_filter\": null, \"library\": null, \"quality\": \"\"}, \"output_options\": {\"__current_case__\": 0, \"adv_output\": {\"collapsecigar\": false, \"readtags\": []}, \"complementary_output\": false, \"output_format\": {\"__current_case__\": 0, \"oformat\": \"input\"}, \"reads_report_type\": \"retained\"}, \"outtype\": \"selected_reads\", \"subsample_config\": {\"subsampling_mode\": {\"__current_case__\": 1, \"seed\": \"7\", \"select_subsample\": \"target\", \"target\": \"2\"}}}"}, "inputs": {"input": {"id": "9b0aace47f069df0", "src": "hda", "uuid": "366a2c7e-195e-47f4-a18e-8be36dbd1e09"}}, "outputs": {"outputsam": {"id": "844808caf7756563", "src": "hda", "uuid": "6e5ceffc-3c20-4a21-b185-4321a1330747"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-12-30 01:08:37", "plugin": "core", "name": "end_epoch", "raw_value": "1735520917.0000000"}, {"title": "Job Start Time", "value": "2024-12-30 01:08:37", "plugin": "core", "name": "start_epoch", "raw_value": "1735520917.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output outputsam: Test output file (test_ds.sam) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "samtools_view/1.9+galaxy3-25", "has_data": true, "data": {"tool_id": "samtools_view", "tool_version": "1.9+galaxy3", "test_index": 25, "time_seconds": 28.785686016082764, "inputs": {"input": {"src": "hda", "id": "cef1ef233d649e68"}, "mode|subsample_config|subsampling_mode|target": "2", "mode|subsample_config|subsampling_mode|seed": "7", "mode|subsample_config|subsampling_mode|select_subsample": "target", "mode|output_options|output_format|oformat": "input", "mode|outtype": "selected_reads"}, "job": {"model_class": "Job", "id": "7a82f5a57734dfaa", "state": "ok", "exit_code": 0, "update_time": "2024-12-30T01:09:15.812245", "create_time": "2024-12-30T01:09:03.766225", "galaxy_version": "23.1", "command_version": "Version: 1.9 (using htslib 1.9)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3", "history_id": "1262154bdd2f9614", "external_id": "gxy-tlm2b", "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/3/4/3/dataset_34320bbd-bfb3-461c-825c-5e3b8202e25c.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/1/b/4/metadata_1b4af7a8-cf6f-4516-a099-e5403719b528.dat' infile.bai && sample_fragment=`samtools idxstats infile | awk '{s+=$4+$3} END {frac=s/2; print(frac > 1 ? 7+1/frac : \".0\")}'` && samtools view -@ $addthreads -b -s ${sample_fragment} -o outfile infile", "traceback": null, "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addref_cond": "{\"__current_case__\": 0, \"addref_select\": \"no\"}", "mode": "{\"__current_case__\": 1, \"filter_config\": {\"cigarcons\": \"\", \"cond_region\": {\"__current_case__\": 0, \"select_region\": \"no\"}, \"cond_rg\": {\"__current_case__\": 0, \"select_rg\": \"no\"}, \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"inclusive_filter\": null, \"library\": null, \"quality\": \"\"}, \"output_options\": {\"__current_case__\": 0, \"adv_output\": {\"collapsecigar\": false, \"readtags\": []}, \"complementary_output\": false, \"output_format\": {\"__current_case__\": 0, \"oformat\": \"input\"}, \"reads_report_type\": \"retained\"}, \"outtype\": \"selected_reads\", \"subsample_config\": {\"subsampling_mode\": {\"__current_case__\": 1, \"seed\": \"7\", \"select_subsample\": \"target\", \"target\": \"2\"}}}"}, "inputs": {"input": {"id": "cef1ef233d649e68", "src": "hda", "uuid": "34320bbd-bfb3-461c-825c-5e3b8202e25c"}}, "outputs": {"outputsam": {"id": "7a82f5a57734dfaa", "src": "hda", "uuid": "3967188f-52e1-44f1-8b86-e0d6665f48d6"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-12-30 01:09:06", "plugin": "core", "name": "end_epoch", "raw_value": "1735520946.0000000"}, {"title": "Job Start Time", "value": "2024-12-30 01:09:05", "plugin": "core", "name": "start_epoch", "raw_value": "1735520945.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output outputsam: Test output file (test_ds.bam) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "samtools_view/1.9+galaxy3-26", "has_data": true, "data": {"tool_id": "samtools_view", "tool_version": "1.9+galaxy3", "test_index": 26, "time_seconds": 26.065353393554688, "inputs": {"input": {"src": "hda", "id": "c52e9dc71b5d2484"}, "mode|subsample_config|subsampling_mode|target": "20", "mode|subsample_config|subsampling_mode|seed": "7", "mode|subsample_config|subsampling_mode|select_subsample": "target", "mode|output_options|output_format|oformat": "input", "mode|outtype": "selected_reads"}, "job": {"model_class": "Job", "id": "8f10fb4d26fa3ad6", "state": "ok", "exit_code": 0, "update_time": "2024-12-30T01:09:42.104564", "create_time": "2024-12-30T01:09:31.283243", "galaxy_version": "23.1", "command_version": "Version: 1.9 (using htslib 1.9)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3", "history_id": "1262154bdd2f9614", "external_id": "gxy-vb4q5", "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/f/0/8/dataset_f081eeb7-dc46-42da-825b-3c951e93066d.