diff --git a/reports/anvil-edge/README.md b/reports/anvil-edge/README.md index 09d9aaf58..aa97cc2ce 100644 --- a/reports/anvil-edge/README.md +++ b/reports/anvil-edge/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 Oct 23 06:24:58 2023Mon Oct 16 06:23:58 2023
1ToolsetMon Oct 23 18:26:34 2023Mon Oct 16 18:29:10 2023
2ToolsetTue Oct 17 06:22:52 2023Tue Oct 10 06:25:54 2023
3ToolsetTue Oct 17 18:30:41 2023Tue Oct 10 18:28:40 2023
4ToolsetWed Oct 18 06:24:04 2023Wed Oct 11 06:23:00 2023
5ToolsetWed Oct 18 18:29:46 2023Wed Oct 11 18:30:44 2023
6ToolsetThu Oct 19 06:23:54 2023Thu Oct 12 06:25:28 2023
7ToolsetThu Oct 19 18:31:15 2023Thu Sep 28 18:27:22 2023
8ToolsetFri Oct 20 06:23:01 2023Fri Oct 13 06:23:52 2023
9ToolsetFri Oct 20 18:29:34 2023Fri Oct 13 18:28:37 2023
10ToolsetSat Oct 21 06:21:06 2023Sat Oct 14 06:24:13 2023
11ToolsetSat Oct 21 18:28:12 2023Sat Oct 14 18:29:05 2023
12ToolsetSun Oct 22 06:21:10 2023Sun Oct 15 06:23:21 2023
13ToolsetSun Oct 22 18:27:29 2023Sun Oct 15 18:29:44 2023
+
Chunk IDTool ListLatest reportPrevious report
0ToolsetMon Oct 23 06:24:58 2023Mon Oct 16 06:23:58 2023
1ToolsetMon Oct 23 18:26:34 2023Mon Oct 16 18:29:10 2023
2ToolsetTue Oct 24 06:23:29 2023Tue Oct 17 06:22:52 2023
3ToolsetTue Oct 17 18:30:41 2023Tue Oct 10 18:28:40 2023
4ToolsetWed Oct 18 06:24:04 2023Wed Oct 11 06:23:00 2023
5ToolsetWed Oct 18 18:29:46 2023Wed Oct 11 18:30:44 2023
6ToolsetThu Oct 19 06:23:54 2023Thu Oct 12 06:25:28 2023
7ToolsetThu Oct 19 18:31:15 2023Thu Sep 28 18:27:22 2023
8ToolsetFri Oct 20 06:23:01 2023Fri Oct 13 06:23:52 2023
9ToolsetFri Oct 20 18:29:34 2023Fri Oct 13 18:28:37 2023
10ToolsetSat Oct 21 06:21:06 2023Sat Oct 14 06:24:13 2023
11ToolsetSat Oct 21 18:28:12 2023Sat Oct 14 18:29:05 2023
12ToolsetSun Oct 22 06:21:10 2023Sun Oct 15 06:23:21 2023
13ToolsetSun Oct 22 18:27:29 2023Sun Oct 15 18:29:44 2023
diff --git a/reports/anvil-edge/tool-tests/chunks.json b/reports/anvil-edge/tool-tests/chunks.json index 8cc797e70..c6b2ba96f 100644 --- a/reports/anvil-edge/tool-tests/chunks.json +++ b/reports/anvil-edge/tool-tests/chunks.json @@ -7,11 +7,11 @@ "date2": "Mon Oct 16 18:29:10 2023" }, "2": { - "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-23-10-17-06-08-1/results.html", - "date1": "Tue Oct 17 06:22:52 2023", - "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-23-10-17-06-08-1/tools.yml", - "run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-23-10-10-06-08-1/results.html", - "date2": "Tue Oct 10 06:25:54 2023" + "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-23-10-24-06-08-1/results.html", + "date1": "Tue Oct 24 06:23:29 2023", + "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-23-10-24-06-08-1/tools.yml", + "run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-23-10-17-06-08-1/results.html", + "date2": "Tue Oct 17 06:22:52 2023" }, "3": { "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-23-10-17-18-13-1/results.html", diff --git a/reports/anvil-edge/tool-tests/edge-23-10-24-06-08-1/chunk.json b/reports/anvil-edge/tool-tests/edge-23-10-24-06-08-1/chunk.json new file mode 100644 index 000000000..652f358e9 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-23-10-24-06-08-1/chunk.json @@ -0,0 +1,7 @@ +{ + "2": { + "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-23-10-24-06-08-1/results.html", + "date1": "Tue Oct 24 06:23:29 2023", + "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-23-10-24-06-08-1/tools.yml" + } +} \ No newline at end of file diff --git a/reports/anvil-edge/tool-tests/edge-23-10-24-06-08-1/chunk.txt b/reports/anvil-edge/tool-tests/edge-23-10-24-06-08-1/chunk.txt new file mode 100644 index 000000000..a97d54fcc --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-23-10-24-06-08-1/chunk.txt @@ -0,0 +1,20 @@ +-t miniasm --tool-version 8dee0218ac7d +-t deeptools_bigwig_compare --tool-version 26e7304d6737 +-t fastq_groomer --tool-version 47e5dbc3e790 +-t sra_tools --tool-version 83c7d564b128 +-t mummer_mummerplot --tool-version ebe3b0f84de9 +-t poretools_qualpos --tool-version 4fe6b96aff72 +-t kallisto_pseudo --tool-version 5ae5c312d718 +-t sam_pileup --tool-version a3b4ad6858ff +-t samtools_calmd --tool-version 06dc50b7b711 +-t music_manipulate_eset --tool-version 22232092be53 +-t droplet_barcode_plot --tool-version 8f605643ccfd +-t scater_plot_exprs_freq --tool-version 058b40656107 +-t scanpy_parameter_iterator --tool-version 0387a2179f88 +-t query_tabular --tool-version cf34c344508d +-t column_remove_by_header --tool-version 372967836e98 +-t snpsift --tool-version 2e497a770bca +-t bcftools_plugin_mendelian --tool-version bf235558f2cf +-t bcftools_csq --tool-version fdd127bd4a32 +-t vcfcommonsamples --tool-version f1852ecef841 +-t vcfdistance --tool-version c506b8275b1a diff --git a/reports/anvil-edge/tool-tests/edge-23-10-24-06-08-1/errors/1b14fde99d7533f4.json b/reports/anvil-edge/tool-tests/edge-23-10-24-06-08-1/errors/1b14fde99d7533f4.json new file mode 100644 index 000000000..78f9546b3 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-23-10-24-06-08-1/errors/1b14fde99d7533f4.json @@ -0,0 +1,100 @@ +{ + "model_class": "Job", + "id": "1b14fde99d7533f4", + "state": "error", + "exit_code": 127, + "update_time": "2023-10-24T06:52:19.846117", + "create_time": "2023-10-24T06:52:05.518898", + "galaxy_version": "23.1", + "command_version": "", + "copied_from_job_id": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.3", + "history_id": "b8e3c9423bdc89f6", + "external_id": "gxy-97tz8", + "command_line": "ln -s '/galaxy/server/database/objects/1/5/b/dataset_15b2290e-dd2b-41d0-b5e4-3af2f3bae9b2.dat' input1.bam && ln -s '/galaxy/server/database/objects/_metadata_files/2/f/f/metadata_2ffd98a9-7424-4f3c-bcd0-a652ef3aa4f1.dat' 'input1.bam.bai' && ln -s '/galaxy/server/database/objects/1/8/5/dataset_18585bf8-66ce-43d3-a8e5-643d1a838a77.dat' reference.fasta && samtools faidx reference.fasta && samtools pileup -M 60 -f reference.fasta input1.bam > '/galaxy/server/database/objects/8/1/1/dataset_811d3f5c-0004-45af-a361-17b8d7e6c31e.dat'", + "traceback": null, + "params": { + "__input_ext": "\"input\"", + "dbkey": "\"equCab2\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/equCab2.len\"", + "c": "{\"__current_case__\": 0, \"consensus\": \"no\"}", + "mapCap": "\"60\"", + "indels": "\"no\"", + "lastCol": "\"no\"", + "refOrHistory": "{\"__current_case__\": 1, \"input1\": {\"values\": [{\"id\": 126, \"src\": \"hda\"}]}, \"ownFile\": {\"values\": [{\"id\": 127, \"src\": \"hda\"}]}, \"reference\": \"history\"}" + }, + "inputs": { + "refOrHistory|input1": { + "id": "0b46f4832cf85eda", + "src": "hda", + "uuid": "15b2290e-dd2b-41d0-b5e4-3af2f3bae9b2" + }, + "refOrHistory|ownFile": { + "id": "606f27db86776ff6", + "src": "hda", + "uuid": "18585bf8-66ce-43d3-a8e5-643d1a838a77" + } + }, + "outputs": { + "output1": { + "id": "26f3b5ab5b8463e6", + "src": "hda", + "uuid": "811d3f5c-0004-45af-a361-17b8d7e6c31e" + } + }, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "samtools: error while loading shared libraries: libncurses.so.5: cannot open shared object file: No such file or directory\n", + "job_stdout": "", + "job_stderr": "", + "stderr": "samtools: error while loading shared libraries: libncurses.so.5: cannot open shared object file: No such file or directory\n", + "stdout": "", + "job_messages": [ + { + "code_desc": "", + "desc": "Fatal error: Exit code 127 ()", + "error_level": 3, + "exit_code": 127, + "type": "exit_code" + } + ], + "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": "2023-10-24 06:52:09", + "plugin": "core", + "name": "end_epoch", + "raw_value": "1698130329.0000000" + }, + { + "title": "Job Start Time", + "value": "2023-10-24 06:52:09", + "plugin": "core", + "name": "start_epoch", + "raw_value": "1698130329.0000000" + }, + { + "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" + } + ] +} diff --git a/reports/anvil-edge/tool-tests/edge-23-10-24-06-08-1/errors/23b59d329824db73.json b/reports/anvil-edge/tool-tests/edge-23-10-24-06-08-1/errors/23b59d329824db73.json new file mode 100644 index 000000000..53b1c7a91 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-23-10-24-06-08-1/errors/23b59d329824db73.json @@ -0,0 +1,48 @@ +{ + "model_class": "Job", + "id": "23b59d329824db73", + "state": "error", + "exit_code": null, + "update_time": "2023-10-24T06:36:11.064450", + "create_time": "2023-10-24T06:36:04.414746", + "galaxy_version": "23.1", + "command_version": null, + "copied_from_job_id": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", + "history_id": "b8e3c9423bdc89f6", + "external_id": "gxy-s6hm5", + "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/e/b/1/dataset_eb1df349-5bf4-4311-ba16-4822ccbbf3dd.dat' sanger '/galaxy/server/database/objects/e/4/5/dataset_e45c9788-b2de-4733-a695-bac9b2cef89f.dat' cssanger None summarize_input --fix-id", + "traceback": null, + "params": { + "__input_ext": "\"fastq\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "options_type": "{\"__current_case__\": 1, \"fix_id\": true, \"force_quality_encoding\": \"None\", \"options_type_selector\": \"advanced\", \"output_type\": \"cssanger\", \"summarize_input\": \"summarize_input\"}", + "input_type": "\"sanger\"" + }, + "inputs": { + "input_file": { + "id": "f8591243569e9382", + "src": "hda", + "uuid": "eb1df349-5bf4-4311-ba16-4822ccbbf3dd" + } + }, + "outputs": { + "output_file": { + "id": "23b59d329824db73", + "src": "hda", + "uuid": "e45c9788-b2de-4733-a695-bac9b2cef89f" + } + }, + "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-edge/tool-tests/edge-23-10-24-06-08-1/errors/31728c841d35499b.json b/reports/anvil-edge/tool-tests/edge-23-10-24-06-08-1/errors/31728c841d35499b.json new file mode 100644 index 000000000..215a8de24 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-23-10-24-06-08-1/errors/31728c841d35499b.json @@ -0,0 +1,44 @@ +{ + "model_class": "Job", + "id": "31728c841d35499b", + "state": "error", + "exit_code": null, + "update_time": "2023-10-24T06:41:39.517836", + "create_time": "2023-10-24T06:41:28.279780", + "galaxy_version": "23.1", + "command_version": null, + "copied_from_job_id": null, + "tool_id": "upload1", + "history_id": "b8e3c9423bdc89f6", + "external_id": "gxy-vbnlp", + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/62/registry.xml' '/galaxy/server/database/jobs_directory/000/62/upload_params.json' '62:/galaxy/server/database/objects/5/d/9/dataset_5d989378-4020-4184-a09d-5cb092a89ccf_files:/galaxy/server/database/objects/5/d/9/dataset_5d989378-4020-4184-a09d-5cb092a89ccf.dat'", + "traceback": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_8krk2pul\"", + "files_metadata": "{\"__current_case__\": 78, \"file_type\": \"fastq\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"wrapping_original_sanger.fastqsanger\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_fzyx79c6\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"fastq\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "31728c841d35499b", + "src": "hda", + "uuid": "5d989378-4020-4184-a09d-5cb092a89ccf" + } + }, + "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-edge/tool-tests/edge-23-10-24-06-08-1/errors/7052fe37f5fb71c3.json b/reports/anvil-edge/tool-tests/edge-23-10-24-06-08-1/errors/7052fe37f5fb71c3.json new file mode 100644 index 000000000..b2fa04839 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-23-10-24-06-08-1/errors/7052fe37f5fb71c3.json @@ -0,0 +1,44 @@ +{ + "model_class": "Job", + "id": "7052fe37f5fb71c3", + "state": "error", + "exit_code": null, + "update_time": "2023-10-24T06:27:54.324527", + "create_time": "2023-10-24T06:27:43.860003", + "galaxy_version": "23.1", + "command_version": null, + "copied_from_job_id": null, + "tool_id": "upload1", + "history_id": "b8e3c9423bdc89f6", + "external_id": "gxy-lm94v", + "command_line": "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/c/6/d/dataset_c6d3bf47-747a-4ff2-980c-4e0ce164af9a_files:/galaxy/server/database/objects/c/6/d/dataset_c6d3bf47-747a-4ff2-980c-4e0ce164af9a.dat'", + "traceback": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_o3xg_31o\"", + "files_metadata": "{\"__current_case__\": 56, \"file_type\": \"bigwig\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"test.bw\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_z7z7aeuc\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"bigwig\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "7052fe37f5fb71c3", + "src": "hda", + "uuid": "c6d3bf47-747a-4ff2-980c-4e0ce164af9a" + } + }, + "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-edge/tool-tests/edge-23-10-24-06-08-1/errors/911c99275447de60.json b/reports/anvil-edge/tool-tests/edge-23-10-24-06-08-1/errors/911c99275447de60.json new file mode 100644 index 000000000..9d4ee4bae --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-23-10-24-06-08-1/errors/911c99275447de60.json @@ -0,0 +1,44 @@ +{ + "model_class": "Job", + "id": "911c99275447de60", + "state": "error", + "exit_code": null, + "update_time": "2023-10-24T06:58:29.896507", + "create_time": "2023-10-24T06:58:20.473923", + "galaxy_version": "23.1", + "command_version": null, + "copied_from_job_id": null, + "tool_id": "upload1", + "history_id": "b8e3c9423bdc89f6", + "external_id": "gxy-5tt8n", + "command_line": "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' '154:/galaxy/server/database/objects/6/a/1/dataset_6a15c4f5-800d-4dbe-9de0-3b9c99026370_files:/galaxy/server/database/objects/6/a/1/dataset_6a15c4f5-800d-4dbe-9de0-3b9c99026370.dat'", + "traceback": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_8prhi7k6\"", + "files_metadata": "{\"__current_case__\": 311, \"file_type\": \"tabular\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"pets.tsv\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_dx4d1o57\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"tabular\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "0170cd6e6911e97e", + "src": "hda", + "uuid": "6a15c4f5-800d-4dbe-9de0-3b9c99026370" + } + }, + "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-edge/tool-tests/edge-23-10-24-06-08-1/errors/9c5885c0875e8135.json b/reports/anvil-edge/tool-tests/edge-23-10-24-06-08-1/errors/9c5885c0875e8135.json new file mode 100644 index 000000000..f56d8bf0a --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-23-10-24-06-08-1/errors/9c5885c0875e8135.json @@ -0,0 +1,59 @@ +{ + "model_class": "Job", + "id": "9c5885c0875e8135", + "state": "error", + "exit_code": null, + "update_time": "2023-10-24T06:59:57.255203", + "create_time": "2023-10-24T06:59:51.843701", + "galaxy_version": "23.1", + "command_version": null, + "copied_from_job_id": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0", + "history_id": "b8e3c9423bdc89f6", + "external_id": "gxy-qb9wr", + "command_line": "cat '/galaxy/server/database/jobs_directory/000/136/configs/tmpkgl6zl5q' && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/cf34c344508d/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/136/configs/tmp_mvqe1xq' -Q '/galaxy/server/database/jobs_directory/000/136/configs/tmpkgl6zl5q' --comment_char='#' -o '/galaxy/server/database/objects/9/d/9/dataset_9d97200a-860c-4cbf-b5d0-f148971d13cc.dat'", + "traceback": null, + "params": { + "__input_ext": "\"tabular\"", + 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b/reports/anvil-edge/tool-tests/edge-23-10-24-06-08-1/job.log @@ -0,0 +1,14743 @@ +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 2023-10-24 06:20:45,371 [pN:job_handler_0,p:8,tN:MainThread] Read job configuration from file: /galaxy/server/config/job_conf.yml +galaxy.jobs INFO 2023-10-24 06:20:45,371 [pN:job_handler_0,p:8,tN:MainThread] Job handler assignment methods set to: db-skip-locked +galaxy.jobs INFO 2023-10-24 06:20:45,371 [pN:job_handler_0,p:8,tN:MainThread] Tag [_default_] handlers: job_handler_0 +galaxy.web_stack.handlers DEBUG 2023-10-24 06:20:45,371 [pN:job_handler_0,p:8,tN:MainThread] default set to child with id or tag 'tpv_dispatcher' +galaxy.jobs DEBUG 2023-10-24 06:20:45,371 [pN:job_handler_0,p:8,tN:MainThread] Done loading job configuration +galaxy.security.vault WARNING 2023-10-24 06:20:45,723 [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 2023-10-24 06:20:45,776 [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 2023-10-24 06:20:45,777 [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 2023-10-24 06:20:45,777 [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 2023-10-24 06:20:45,777 [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 2023-10-24 06:20:45,777 [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 2023-10-24 06:20:45,777 [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 2023-10-24 06:20:45,778 [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 2023-10-24 06:20:45,778 [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 2023-10-24 06:20:45,778 [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 2023-10-24 06:20:45,778 [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 2023-10-24 06:20:45,778 [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 2023-10-24 06:20:45,779 [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 2023-10-24 06:20:45,780 [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 2023-10-24 06:20:45,780 [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 2023-10-24 06:20:45,780 [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 2023-10-24 06:20:45,781 [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 2023-10-24 06:20:45,781 [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 2023-10-24 06:20:45,781 [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 2023-10-24 06:20:45,781 [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 2023-10-24 06:20:45,781 [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 2023-10-24 06:20:45,781 [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 2023-10-24 06:20:45,781 [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 2023-10-24 06:20:45,781 [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 2023-10-24 06:20:45,781 [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 2023-10-24 06:20:45,781 [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 2023-10-24 06:20:45,782 [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 2023-10-24 06:20:45,782 [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 2023-10-24 06:20:45,782 [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 2023-10-24 06:20:45,782 [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 2023-10-24 06:20:45,782 [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 2023-10-24 06:20:45,782 [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 2023-10-24 06:20:45,782 [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 2023-10-24 06:20:45,782 [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 2023-10-24 06:20:45,783 [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 2023-10-24 06:20:45,783 [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 2023-10-24 06:20:45,783 [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 2023-10-24 06:20:45,783 [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 2023-10-24 06:20:45,783 [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 2023-10-24 06:20:45,783 [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 2023-10-24 06:20:45,784 [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 2023-10-24 06:20:45,784 [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 2023-10-24 06:20:45,784 [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 2023-10-24 06:20:45,784 [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 2023-10-24 06:20:45,784 [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 2023-10-24 06:20:45,784 [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 2023-10-24 06:20:45,784 [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 2023-10-24 06:20:45,785 [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 2023-10-24 06:20:45,785 [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 2023-10-24 06:20:45,785 [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 2023-10-24 06:20:45,785 [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 2023-10-24 06:20:45,786 [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 2023-10-24 06:20:45,786 [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 2023-10-24 06:20:45,786 [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 2023-10-24 06:20:45,786 [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 2023-10-24 06:20:45,786 [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 2023-10-24 06:20:45,786 [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 2023-10-24 06:20:45,787 [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 2023-10-24 06:20:45,787 [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 2023-10-24 06:20:45,787 [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 2023-10-24 06:20:45,787 [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 2023-10-24 06:20:45,787 [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 2023-10-24 06:20:45,788 [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 2023-10-24 06:20:45,788 [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 2023-10-24 06:20:45,788 [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 2023-10-24 06:20:45,789 [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 2023-10-24 06:20:45,789 [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 2023-10-24 06:20:45,789 [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 2023-10-24 06:20:45,789 [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 2023-10-24 06:20:45,789 [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 2023-10-24 06:20:45,790 [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 2023-10-24 06:20:45,790 [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 2023-10-24 06:20:45,790 [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 2023-10-24 06:20:45,790 [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 2023-10-24 06:20:45,790 [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 2023-10-24 06:20:45,791 [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 2023-10-24 06:20:45,791 [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 2023-10-24 06:20:45,791 [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 2023-10-24 06:20:45,791 [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 2023-10-24 06:20:45,792 [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 2023-10-24 06:20:45,792 [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 2023-10-24 06:20:45,793 [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 2023-10-24 06:20:45,793 [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 2023-10-24 06:20:45,793 [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 2023-10-24 06:20:45,793 [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 2023-10-24 06:20:45,793 [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 2023-10-24 06:20:45,794 [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 2023-10-24 06:20:45,794 [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 2023-10-24 06:20:45,794 [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 2023-10-24 06:20:45,794 [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 2023-10-24 06:20:45,795 [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 2023-10-24 06:20:45,795 [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 2023-10-24 06:20:45,795 [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 2023-10-24 06:20:45,795 [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 2023-10-24 06:20:45,795 [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 2023-10-24 06:20:45,796 [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 2023-10-24 06:20:45,796 [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 2023-10-24 06:20:45,796 [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 2023-10-24 06:20:45,796 [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 2023-10-24 06:20:45,796 [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 2023-10-24 06:20:45,796 [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 2023-10-24 06:20:45,796 [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 2023-10-24 06:20:45,796 [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 2023-10-24 06:20:45,797 [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 2023-10-24 06:20:45,797 [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 2023-10-24 06:20:45,797 [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 2023-10-24 06:20:45,797 [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 2023-10-24 06:20:45,797 [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 2023-10-24 06:20:45,797 [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 2023-10-24 06:20:45,797 [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 2023-10-24 06:20:45,908 [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 2023-10-24 06:20:45,908 [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 2023-10-24 06:20:45,909 [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 2023-10-24 06:20:45,909 [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 2023-10-24 06:20:45,909 [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 2023-10-24 06:20:45,909 [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 2023-10-24 06:20:45,909 [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 2023-10-24 06:20:45,909 [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 2023-10-24 06:20:45,910 [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 2023-10-24 06:20:45,910 [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 2023-10-24 06:20:45,910 [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 2023-10-24 06:20:45,910 [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 2023-10-24 06:20:45,910 [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 2023-10-24 06:20:45,910 [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 2023-10-24 06:20:45,910 [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 2023-10-24 06:20:45,911 [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 2023-10-24 06:20:45,911 [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 2023-10-24 06:20:45,911 [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 2023-10-24 06:20:45,911 [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 2023-10-24 06:20:45,911 [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 2023-10-24 06:20:45,911 [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 2023-10-24 06:20:45,911 [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 2023-10-24 06:20:45,911 [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 2023-10-24 06:20:45,912 [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 2023-10-24 06:20:45,912 [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 2023-10-24 06:20:45,912 [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 2023-10-24 06:20:45,912 [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 2023-10-24 06:20:45,912 [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 2023-10-24 06:20:45,912 [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 2023-10-24 06:20:45,912 [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 2023-10-24 06:20:45,912 [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 2023-10-24 06:20:45,912 [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 2023-10-24 06:20:45,912 [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 2023-10-24 06:20:45,912 [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 2023-10-24 06:20:45,912 [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 2023-10-24 06:20:45,912 [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 2023-10-24 06:20:45,913 [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 2023-10-24 06:20:45,913 [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 2023-10-24 06:20:45,914 [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 2023-10-24 06:20:45,914 [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 2023-10-24 06:20:45,914 [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 2023-10-24 06:20:45,915 [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 2023-10-24 06:20:45,915 [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 2023-10-24 06:20:45,915 [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 2023-10-24 06:20:45,915 [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 2023-10-24 06:20:45,915 [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 2023-10-24 06:20:45,915 [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 2023-10-24 06:20:45,918 [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 2023-10-24 06:20:45,918 [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 2023-10-24 06:20:45,919 [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 2023-10-24 06:20:45,919 [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 2023-10-24 06:20:45,919 [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 2023-10-24 06:20:45,919 [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 2023-10-24 06:20:45,919 [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 2023-10-24 06:20:45,919 [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 2023-10-24 06:20:45,919 [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 2023-10-24 06:20:45,919 [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 2023-10-24 06:20:45,919 [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 2023-10-24 06:20:45,919 [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 2023-10-24 06:20:45,920 [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 2023-10-24 06:20:45,920 [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 2023-10-24 06:20:45,920 [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 2023-10-24 06:20:45,920 [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 2023-10-24 06:20:45,920 [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 2023-10-24 06:20:45,920 [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 2023-10-24 06:20:45,920 [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 2023-10-24 06:20:45,920 [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 2023-10-24 06:20:45,920 [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 2023-10-24 06:20:45,920 [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 2023-10-24 06:20:45,920 [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 2023-10-24 06:20:45,920 [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 2023-10-24 06:20:45,921 [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 2023-10-24 06:20:45,921 [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 2023-10-24 06:20:45,921 [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 2023-10-24 06:20:45,921 [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 2023-10-24 06:20:45,921 [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 2023-10-24 06:20:45,921 [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 2023-10-24 06:20:45,921 [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 2023-10-24 06:20:45,921 [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 2023-10-24 06:20:45,921 [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 2023-10-24 06:20:45,921 [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 2023-10-24 06:20:45,921 [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 2023-10-24 06:20:45,921 [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 2023-10-24 06:20:45,922 [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 2023-10-24 06:20:45,922 [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 2023-10-24 06:20:45,922 [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 2023-10-24 06:20:45,922 [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 2023-10-24 06:20:45,922 [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 2023-10-24 06:20:45,922 [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 2023-10-24 06:20:45,922 [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 2023-10-24 06:20:45,922 [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 2023-10-24 06:20:45,922 [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 2023-10-24 06:20:45,922 [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 2023-10-24 06:20:45,922 [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 2023-10-24 06:20:45,922 [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 2023-10-24 06:20:45,923 [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 2023-10-24 06:20:45,923 [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 2023-10-24 06:20:45,923 [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 2023-10-24 06:20:45,923 [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 2023-10-24 06:20:45,923 [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 2023-10-24 06:20:45,923 [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 2023-10-24 06:20:45,923 [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 2023-10-24 06:20:45,923 [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 2023-10-24 06:20:45,923 [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 2023-10-24 06:20:45,923 [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 2023-10-24 06:20:45,923 [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 2023-10-24 06:20:45,923 [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 2023-10-24 06:20:45,924 [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 2023-10-24 06:20:45,924 [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 2023-10-24 06:20:45,924 [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 2023-10-24 06:20:45,924 [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 2023-10-24 06:20:45,924 [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 2023-10-24 06:20:45,924 [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 2023-10-24 06:20:45,924 [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 2023-10-24 06:20:45,924 [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 2023-10-24 06:20:45,924 [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 2023-10-24 06:20:45,924 [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 2023-10-24 06:20:45,924 [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 2023-10-24 06:20:45,924 [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 2023-10-24 06:20:45,925 [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 2023-10-24 06:20:45,925 [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 2023-10-24 06:20:45,925 [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 2023-10-24 06:20:45,925 [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 2023-10-24 06:20:45,925 [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 2023-10-24 06:20:45,925 [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 2023-10-24 06:20:45,925 [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 2023-10-24 06:20:45,926 [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 2023-10-24 06:20:45,926 [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 2023-10-24 06:20:45,926 [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 2023-10-24 06:20:45,926 [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 2023-10-24 06:20:45,926 [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 2023-10-24 06:20:45,926 [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 2023-10-24 06:20:45,926 [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 2023-10-24 06:20:45,926 [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 2023-10-24 06:20:45,927 [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 2023-10-24 06:20:45,927 [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 2023-10-24 06:20:45,927 [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 2023-10-24 06:20:45,927 [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 2023-10-24 06:20:45,928 [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 2023-10-24 06:20:45,928 [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 2023-10-24 06:20:45,928 [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 2023-10-24 06:20:45,928 [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 2023-10-24 06:20:45,928 [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 2023-10-24 06:20:45,928 [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 2023-10-24 06:20:45,929 [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 2023-10-24 06:20:45,929 [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 2023-10-24 06:20:45,929 [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 2023-10-24 06:20:45,929 [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 2023-10-24 06:20:45,929 [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 2023-10-24 06:20:45,930 [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 2023-10-24 06:20:45,930 [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 2023-10-24 06:20:45,930 [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 2023-10-24 06:20:45,930 [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 2023-10-24 06:20:45,930 [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 2023-10-24 06:20:45,930 [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 2023-10-24 06:20:45,930 [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 2023-10-24 06:20:45,930 [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 2023-10-24 06:20:45,930 [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 2023-10-24 06:20:45,931 [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 2023-10-24 06:20:45,931 [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 2023-10-24 06:20:45,931 [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 2023-10-24 06:20:45,931 [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 2023-10-24 06:20:45,931 [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 2023-10-24 06:20:45,931 [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 2023-10-24 06:20:45,931 [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 2023-10-24 06:20:45,931 [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 2023-10-24 06:20:45,931 [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 2023-10-24 06:20:45,931 [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 2023-10-24 06:20:45,931 [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 2023-10-24 06:20:45,932 [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 2023-10-24 06:20:45,932 [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 2023-10-24 06:20:45,932 [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 2023-10-24 06:20:45,932 [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 2023-10-24 06:20:45,932 [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 2023-10-24 06:20:45,932 [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 2023-10-24 06:20:45,932 [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 2023-10-24 06:20:45,932 [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 2023-10-24 06:20:45,932 [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 2023-10-24 06:20:45,932 [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 2023-10-24 06:20:45,932 [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 2023-10-24 06:20:45,933 [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 2023-10-24 06:20:45,933 [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 2023-10-24 06:20:45,933 [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 2023-10-24 06:20:45,933 [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 2023-10-24 06:20:45,933 [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 