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/6/c/f/metadata_6cf1a4a3-c48d-4415-bf96-49da3a043d08.dat' infile.bai && sample_fragment=`samtools idxstats infile | awk '{s+=$4+$3} END {frac=s/20; print(frac > 1 ? 7+1/frac : \".0\")}'` && samtools view -@ $addthreads -b -s ${sample_fragment} -o outfile infile", "traceback": null, "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addref_cond": "{\"__current_case__\": 0, \"addref_select\": \"no\"}", "mode": "{\"__current_case__\": 1, \"filter_config\": {\"cigarcons\": \"\", \"cond_region\": {\"__current_case__\": 0, \"select_region\": \"no\"}, \"cond_rg\": {\"__current_case__\": 0, \"select_rg\": \"no\"}, \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"inclusive_filter\": null, \"library\": null, \"quality\": \"\"}, \"output_options\": {\"__current_case__\": 0, \"adv_output\": {\"collapsecigar\": false, \"readtags\": []}, \"complementary_output\": false, \"output_format\": {\"__current_case__\": 0, \"oformat\": \"input\"}, \"reads_report_type\": \"retained\"}, \"outtype\": \"selected_reads\", \"subsample_config\": {\"subsampling_mode\": {\"__current_case__\": 1, \"seed\": \"7\", \"select_subsample\": \"target\", \"target\": \"20\"}}}"}, "inputs": {"input": {"id": "c52e9dc71b5d2484", "src": "hda", "uuid": "f081eeb7-dc46-42da-825b-3c951e93066d"}}, "outputs": {"outputsam": {"id": "8f10fb4d26fa3ad6", "src": "hda", "uuid": "c891af48-12bc-4981-b0d6-c01990b56bef"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-12-30 01:09:32", "plugin": "core", "name": "end_epoch", "raw_value": "1735520972.0000000"}, {"title": "Job Start Time", "value": "2024-12-30 01:09:32", "plugin": "core", "name": "start_epoch", "raw_value": "1735520972.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output outputsam: Test output file (test.bam) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "samtools_view/1.9+galaxy3-27", "has_data": true, "data": {"tool_id": "samtools_view", "tool_version": "1.9+galaxy3", "test_index": 27, "time_seconds": 28.366541862487793, "inputs": {"input": {"src": "hda", "id": "adbdc15bd6b7ce52"}, "mode|subsample_config|subsampling_mode|factor": "5", "mode|subsample_config|subsampling_mode|seed": "7", "mode|subsample_config|subsampling_mode|select_subsample": "fraction", "mode|output_options|output_format|oformat": "input", "mode|outtype": "selected_reads"}, "job": {"model_class": "Job", "id": "4cd5e4fc0a8b1f5f", "state": "ok", "exit_code": 0, "update_time": "2024-12-30T01:10:10.612083", "create_time": "2024-12-30T01:09:58.644919", "galaxy_version": "23.1", "command_version": "Version: 1.9 (using htslib 1.9)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3", "history_id": "1262154bdd2f9614", "external_id": "gxy-d5xx5", "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/3/6/3/dataset_36357b41-62d7-4da7-8c70-2c487ecdf0ea.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/c/7/a/metadata_c7a4e5c8-fe59-48f0-860f-ff69d7a43b36.dat' infile.bai && samtools view -@ $addthreads -b -s 7.2 -o outfile infile", "traceback": null, "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addref_cond": "{\"__current_case__\": 0, \"addref_select\": \"no\"}", "mode": "{\"__current_case__\": 1, \"filter_config\": {\"cigarcons\": \"\", \"cond_region\": {\"__current_case__\": 0, \"select_region\": \"no\"}, \"cond_rg\": {\"__current_case__\": 0, \"select_rg\": \"no\"}, \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"inclusive_filter\": null, \"library\": null, \"quality\": \"\"}, \"output_options\": {\"__current_case__\": 0, \"adv_output\": {\"collapsecigar\": false, \"readtags\": []}, \"complementary_output\": false, \"output_format\": {\"__current_case__\": 0, \"oformat\": \"input\"}, \"reads_report_type\": \"retained\"}, \"outtype\": \"selected_reads\", \"subsample_config\": {\"subsampling_mode\": {\"__current_case__\": 0, \"factor\": \"5.0\", \"seed\": \"7\", \"select_subsample\": \"fraction\"}}}"}, "inputs": {"input": {"id": "adbdc15bd6b7ce52", "src": "hda", "uuid": "36357b41-62d7-4da7-8c70-2c487ecdf0ea"}}, "outputs": {"outputsam": {"id": "4cd5e4fc0a8b1f5f", "src": "hda", "uuid": "e1df2083-2462-4a96-9964-343af95751cb"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-12-30 01:10:00", "plugin": "core", "name": "end_epoch", "raw_value": "1735521000.0000000"}, {"title": "Job Start Time", "value": "2024-12-30 01:10:00", "plugin": "core", "name": "start_epoch", "raw_value": "1735521000.