2023-10-24 06:20:45,933 [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 2023-10-24 06:20:45,934 [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 2023-10-24 06:20:45,934 [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 2023-10-24 06:20:45,934 [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 2023-10-24 06:20:45,934 [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 2023-10-24 06:20:45,934 [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 2023-10-24 06:20:45,934 [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 2023-10-24 06:20:45,934 [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 2023-10-24 06:20:45,934 [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 2023-10-24 06:20:45,934 [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 2023-10-24 06:20:45,934 [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 2023-10-24 06:20:45,934 [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 2023-10-24 06:20:45,935 [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 2023-10-24 06:20:45,935 [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 2023-10-24 06:20:45,935 [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 2023-10-24 06:20:45,935 [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 2023-10-24 06:20:45,935 [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 2023-10-24 06:20:45,935 [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 2023-10-24 06:20:45,935 [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 2023-10-24 06:20:45,935 [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 2023-10-24 06:20:45,935 [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 2023-10-24 06:20:45,936 [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 2023-10-24 06:20:45,936 [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 2023-10-24 06:20:45,936 [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 2023-10-24 06:20:45,936 [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 2023-10-24 06:20:45,936 [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 2023-10-24 06:20:45,936 [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 2023-10-24 06:20:45,936 [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 2023-10-24 06:20:45,936 [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 2023-10-24 06:20:45,937 [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 2023-10-24 06:20:45,937 [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 2023-10-24 06:20:45,937 [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 2023-10-24 06:20:45,937 [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 2023-10-24 06:20:45,937 [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 2023-10-24 06:20:45,937 [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 2023-10-24 06:20:45,937 [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 2023-10-24 06:20:45,937 [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 2023-10-24 06:20:45,937 [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 2023-10-24 06:20:45,937 [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 2023-10-24 06:20:45,937 [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 2023-10-24 06:20:45,938 [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 2023-10-24 06:20:45,938 [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 2023-10-24 06:20:45,940 [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 2023-10-24 06:20:45,943 [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 2023-10-24 06:20:45,943 [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 2023-10-24 06:20:45,943 [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 2023-10-24 06:20:45,944 [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 2023-10-24 06:20:45,944 [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 2023-10-24 06:20:45,944 [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 2023-10-24 06:20:45,944 [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 2023-10-24 06:20:45,944 [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 2023-10-24 06:20:45,945 [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 2023-10-24 06:20:45,945 [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 2023-10-24 06:20:45,945 [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 2023-10-24 06:20:45,945 [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 2023-10-24 06:20:45,945 [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 2023-10-24 06:20:45,945 [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 2023-10-24 06:20:45,946 [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 2023-10-24 06:20:45,946 [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 2023-10-24 06:20:45,946 [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 2023-10-24 06:20:45,946 [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 2023-10-24 06:20:45,946 [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 2023-10-24 06:20:45,946 [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 2023-10-24 06:20:45,947 [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 2023-10-24 06:20:45,948 [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 2023-10-24 06:20:45,948 [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 2023-10-24 06:20:45,949 [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 2023-10-24 06:20:45,949 [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 2023-10-24 06:20:45,949 [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 2023-10-24 06:20:45,949 [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 2023-10-24 06:20:45,949 [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 2023-10-24 06:20:45,949 [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 2023-10-24 06:20:45,949 [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 2023-10-24 06:20:45,950 [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 2023-10-24 06:20:45,950 [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 2023-10-24 06:20:45,950 [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 2023-10-24 06:20:45,950 [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 2023-10-24 06:20:45,950 [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 2023-10-24 06:20:45,950 [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 2023-10-24 06:20:45,950 [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 2023-10-24 06:20:45,950 [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 2023-10-24 06:20:45,950 [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 2023-10-24 06:20:45,951 [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 2023-10-24 06:20:45,951 [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 2023-10-24 06:20:45,951 [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 2023-10-24 06:20:45,951 [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 2023-10-24 06:20:45,951 [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 2023-10-24 06:20:45,951 [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 2023-10-24 06:20:45,951 [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 2023-10-24 06:20:45,951 [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 2023-10-24 06:20:45,951 [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 2023-10-24 06:20:45,951 [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 2023-10-24 06:20:45,951 [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 2023-10-24 06:20:45,952 [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 2023-10-24 06:20:45,952 [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 2023-10-24 06:20:45,952 [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 2023-10-24 06:20:45,952 [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 2023-10-24 06:20:45,952 [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 2023-10-24 06:20:45,952 [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 2023-10-24 06:20:45,952 [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 2023-10-24 06:20:45,952 [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 2023-10-24 06:20:45,952 [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 2023-10-24 06:20:45,952 [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 2023-10-24 06:20:45,953 [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 2023-10-24 06:20:45,953 [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 2023-10-24 06:20:45,953 [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 2023-10-24 06:20:45,953 [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 2023-10-24 06:20:45,953 [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 2023-10-24 06:20:45,953 [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 2023-10-24 06:20:45,953 [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 2023-10-24 06:20:45,953 [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 2023-10-24 06:20:45,953 [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 2023-10-24 06:20:45,953 [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 2023-10-24 06:20:45,954 [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 2023-10-24 06:20:45,954 [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 2023-10-24 06:20:45,954 [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 2023-10-24 06:20:45,954 [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 2023-10-24 06:20:45,954 [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 2023-10-24 06:20:45,954 [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 2023-10-24 06:20:45,954 [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 2023-10-24 06:20:45,954 [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 2023-10-24 06:20:45,954 [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 2023-10-24 06:20:45,954 [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 2023-10-24 06:20:45,955 [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 2023-10-24 06:20:45,955 [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 2023-10-24 06:20:45,955 [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 2023-10-24 06:20:45,955 [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 2023-10-24 06:20:45,955 [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 2023-10-24 06:20:45,955 [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 2023-10-24 06:20:45,955 [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 2023-10-24 06:20:45,955 [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 2023-10-24 06:20:45,955 [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 2023-10-24 06:20:45,956 [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 2023-10-24 06:20:45,956 [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 2023-10-24 06:20:45,956 [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 2023-10-24 06:20:45,956 [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 2023-10-24 06:20:45,956 [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 2023-10-24 06:20:45,956 [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 2023-10-24 06:20:45,956 [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 2023-10-24 06:20:45,956 [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 2023-10-24 06:20:45,956 [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 2023-10-24 06:20:45,956 [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 2023-10-24 06:20:45,957 [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 2023-10-24 06:20:45,957 [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 2023-10-24 06:20:45,957 [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 2023-10-24 06:20:45,957 [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 2023-10-24 06:20:45,957 [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 2023-10-24 06:20:45,957 [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 2023-10-24 06:20:45,957 [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 2023-10-24 06:20:45,957 [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 2023-10-24 06:20:45,958 [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 2023-10-24 06:20:45,958 [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 2023-10-24 06:20:45,958 [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 2023-10-24 06:20:45,958 [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 2023-10-24 06:20:45,958 [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 2023-10-24 06:20:45,959 [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 2023-10-24 06:20:45,959 [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 2023-10-24 06:20:45,959 [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 2023-10-24 06:20:45,959 [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 2023-10-24 06:20:45,959 [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 2023-10-24 06:20:45,960 [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 2023-10-24 06:20:45,960 [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 2023-10-24 06:20:45,961 [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 2023-10-24 06:20:45,961 [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 2023-10-24 06:20:45,961 [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 2023-10-24 06:20:45,961 [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 