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output outputsam: Test output file (test_ds.bam) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "samtools_view/1.9+galaxy3-28", "has_data": true, "data": {"tool_id": "samtools_view", "tool_version": "1.9+galaxy3", "test_index": 28, "time_seconds": 26.392157554626465, "inputs": {"input": {"src": "hda", "id": "0aaea8878b8fea5b"}, "mode|subsample_config|subsampling_mode|factor": "1.25", "mode|subsample_config|subsampling_mode|seed": "7", "mode|subsample_config|subsampling_mode|select_subsample": "fraction", "mode|output_options|output_format|oformat": "input", "mode|output_options|reads_report_type": "dropped", "mode|outtype": "selected_reads"}, "job": {"model_class": "Job", "id": "8c56311ea3240b50", "state": "ok", "exit_code": 0, "update_time": "2024-12-30T01:10:36.759007", "create_time": "2024-12-30T01:10:25.825155", "galaxy_version": "23.1", "command_version": "Version: 1.9 (using htslib 1.9)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3", "history_id": "1262154bdd2f9614", "external_id": "gxy-rc7k8", "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/4/4/0/dataset_440ad6f8-dc03-403b-92bc-d3948fd1f884.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/5/7/3/metadata_573cfc1b-413f-49a2-b21f-dbdbd92c7e16.dat' infile.bai && samtools view -@ $addthreads -b -s 7.8 -U outfile -o /dev/null infile", "traceback": null, "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addref_cond": "{\"__current_case__\": 0, \"addref_select\": \"no\"}", "mode": "{\"__current_case__\": 1, \"filter_config\": {\"cigarcons\": \"\", \"cond_region\": {\"__current_case__\": 0, \"select_region\": \"no\"}, \"cond_rg\": {\"__current_case__\": 0, \"select_rg\": \"no\"}, \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"inclusive_filter\": null, \"library\": null, \"quality\": \"\"}, \"output_options\": {\"__current_case__\": 1, \"adv_output\": {\"collapsecigar\": false, \"readtags\": []}, \"complementary_output\": false, \"output_format\": {\"__current_case__\": 0, \"oformat\": \"input\"}, \"reads_report_type\": \"dropped\"}, \"outtype\": \"selected_reads\", \"subsample_config\": {\"subsampling_mode\": {\"__current_case__\": 0, \"factor\": \"1.25\", \"seed\": \"7\", \"select_subsample\": \"fraction\"}}}"}, "inputs": {"input": {"id": "0aaea8878b8fea5b", "src": "hda", "uuid": "440ad6f8-dc03-403b-92bc-d3948fd1f884"}}, "outputs": {"outputsam": {"id": "8c56311ea3240b50", "src": "hda", "uuid": "98c860a0-9501-4576-90aa-7bc5a2ecb386"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-12-30 01:10:27", "plugin": "core", "name": "end_epoch", "raw_value": "1735521027.0000000"}, {"title": "Job Start Time", "value": "2024-12-30 01:10:27", "plugin": "core", "name": "start_epoch", "raw_value": "1735521027.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output outputsam: Test output file (test_ds.bam) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "samtools_view/1.9+galaxy3-3", "has_data": true, "data": {"tool_id": "samtools_view", "tool_version": "1.9+galaxy3", "test_index": 3, "time_seconds": 29.110257148742676, "inputs": {"input": {"src": "hda", "id": "5aba81aa33ae9c65"}, "addref_cond|ref": {"src": "hda", "id": "c94fc708be99abd0"}, "addref_cond|addref_select": "history"}, "job": {"model_class": "Job", "id": "5239fad89d935397", "state": "ok", "exit_code": 0, "update_time": "2024-12-30T00:59:36.370108", "create_time": "2024-12-30T00:59:24.412973", "galaxy_version": "23.1", "command_version": "Version: 1.9 (using htslib 1.9)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3", "history_id": "1262154bdd2f9614", "external_id": "gxy-5zc89", "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/1/5/1/dataset_15145316-4dbd-405c-8120-95224b22d731.dat' reference.fa && samtools faidx reference.fa && ln -s '/galaxy/server/database/objects/8/2/f/dataset_82f68dc0-4041-44c8-b4d7-afb9e5550e29.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/5/b/b/metadata_5bb2679b-65fa-4f8f-b100-2c269866be67.dat' infile.crai && samtools view -@ $addthreads -b -o outfile -T 'reference.fa' -t 'reference.fa.fai' infile && samtools sort -@ $addthreads -m $addmemory\"M\" -T \"${TMPDIR:-.