2023-10-24 06:20:45,961 [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 2023-10-24 06:20:45,961 [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 2023-10-24 06:20:45,961 [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 2023-10-24 06:20:45,961 [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 2023-10-24 06:20:45,962 [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 2023-10-24 06:20:45,962 [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 2023-10-24 06:20:45,962 [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 2023-10-24 06:20:45,962 [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 2023-10-24 06:20:45,962 [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 2023-10-24 06:20:45,963 [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 2023-10-24 06:20:45,963 [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 2023-10-24 06:20:45,963 [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 2023-10-24 06:20:45,964 [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 2023-10-24 06:20:45,964 [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 2023-10-24 06:20:45,964 [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 2023-10-24 06:20:45,964 [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 2023-10-24 06:20:45,964 [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 2023-10-24 06:20:45,964 [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 2023-10-24 06:20:45,965 [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 2023-10-24 06:20:45,965 [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 2023-10-24 06:20:45,965 [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 2023-10-24 06:20:45,965 [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 2023-10-24 06:20:45,965 [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 2023-10-24 06:20:45,965 [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 2023-10-24 06:20:45,965 [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 2023-10-24 06:20:45,965 [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 2023-10-24 06:20:45,966 [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 2023-10-24 06:20:45,966 [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 2023-10-24 06:20:45,966 [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 2023-10-24 06:20:45,966 [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 2023-10-24 06:20:45,967 [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 2023-10-24 06:20:45,967 [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 2023-10-24 06:20:45,967 [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 2023-10-24 06:20:45,967 [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 2023-10-24 06:20:45,967 [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 2023-10-24 06:20:45,967 [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 2023-10-24 06:20:45,969 [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 2023-10-24 06:20:45,969 [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 2023-10-24 06:20:45,969 [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 2023-10-24 06:20:45,969 [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 2023-10-24 06:20:45,969 [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 2023-10-24 06:20:45,969 [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 2023-10-24 06:20:45,969 [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 2023-10-24 06:20:45,969 [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 2023-10-24 06:20:45,970 [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 2023-10-24 06:20:45,971 [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 2023-10-24 06:20:45,972 [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 2023-10-24 06:20:45,972 [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 2023-10-24 06:20:45,972 [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 2023-10-24 06:20:45,972 [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 2023-10-24 06:20:45,972 [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 2023-10-24 06:20:45,972 [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 2023-10-24 06:20:45,972 [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 2023-10-24 06:20:45,972 [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 2023-10-24 06:20:45,973 [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 2023-10-24 06:20:45,973 [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 2023-10-24 06:20:45,973 [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 2023-10-24 06:20:45,973 [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 2023-10-24 06:20:45,973 [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 2023-10-24 06:20:45,973 [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 2023-10-24 06:20:45,973 [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 2023-10-24 06:20:45,973 [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 2023-10-24 06:20:45,973 [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 2023-10-24 06:20:45,973 [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 2023-10-24 06:20:45,973 [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 2023-10-24 06:20:45,973 [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 2023-10-24 06:20:45,974 [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 2023-10-24 06:20:45,974 [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 2023-10-24 06:20:45,974 [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 2023-10-24 06:20:45,974 [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 2023-10-24 06:20:45,974 [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 2023-10-24 06:20:45,974 [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 2023-10-24 06:20:45,974 [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 2023-10-24 06:20:45,974 [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 2023-10-24 06:20:45,974 [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 2023-10-24 06:20:45,975 [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 2023-10-24 06:20:45,975 [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 2023-10-24 06:20:45,975 [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 2023-10-24 06:20:45,975 [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 2023-10-24 06:20:45,975 [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 2023-10-24 06:20:45,975 [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 2023-10-24 06:20:45,975 [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 2023-10-24 06:20:45,976 [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 2023-10-24 06:20:45,976 [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 2023-10-24 06:20:45,976 [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 2023-10-24 06:20:45,976 [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 2023-10-24 06:20:45,976 [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 2023-10-24 06:20:45,976 [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 2023-10-24 06:20:45,976 [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 2023-10-24 06:20:45,976 [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 2023-10-24 06:20:45,976 [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 2023-10-24 06:20:45,977 [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 2023-10-24 06:20:45,977 [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 2023-10-24 06:20:45,977 [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 2023-10-24 06:20:45,977 [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 2023-10-24 06:20:45,977 [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 2023-10-24 06:20:45,977 [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 2023-10-24 06:20:45,977 [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 2023-10-24 06:20:45,977 [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 2023-10-24 06:20:45,977 [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 2023-10-24 06:20:45,977 [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 2023-10-24 06:20:45,978 [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 2023-10-24 06:20:45,978 [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 2023-10-24 06:20:45,978 [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 2023-10-24 06:20:45,978 [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 2023-10-24 06:20:45,978 [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 2023-10-24 06:20:45,978 [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 2023-10-24 06:20:45,978 [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 2023-10-24 06:20:45,978 [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 2023-10-24 06:20:45,978 [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 2023-10-24 06:20:45,979 [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 2023-10-24 06:20:45,979 [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 2023-10-24 06:20:45,979 [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 2023-10-24 06:20:45,979 [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 2023-10-24 06:20:45,979 [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 2023-10-24 06:20:45,979 [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 2023-10-24 06:20:45,980 [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 2023-10-24 06:20:45,980 [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 2023-10-24 06:20:45,980 [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 2023-10-24 06:20:45,981 [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 2023-10-24 06:20:45,981 [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 2023-10-24 06:20:45,982 [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 2023-10-24 06:20:45,982 [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 2023-10-24 06:20:45,982 [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 2023-10-24 06:20:45,982 [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 2023-10-24 06:20:45,982 [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 2023-10-24 06:20:45,982 [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 2023-10-24 06:20:45,982 [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 2023-10-24 06:20:45,983 [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 2023-10-24 06:20:45,983 [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 2023-10-24 06:20:45,983 [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 2023-10-24 06:20:45,983 [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 2023-10-24 06:20:45,983 [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 2023-10-24 06:20:45,984 [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 2023-10-24 06:20:45,984 [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 2023-10-24 06:20:45,984 [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 2023-10-24 06:20:45,984 [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 2023-10-24 06:20:45,984 [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 2023-10-24 06:20:45,984 [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 2023-10-24 06:20:45,984 [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 2023-10-24 06:20:45,984 [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 2023-10-24 06:20:45,984 [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 2023-10-24 06:20:45,985 [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 2023-10-24 06:20:45,985 [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 2023-10-24 06:20:45,985 [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 2023-10-24 06:20:45,986 [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 2023-10-24 06:20:45,986 [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 2023-10-24 06:20:45,986 [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 2023-10-24 06:20:45,986 [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 2023-10-24 06:20:45,986 [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 2023-10-24 06:20:45,986 [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 2023-10-24 06:20:45,986 [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 2023-10-24 06:20:45,987 [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 2023-10-24 06:20:45,987 [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 2023-10-24 06:20:45,994 [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 2023-10-24 06:20:45,994 [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 2023-10-24 06:20:45,994 [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 2023-10-24 06:20:45,994 [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 2023-10-24 06:20:45,994 [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 2023-10-24 06:20:45,994 [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 2023-10-24 06:20:45,995 [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 2023-10-24 06:20:45,995 [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 2023-10-24 06:20:45,995 [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 2023-10-24 06:20:45,995 [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 2023-10-24 06:20:45,995 [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 2023-10-24 06:20:45,995 [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 2023-10-24 06:20:45,995 [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 2023-10-24 06:20:45,996 [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 2023-10-24 06:20:45,996 [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 2023-10-24 06:20:45,996 [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 2023-10-24 06:20:45,996 [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 2023-10-24 06:20:45,996 [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 2023-10-24 06:20:45,996 [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 2023-10-24 06:20:45,996 [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 2023-10-24 06:20:45,996 [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 2023-10-24 06:20:45,996 [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 2023-10-24 06:20:45,996 [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 2023-10-24 06:20:45,997 [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 2023-10-24 06:20:45,997 [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 2023-10-24 06:20:45,997 [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 2023-10-24 06:20:45,997 [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 2023-10-24 06:20:45,997 [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 2023-10-24 06:20:45,997 [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 2023-10-24 06:20:45,997 [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 2023-10-24 06:20:45,997 [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 2023-10-24 06:20:45,997 [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 2023-10-24 06:20:45,997 [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 2023-10-24 06:20:45,997 [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 2023-10-24 06:20:45,997 [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 2023-10-24 06:20:45,998 [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 2023-10-24 06:20:45,998 [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 2023-10-24 06:20:45,998 [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 2023-10-24 06:20:45,998 [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 2023-10-24 06:20:45,998 [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 2023-10-24 06:20:45,998 [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 2023-10-24 06:20:45,998 [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 2023-10-24 06:20:45,999 [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 2023-10-24 06:20:45,999 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.plant_tribes:PlantTribesKsComponents' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:45,999 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.plant_tribes:Smat' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:45,999 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Sabund' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:45,999 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Otu' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:45,999 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:GroupAbund' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:45,999 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:SecondaryStructureMap' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:45,999 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:LowerTriangleDistanceMatrix' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:45,999 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:SquareDistanceMatrix' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:45,999 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:PairwiseDistanceMatrix' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,000 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Oligos' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,000 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Quantile' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,000 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Frequency' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,001 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:LaneMask' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,001 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:RefTaxonomy' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,001 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Axes' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,001 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyAscii' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,001 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyBinary' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,001 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkAscii' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,001 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkBinary' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,001 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:NeperTess' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,001 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:NeperTesr' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,001 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:GmshMsh' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,001 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.goldenpath:GoldenPath' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,001 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:ScIdx' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,002 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:Vcf' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,002 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:JP2' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,002 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:TwoBit' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,002 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:GeminiSQLite' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,002 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:SQmass' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,002 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:MzSQlite' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,002 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OSW' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,002 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:PQP' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,002 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:IdpDB' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,002 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:ElibSQlite' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,002 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:DlibSQlite' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,002 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:BlibSQlite' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,002 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:ChiraSQLite' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,003 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:CuffDiffSQlite' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,003 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:GAFASQLite' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,003 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:NcbiTaxonomySQlite' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,003 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:SQlite' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,003 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:H5MLM' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,003 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Cool' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,003 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:MCool' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,003 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Loom' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,003 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Anndata' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,003 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Biom2' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,003 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:HexrdMaterials' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,004 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:H5' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,004 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Grib' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,004 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:HexrdImagesNpz' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,004 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:HexrdEtaOmeNpz' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,004 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Npz' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,004 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Bam' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,004 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:BamQuerynameSorted' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,004 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:BamNative' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,004 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:CRAM' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,004 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Sff' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,004 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Sra' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,004 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:NetCDF' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,004 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:DAA' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,004 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:RMA6' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,004 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:DMND' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,004 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Parquet' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,004 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:BafTar' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,004 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:TdfTar' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,004 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:MassHunterTar' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,005 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:MassLynxTar' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,005 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:YepTar' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,005 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:WiffTar' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,005 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5ArchiveGz' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,005 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5ArchiveBz2' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,005 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5Archive' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,005 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Meryldb' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,005 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Bref3' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,005 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:PostgresqlArchive' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,005 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:ICM' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,005 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Idat' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,005 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Trr' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,005 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Dcd' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,005 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Xtc' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,006 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Cpt' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,006 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Edr' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,006 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Vel' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,006 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Xlsx' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,006 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.qiime2:QIIME2Metadata' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,006 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.qiime2:QIIME2Artifact' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,006 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.qiime2:QIIME2Visualization' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,006 