}\" -O bam -o tmpsam outfile && mv tmpsam outfile", "traceback": null, "params": {"__input_ext": "\"cram\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addref_cond": "{\"__current_case__\": 1, \"addref_select\": \"history\", \"ref\": {\"values\": [{\"id\": 24, \"src\": \"hda\"}]}}", "mode": "{\"__current_case__\": 0, \"output_options\": {\"__current_case__\": 0, \"adv_output\": {\"collapsecigar\": false, \"readtags\": []}, \"output_format\": {\"__current_case__\": 2, \"oformat\": \"bam\"}, \"reads_report_type\": \"retained\"}, \"outtype\": \"all_reads\"}"}, "inputs": {"input": {"id": "5aba81aa33ae9c65", "src": "hda", "uuid": "82f68dc0-4041-44c8-b4d7-afb9e5550e29"}, "addref_cond|ref": {"id": "c94fc708be99abd0", "src": "hda", "uuid": "15145316-4dbd-405c-8120-95224b22d731"}}, "outputs": {"outputsam": {"id": "5239fad89d935397", "src": "hda", "uuid": "2efacf8e-75e1-4748-9d81-6916a7a3fb44"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Job Start Time", "value": "2024-12-30 00:59:26", "plugin": "core", "name": "start_epoch", "raw_value": "1735520366.0000000"}, {"title": "Job End Time", "value": "2024-12-30 00:59:26", "plugin": "core", "name": "end_epoch", "raw_value": "1735520366.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "output_problems": ["Output outputsam: Test output file (test.bam) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "samtools_view/1.9+galaxy3-4", "has_data": true, "data": {"tool_id": "samtools_view", "tool_version": "1.9+galaxy3", "test_index": 4, "time_seconds": 28.704160690307617, "inputs": {"input": {"src": "hda", "id": "f3aa40edd8d2ea49"}}, "job": {"model_class": "Job", "id": "7e3077fb34b289c9", "state": "ok", "exit_code": 0, "update_time": "2024-12-30T01:00:05.188721", "create_time": "2024-12-30T00:59:52.676005", "galaxy_version": "23.1", "command_version": "Version: 1.9 (using htslib 1.9)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3", "history_id": "1262154bdd2f9614", "external_id": "gxy-jsj2h", "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/3/4/c/dataset_34c83c44-d6e9-4318-9a91-53b0c43c419a.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/b/1/9/metadata_b1974381-2ba2-4623-88e3-61636470b2bf.dat' infile.bai && samtools view -@ $addthreads -b -o outfile infile", "traceback": null, "params": {"mode": "{\"__current_case__\": 0, \"output_options\": {\"__current_case__\": 0, \"adv_output\": {\"collapsecigar\": false, \"readtags\": []}, \"output_format\": {\"__current_case__\": 2, \"oformat\": \"bam\"}, \"reads_report_type\": \"retained\"}, \"outtype\": \"all_reads\"}", "addref_cond": "{\"__current_case__\": 0, \"addref_select\": \"no\"}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"bam\""}, "inputs": {"input": {"id": "f3aa40edd8d2ea49", "src": "hda", "uuid": "34c83c44-d6e9-4318-9a91-53b0c43c419a"}}, "outputs": {"outputsam": {"id": "7e3077fb34b289c9", "src": "hda", "uuid": "1b808570-2846-47c5-b673-69d7156cf648"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-12-30 00:59:54", "plugin": "core", "name": "end_epoch", "raw_value": "1735520394.0000000"}, {"title": "Job Start Time", "value": "2024-12-30 00:59:54", "plugin": "core", "name": "start_epoch", "raw_value": "1735520394.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output outputsam: Test output file (1_sort.bam) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "samtools_view/1.9+galaxy3-5", "has_data": true, "data": {"tool_id": "samtools_view", "tool_version": "1.9+galaxy3", "test_index": 5, "time_seconds": 29.859018087387085, "inputs": {"input": {"src": "hda", "id": "3c170082823cf887"}, "mode|output_options|output_format|oformat": "input"}, "job": {"model_class": "Job", "id": "18e5c9145b338dad", "state": "ok", "exit_code": 0, "update_time": "2024-12-30T01:00:34.982862", "create_time": "2024-12-30T01:00:23.262523", "galaxy_version": "23.1", "command_version": "Version: 1.9 (using htslib 1.9)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3", "history_id": "1262154bdd2f9614", "external_id": "gxy-mcqcb", "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/3/f/1/dataset_3f1a80b0-52ae-464b-ade4-8e8e29d9ec18.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/5/1/6/metadata_51686606-7655-42ce-80b7-29bdb8709f83.dat' infile.bai && samtools view -@ $addthreads -b -o outfile infile", "traceback": null, "params": {"mode": "{\"__current_case__\": 0, \"output_options\": {\"__current_case__\": 0, \"adv_output\": {\"collapsecigar\": false, \"readtags\": []}, \"output_format\": {\"__current_case__\": 0, \"oformat\": \"input\"}, \"reads_report_type\": \"retained\"}, \"outtype\": \"all_reads\"}", "addref_cond": "{\"__current_case__\": 0, \"addref_select\": \"no\"}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"bam\""}, "inputs": {"input": {"id": "3c170082823cf887", "src": "hda", "uuid": "3f1a80b0-52ae-464b-ade4-8e8e29d9ec18"}}, "outputs": {"outputsam": {"id": "18e5c9145b338dad", "src": "hda", "uuid": "c93549d3-dc3e-4ef0-9316-3962a786abc9"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-12-30 01:00:25", "plugin": "core", "name": "end_epoch", "raw_value": "1735520425.0000000"}, {"title": "Job Start Time", "value": "2024-12-30 01:00:25", "plugin": "core", "name": "start_epoch", "raw_value": "1735520425.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output outputsam: Test output file (1_sort.bam) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "samtools_view/1.9+galaxy3-6", "has_data": true, "data": {"tool_id": "samtools_view", "tool_version": "1.9+galaxy3", "test_index": 6, "time_seconds": 27.296958684921265, "inputs": {"input": {"src": "hda", "id": "fca20421263140dc"}}, "job": {"model_class": "Job", "id": "48bb38aa499c3a0b", "state": "ok", "exit_code": 0, "update_time": "2024-12-30T01:01:02.359397", "create_time": "2024-12-30T01:00:50.370079", "galaxy_version": "23.1", "command_version": "Version: 1.9 (using htslib 1.9)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3", "history_id": "1262154bdd2f9614", "external_id": "gxy-q5fth", "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/6/f/5/dataset_6f531b03-1517-465e-9632-bbdac4d1fce2.dat' infile && samtools view -@ $addthreads -b -o outfile infile && samtools sort -@ $addthreads -m $addmemory\"M\" -T \"${TMPDIR:-.}\" -O bam -o tmpsam outfile && mv tmpsam outfile", "traceback": null, "params": {"mode": "{\"__current_case__\": 0, \"output_options\": {\"__current_case__\": 0, \"adv_output\": {\"collapsecigar\": false, \"readtags\": []}, \"output_format\": {\"__current_case__\": 2, \"oformat\": \"bam\"}, \"reads_report_type\": \"retained\"}, \"outtype\": \"all_reads\"}", "addref_cond": "{\"__current_case__\": 0, \"addref_select\": \"no\"}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"qname_sorted.bam\""}, "inputs": {"input": {"id": "fca20421263140dc", "src": "hda", "uuid": "6f531b03-1517-465e-9632-bbdac4d1fce2"}}, "outputs": {"outputsam": {"id": "48bb38aa499c3a0b", "src": "hda", "uuid": "b7d20c47-3c50-46e8-b2e3-14561bfea4be"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-12-30 01:00:52", "plugin": "core", "name": "end_epoch", "raw_value": "1735520452.0000000"}, {"title": "Job Start Time", "value": "2024-12-30 01:00:52", "plugin": "core", "name": "start_epoch", "raw_value": "1735520452.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output outputsam: Test output file (1_sort.bam) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "samtools_view/1.9+galaxy3-7", "has_data": true, "data": {"tool_id": "samtools_view", "tool_version": "1.9+galaxy3", "test_index": 7, "time_seconds": 27.938210248947144, "inputs": {"input": {"src": "hda", "id": "4aaf880e0f6f3a5c"}, "mode|output_options|output_format|oformat": "input"}, "job": {"model_class": "Job", "id": "91ba9c0545237ea2", "state": "ok", "exit_code": 0, "update_time": "2024-12-30T01:01:30.227883", "create_time": "2024-12-30T01:01:18.187282", "galaxy_version": "23.1", "command_version": "Version: 1.9 (using htslib 1.9)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3", "history_id": "1262154bdd2f9614", "external_id": "gxy-8bxtx", "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/8/6/7/dataset_867f6e65-c516-44bc-ad66-a6c71a93cf2b.dat' infile && samtools view -@ $addthreads -h -o outfile infile", "traceback": null, "params": {"mode": "{\"__current_case__\": 0, \"output_options\": {\"__current_case__\": 0, \"adv_output\": {\"collapsecigar\": false, \"readtags\": []}, \"output_format\": {\"__current_case__\": 0, \"oformat\": \"input\"}, \"reads_report_type\": \"retained\"}, \"outtype\": \"all_reads\"}", "addref_cond": "{\"__current_case__\": 0, \"addref_select\": \"no\"}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"qname_sorted.bam\""}, "inputs": {"input": {"id": "4aaf880e0f6f3a5c", "src": "hda", "uuid": "867f6e65-c516-44bc-ad66-a6c71a93cf2b"}}, "outputs": {"outputsam": {"id": "91ba9c0545237ea2", "src": "hda", "uuid": "648379be-ae90-4283-9b62-be8ce86ac851"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-12-30 01:01:20", "plugin": "core", "name": "end_epoch", "raw_value": "1735520480.0000000"}, {"title": "Job Start Time", "value": "2024-12-30 01:01:20", "plugin": "core", "name": "start_epoch", "raw_value": "1735520480.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output outputsam: Test output file (1_sort_read_names.bam) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "samtools_view/1.9+galaxy3-8", "has_data": true, "data": {"tool_id": "samtools_view", "tool_version": "1.9+galaxy3", "test_index": 8, "time_seconds": 26.472511529922485, "inputs": {"input": {"src": "hda", "id": "bd160df99ae4cf99"}}, "job": {"model_class": "Job", "id": "5382d35a68c9df5e", "state": "ok", "exit_code": 0, "update_time": "2024-12-30T01:01:57.000580", "create_time": "2024-12-30T01:01:45.235284", "galaxy_version": "23.1", "command_version": "Version: 1.9 (using htslib 1.9)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3", "history_id": "1262154bdd2f9614", "external_id": "gxy-p2zbt", "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/c/f/0/dataset_cf08de5f-7c96-43fe-a5fc-5f5fd218e798.dat' infile && samtools view -@ $addthreads -b -o outfile infile && samtools sort -@ $addthreads -m $addmemory\"M\" -T \"${TMPDIR:-.