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:CompressedZipArchive' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,006 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Pretext' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,006 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.annotation:Augustus' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,006 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.xml:Owl' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,006 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.triples:Rdf' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,006 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.blast:BlastXml' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,006 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Gifti' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,006 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.xml:Phyloxml' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,006 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.xml:Dzi' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,006 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.xml:Sbml' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,007 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Dta2d' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,007 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Edta' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,007 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ConsensusXML' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,007 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:IdXML' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,007 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:FeatureXML' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,007 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MascotXML' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,007 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Mgf' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,007 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Ms2' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,007 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Msp' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,007 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzData' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,007 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzIdentML' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,007 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzML' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,007 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzQuantML' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,007 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzTab' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,007 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzTab2' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,007 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ParamXml' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,008 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzXML' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,008 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:NmrML' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,008 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Kroenik' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,008 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PepList' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,008 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PSMS' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,008 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PepXml' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,008 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ProtXML' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,008 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:SPLib' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,008 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TandemXML' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,008 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ThermoRAW' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,008 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TraML' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,008 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TrafoXML' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,008 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:UniProtXML' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,008 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:XquestXML' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,009 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:XquestSpecXML' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,009 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:QCML' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,009 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Wiff' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,009 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PEFF' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,009 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:CML' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,009 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.xml:GenericXml' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,009 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.triples:HDT' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,009 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.triples:Turtle' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,009 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.triples:NTriples' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,009 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.triples:Jsonld' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,009 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Maf' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,009 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Lav' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,009 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:MemePsp' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,009 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastg' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,009 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:csFasta' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,009 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,010 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,010 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:SDF' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,288 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:PDB' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,288 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:Cell' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,288 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:CIF' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,288 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:ExtendedXYZ' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,288 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:XYZ' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,288 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:MOL2' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,289 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:InChI' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,289 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:FPS' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,289 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:PQR' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,289 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:GRO' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,289 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.phylip:Phylip' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,289 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fasta' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,289 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqCSSanger' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,289 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqSanger' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,289 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastq' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,289 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:Wiggle' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,289 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Html' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,289 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Pdf' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,289 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Axt' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,289 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Genbank' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,290 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:Bed' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,290 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:CustomTrack' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,290 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:Gtf' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,290 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,290 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff3' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,290 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:Pileup' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,290 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:Psl' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,290 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Paf' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,290 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:Interval' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,290 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:Sam' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,290 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.data:Newick' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,290 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.data:Nexus' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,290 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:IQTree' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,290 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Obo' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,291 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Arff' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,291 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Ipynb' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,291 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Biom1' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,291 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:ImgtJson' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,291 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:GeoJson' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,291 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:PithyaResult' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,291 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:BCSLts' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,291 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Json' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,291 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.genetics:GenotypeMatrix' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,291 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.genetics:DataIn' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,291 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.genetics:MarkerMap' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,291 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.genetics:AllegroLOD' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,291 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:RNADotPlotMatrix' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,291 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:DotBracket' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,291 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:CMAP' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,292 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:ConnectivityTable' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,292 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:CSV' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,292 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.metacyto:mSummary' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,292 