}\" -O bam -o tmpsam outfile && mv tmpsam outfile", "traceback": null, "params": {"mode": "{\"__current_case__\": 0, \"output_options\": {\"__current_case__\": 0, \"adv_output\": {\"collapsecigar\": false, \"readtags\": []}, \"output_format\": {\"__current_case__\": 2, \"oformat\": \"bam\"}, \"reads_report_type\": \"retained\"}, \"outtype\": \"all_reads\"}", "addref_cond": "{\"__current_case__\": 0, \"addref_select\": \"no\"}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"unsorted.bam\""}, "inputs": {"input": {"id": "bd160df99ae4cf99", "src": "hda", "uuid": "cf08de5f-7c96-43fe-a5fc-5f5fd218e798"}}, "outputs": {"outputsam": {"id": "5382d35a68c9df5e", "src": "hda", "uuid": "cd54992a-ba21-46dc-b3a8-c99888bd1a6f"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-12-30 01:01:47", "plugin": "core", "name": "end_epoch", "raw_value": "1735520507.0000000"}, {"title": "Job Start Time", "value": "2024-12-30 01:01:47", "plugin": "core", "name": "start_epoch", "raw_value": "1735520507.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output outputsam: Test output file (1_sort.bam) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "samtools_view/1.9+galaxy3-9", "has_data": true, "data": {"tool_id": "samtools_view", "tool_version": "1.9+galaxy3", "test_index": 9, "time_seconds": 27.426937580108643, "inputs": {"input": {"src": "hda", "id": "37aec2ce0608f047"}, "mode|output_options|output_format|oformat": "input"}, "job": {"model_class": "Job", "id": "611a05f0e2887df6", "state": "ok", "exit_code": 0, "update_time": "2024-12-30T01:02:24.296825", "create_time": "2024-12-30T01:02:12.640792", "galaxy_version": "23.1", "command_version": "Version: 1.9 (using htslib 1.9)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3", "history_id": "1262154bdd2f9614", "external_id": "gxy-knjc6", "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/f/f/9/dataset_ff9e3630-42b4-416e-acd3-2f51776a3369.dat' infile && samtools view -@ $addthreads -h -o outfile infile", "traceback": null, "params": {"mode": "{\"__current_case__\": 0, \"output_options\": {\"__current_case__\": 0, \"adv_output\": {\"collapsecigar\": false, \"readtags\": []}, \"output_format\": {\"__current_case__\": 0, \"oformat\": \"input\"}, \"reads_report_type\": \"retained\"}, \"outtype\": \"all_reads\"}", "addref_cond": "{\"__current_case__\": 0, \"addref_select\": \"no\"}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"unsorted.bam\""}, "inputs": {"input": {"id": "37aec2ce0608f047", "src": "hda", "uuid": "ff9e3630-42b4-416e-acd3-2f51776a3369"}}, "outputs": {"outputsam": {"id": "611a05f0e2887df6", "src": "hda", "uuid": "be153424-88f0-4307-873b-7a5dd534472e"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-12-30 01:02:14", "plugin": "core", "name": "end_epoch", "raw_value": "1735520534.0000000"}, {"title": "Job Start Time", "value": "2024-12-30 01:02:14", "plugin": "core", "name": "start_epoch", "raw_value": "1735520534.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output outputsam: Test output file (1_sort_read_names.bam) is missing. 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"\"vcf\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\""}, "inputs": {"input1": {"id": "a1103d5912b69db6", "src": "hda", "uuid": "a45fba20-919d-4a06-a036-a1097b9ed7fe"}}, "outputs": {"out_file1": {"id": "b199453d55d1008b", "src": "hda", "uuid": "f799635b-3404-4f7d-bd84-1b767736ec4f"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-12-30 01:18:26", "plugin": "core", "name": "end_epoch", "raw_value": "1735521506.0000000"}, {"title": "Job Start Time", "value": "2024-12-30 01:18:26", "plugin": "core", "name": "start_epoch", "raw_value": "1735521506.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "vcftools_annotate/0.1-0", "has_data": true, "data": {"tool_id": "vcftools_annotate", "tool_version": "0.1", "test_index": 0, "time_seconds": 31.34779977798462, "inputs": {"input": {"src": "hda", "id": "63ec486a59172927"}, "tag": "FORMAT/FREQ", "description": "MinAF [7]", "filter": "MinAF", "condition": ">= 7"}, "job": {"model_class": "Job", "id": "798ce302529f6e3f", "state": "ok", "exit_code": 127, "update_time": "2024-12-30T01:19:08.759922", "create_time": "2024-12-30T01:18:52.639783", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/vcftools_annotate/vcftools_annotate/0.1", "history_id": "1262154bdd2f9614", "external_id": "gxy-6mg4v", "command_line": "echo \"{ tag => 'FORMAT/FREQ', name => 'MinAF', desc => 'MinAF [7]', test => sub { my @t = split('%', @\\$MATCH[0]); return @t[0] >= 7 ? \\$PASS : \\$FAIL }, },\" > f.txt ; vcf-annotate -f f.txt /galaxy/server/database/objects/1/d/9/dataset_1d9f2eb0-c28b-4a7c-9e2e-2c663729747f.dat > /galaxy/server/database/objects/4/4/2/dataset_44201c8e-7902-4b0d-b11f-21cad2194d61.dat", "traceback": null, "params": {"__input_ext": "\"vcf\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "condition": "\">= 7\"", "filter": "\"MinAF\"", "description": "\"MinAF [7]\"", "tag": "\"FORMAT/FREQ\""}, "inputs": {"input": {"id": "63ec486a59172927", "src": "hda", "uuid": "1d9f2eb0-c28b-4a7c-9e2e-2c663729747f"}}, "outputs": {"output": {"id": "798ce302529f6e3f", "src": "hda", "uuid": "44201c8e-7902-4b0d-b11f-21cad2194d61"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "/galaxy/server/database/jobs_directory/000/127/tool_script.sh: line 22: vcf-annotate: command not found\n", "job_stdout": "", "job_stderr": "", "stderr": "/galaxy/server/database/jobs_directory/000/127/tool_script.sh: line 22: vcf-annotate: command not found\n", "stdout": "", "job_messages": [{"code_desc": "tool progress", "desc": "Log: tool progress", "error_level": 1, "match": "/galaxy/server/database/jobs_directory/000/127/tool_script.sh: line 22: vcf-annotate: command not found", "stream": "stderr", "type": "regex"}, {"code_desc": "tool progress", "desc": "Log: tool progress", "error_level": 1, "match": "", "stream": "stdout", "type": "regex"}], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-12-30 01:18:58", "plugin": "core", "name": "end_epoch", "raw_value": "1735521538.0000000"}, {"title": "Job Start Time", "value": "2024-12-30 01:18:58", "plugin": "core", "name": "start_epoch", "raw_value": "1735521538.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output output: different than expected, difference (using diff):\n( /tmp/tmp2bv17c82test_out1.vcf v. /tmp/tmpaigycup4test_out1.vcf )\n--- local_file\n+++ history_data\n@@ -1,30 +0,0 @@\n-##fileformat=VCFv4.1\n-##FILTER=\n-##source_20130813.1=vcf-annotate(r797) -f f.txt \n-#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tSample1\n-chr1\t14470\t.\tG\tA\t.\tPASS\tADP=25;WT=0;HET=1;HOM=0;NC=0\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:28:25:23:2:8%:9.8E-1:33:39:22:1:2:0\n-chr1\t14513\t.\tG\tA\t.\tPASS\tADP=32;WT=0;HET=1;HOM=0;NC=0\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:36:32:24:8:25%:9.8E-1:31:22:16:8:7:1\n-chr1\t14626\t.\tG\tC\t.\tPASS\tADP=44;WT=0;HET=1;HOM=0;NC=0\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:45:44:40:4:9.09%:9.8E-1:34:36:14:26:0:4\n-chr1\t14677\t.\tG\tA\t.\tPASS\tADP=70;WT=0;HET=1;HOM=0;NC=0\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:82:70:63:7:10%:9.8E-1:33:17:44:19:7:0\n-chr1\t14813\t.\tT\tG\t.\tMinAF\tADP=105;WT=0;HET=1;HOM=0;NC=0\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:121:105:103:2:1.9%:9.8E-1:32:22:42:61:1:1\n-chr1\t14815\t.\tC\tT\t.\tMinAF\tADP=117;WT=0;HET=1;HOM=0;NC=0\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:122:117:109:8:6.84%:9.8E-1:33:29:50:59:4:4\n-chr1\t14907\t.\tA\tG\t.\tPASS\tADP=104;WT=0;HET=1;HOM=0;NC=0\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:108:104:19:16:45.71%:9.8E-1:37:18:10:9:8:8\n-chr1\t14930\t.\tA\tG\t.\tPASS\tADP=103;WT=0;HET=1;HOM=0;NC=0\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:110:103:17:17:50%:9.8E-1:37:24:8:9:8:9\n-chr1\t15015\t.\tG\tC\t.\tPASS\tADP=52;WT=0;HET=1;HOM=0;NC=0\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:55:52:44:8:15.38%:9.8E-1:34:35:5:39:1:7\n-chr1\t15211\t.\tT\tG\t.\tPASS\tADP=21;WT=0;HET=0;HOM=1;NC=0\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t1/1:0:23:21:0:2:100%:9.8E-1:0:26:0:0:1:1\n-chr1\t15527\t.\tG\tA\t.\tPASS\tADP=53;WT=0;HET=1;HOM=0;NC=0\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:57:53:29:5:14.71%:9.8E-1:32:23:19:10:3:2\n-chr1\t15688\t.\tC\tT\t.\tPASS\tADP=34;WT=0;HET=1;HOM=0;NC=0\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:36:34:11:4:26.67%:9.8E-1:35:26:6:5:1:3\n-chr1\t16257\t.\tG\tC\t.\tPASS\tADP=23;WT=0;HET=1;HOM=0;NC=0\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:26:23:20:2:9.09%:9.8E-1:35:17:7:13:0:2\n-chr1\t16288\t.\tC\tG\t.\tPASS\tADP=15;WT=0;HET=1;HOM=0;NC=0\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:16:15:11:3:21.43%:9.8E-1:34:36:3:8:1:2\n-chr1\t16298\t.\tC\tT\t.\tPASS\tADP=12;WT=0;HET=1;HOM=0;NC=0\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:12:12:9:2:18.18%:9.8E-1:34:30:2:7:1:1\n-chr1\t16378\t.\tT\tC\t.\tPASS\tADP=24;WT=0;HET=1;HOM=0;NC=0\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:24:24:11:12:52.17%:9.8E-1:37:34:7:4:8:4\n-chr1\t16495\t.\tG\tC\t.\tPASS\tADP=21;WT=0;HET=1;HOM=0;NC=0\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:22:21:14:6:30%:9.8E-1:31:25:5:9:2:4\n-chr1\t16534\t.\tC\tT\t.\tPASS\tADP=11;WT=0;HET=1;HOM=0;NC=0\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:11:11:6:4:40%:9.8E-1:32:37:1:5:0:4\n-chr1\t16571\t.\tG\tA\t.\tPASS\tADP=8;WT=0;HET=1;HOM=0;NC=0\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:8:8:5:2:28.57%:9.8E-1:31:34:2:3:0:2\n-chr1\t16737\t.\tG\tT\t.\tPASS\tADP=27;WT=0;HET=1;HOM=0;NC=0\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:30:27:22:5:18.52%:9.8E-1:37:34:21:1:5:0\n-chr1\t16742\t.\tG\tC\t.\tPASS\tADP=30;WT=0;HET=1;HOM=0;NC=0\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:30:30:23:7:23.33%:9.8E-1:32:37:21:2:7:0\n-chr1\t16900\t.\tT\tC\t.\tMinAF\tADP=140;WT=0;HET=1;HOM=0;NC=0\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:150:140:135:5:3.57%:9.8E-1:35:25:119:16:5:0\n-chr1\t16963\t.\tG\tA\t.\tPASS\tADP=338;WT=0;HET=1;HOM=0;NC=0\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:354:338:297:41:12.13%:9.8E-1:32:34:218:79:26:15\n-chr1\t16977\t.\tG\tA\t.\tPASS\tADP=368;WT=0;HET=1;HOM=0;NC=0\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:384:368:270:98:26.63%:9.8E-1:34:25:186:84:63:35\n-chr1\t16996\t.\tT\tC\t.\tPASS\tADP=356;WT=0;HET=1;HOM=0;NC=0\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:371:356:269:87:24.44%:9.8E-1:35:34:147:122:58:29\n-chr1\t17020\t.\tG\tA\t.\tMinAF\tADP=355;WT=0;HET=1;HOM=0;NC=0\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:380:355:347:8:2.25%:9.8E-1:33:29:164:183:4:4\n"], "status": "failure"}}], "galaxy_url": "http://104.196.55.178:8000/galaxy/"} \ No newline at end of file diff --git a/reports/anvil-production/tool-tests/prod-24-12-30-00-37-1/results.xunit b/reports/anvil-production/tool-tests/prod-24-12-30-00-37-1/results.xunit new file mode 100644 index 000000000..db9594454 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-12-30-00-37-1/results.xunit @@ -0,0 +1,1056 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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100644 index 000000000..3b1fddaa9 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-12-30-00-37-1/tools.yml @@ -0,0 +1,98 @@ +chunk: 0 +tools: +- name: sra_tools + owner: iuc + revisions: + - e08a7ad4378b + tool_panel_section_label: Get Data + tool_shed_url: toolshed.g2.bx.psu.edu +- name: split_file_on_column + owner: bgruening + revisions: + - 37a53100b67e + tool_panel_section_label: Text Manipulation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastq_filter + owner: devteam + revisions: + - 81a9090d6df3 + tool_panel_section_label: FASTA/FASTQ + tool_shed_url: toolshed.g2.bx.psu.edu +- name: samtools_view + owner: iuc + revisions: + - b72793637686 + tool_panel_section_label: SAM/BAM + tool_shed_url: toolshed.g2.bx.psu.edu +- name: samtools_split + owner: devteam + revisions: + - 135c85f4cfaf + tool_panel_section_label: SAM/BAM + tool_shed_url: toolshed.g2.bx.psu.edu +- name: sam_merge + owner: devteam + revisions: + - 1977f1637890 + tool_panel_section_label: SAM/BAM + tool_shed_url: toolshed.g2.bx.psu.edu +- name: bcftools_concat + owner: iuc + revisions: + - d40d4bf05718 + tool_panel_section_label: VCF/BCF + tool_shed_url: toolshed.g2.bx.psu.edu +- name: bcftools_annotate + owner: iuc + revisions: + - 403553ae19f6 + tool_panel_section_label: VCF/BCF + tool_shed_url: toolshed.g2.bx.psu.edu +- name: vcffixup + owner: devteam + revisions: + - 11f62f071125 + tool_panel_section_label: VCF/BCF + tool_shed_url: toolshed.g2.bx.psu.edu +- name: vcftools_annotate + owner: devteam + revisions: + - 57a6550df582 + tool_panel_section_label: VCF/BCF + tool_shed_url: toolshed.g2.bx.psu.edu +- name: porechop + owner: iuc + revisions: + - 93d623d9979c + tool_panel_section_label: Nanopore + tool_shed_url: toolshed.g2.bx.psu.edu +- name: deeptools_compute_gc_bias + owner: bgruening + revisions: + - 2bc10a9ca58b + tool_panel_section_label: deepTools + tool_shed_url: toolshed.g2.bx.psu.edu +- name: bwa + owner: devteam + revisions: + - 3fe632431b68 + tool_panel_section_label: Mapping + tool_shed_url: toolshed.g2.bx.psu.edu +- name: snpsift_dbnsfp + owner: iuc + revisions: + - 4e21e4f2bc48 + tool_panel_section_label: Variant Calling + tool_shed_url: toolshed.g2.bx.psu.edu +- name: limma_voom + owner: iuc + revisions: + - 0921444c832d + tool_panel_section_label: RNA-seq + tool_shed_url: toolshed.g2.bx.psu.edu +- name: mummer_delta_filter + owner: iuc + revisions: + - b3acbb3a6af0 + tool_panel_section_label: Multiple Alignments + tool_shed_url: toolshed.g2.bx.psu.edu