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.metacyto:mStats' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,292 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:TSV' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,292 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:MatrixMarket' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,292 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer2' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,292 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer3' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,292 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.msa:Stockholm_1_0' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,292 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.msa:MauveXmfa' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,292 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.msa:InfernalCM' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,292 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.annotation:SnapHmm' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,292 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.microarrays:Cel' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,293 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.microarrays:Gpr' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,293 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.microarrays:Gal' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,293 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:RData' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,293 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:RDS' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,293 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Mrc2014' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,293 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Jpg' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,293 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Png' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,293 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:OMETiff' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,293 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Tiff' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,293 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Bmp' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,293 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Gif' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,293 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Im' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,293 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Pcd' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,293 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Pcx' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,294 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Ppm' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,294 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Psd' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,294 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Xbm' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,294 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Rgb' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,294 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,294 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,294 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,294 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Eps' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,294 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Rast' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,294 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Tck' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,294 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Trk' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,294 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Nifti1' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,294 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Nifti2' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,295 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Star' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,295 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Wav' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,295 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Mkv' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,295 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Mp3' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,295 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Mp4' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,295 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Flv' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,295 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Mpg' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,295 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.speech:TextGrid' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,295 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.speech:BPF' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,295 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Castep' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,295 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:CTLresult' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,295 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:FormattedDensity' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,295 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Param' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,296 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Yaml' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,296 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliCountGraph' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,296 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliNodeGraph' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,296 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliTagSet' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,296 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliStopTags' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,296 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliSubset' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,296 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliGraphLabels' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,296 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:FITS' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,296 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.neo4j:Neo4jDBzip' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,296 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:PithyaProperty' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,296 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:PithyaModel' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,296 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:BCSLmodel' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,297 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:StormSample' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,297 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:StormCheck' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:46,301 [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 2023-10-24 06:20:46,301 [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 2023-10-24 06:20:46,301 [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 2023-10-24 06:20:46,301 [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 2023-10-24 06:20:46,301 [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 2023-10-24 06:20:46,301 [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 2023-10-24 06:20:46,302 [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 2023-10-24 06:20:46,302 [pN:job_handler_0,p:8,tN:MainThread] Loaded reference to tool shed: Galaxy Main Tool Shed +galaxy.web_stack DEBUG 2023-10-24 06:20:46,304 [pN:job_handler_0,p:8,tN:MainThread] server_name set to: job_handler_0 +galaxy.queue_worker INFO 2023-10-24 06:20:46,308 [pN:job_handler_0,p:8,tN:MainThread] Initializing job_handler_0 Galaxy Queue Worker on amqp://default_user_x1khT-Z2T22fX6s6eEA:********@edge-23-10-24-06-08-1-galaxy-rabbitmq-server:5672 +galaxy.tool_util.data WARNING 2023-10-24 06:20:46,324 [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 2023-10-24 06:20:46,324 [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 2023-10-24 06:20:46,324 [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 2023-10-24 06:20:46,324 [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 2023-10-24 06:20:46,324 [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 2023-10-24 06:20:46,324 [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 2023-10-24 06:20:46,324 [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 2023-10-24 06:20:46,325 [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 2023-10-24 06:20:46,325 [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 2023-10-24 06:20:46,325 [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 2023-10-24 06:20:46,325 [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 2023-10-24 06:20:46,325 [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 2023-10-24 06:20:46,325 [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 2023-10-24 06:20:46,325 [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 2023-10-24 06:20:46,325 [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 2023-10-24 06:20:46,325 [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 2023-10-24 06:20:46,326 [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 2023-10-24 06:20:46,326 [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 2023-10-24 06:20:46,326 [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 2023-10-24 06:20:46,326 [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 2023-10-24 06:20:46,326 [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 2023-10-24 06:20:46,326 [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 2023-10-24 06:20:46,326 [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 2023-10-24 06:20:46,326 [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 2023-10-24 06:20:46,327 [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 2023-10-24 06:20:46,327 [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 2023-10-24 06:20:46,327 [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 2023-10-24 06:20:46,327 [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 2023-10-24 06:20:46,327 [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 2023-10-24 06:20:46,327 [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 2023-10-24 06:20:46,328 [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 2023-10-24 06:20:46,328 [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 2023-10-24 06:20:46,328 [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 2023-10-24 06:20:46,328 [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 2023-10-24 06:20:46,328 [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 2023-10-24 06:20:46,328 [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 2023-10-24 06:20:46,328 [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 2023-10-24 06:20:46,329 [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 2023-10-24 06:20:46,329 [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 2023-10-24 06:20:46,329 [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 2023-10-24 06:20:46,329 [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 2023-10-24 06:20:46,329 [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 2023-10-24 06:20:46,329 [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 2023-10-24 06:20:46,329 [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 2023-10-24 06:20:46,330 [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 2023-10-24 06:20:46,330 [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 2023-10-24 06:20:46,330 [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 2023-10-24 06:20:46,330 [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 2023-10-24 06:20:46,330 [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 2023-10-24 06:20:46,330 [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 2023-10-24 06:20:46,330 [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 2023-10-24 06:20:46,331 [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 2023-10-24 06:20:46,331 [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 2023-10-24 06:20:46,331 [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 2023-10-24 06:20:46,331 [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 2023-10-24 06:20:46,331 [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 2023-10-24 06:20:46,331 [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 2023-10-24 06:20:46,331 [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 2023-10-24 06:20:46,331 [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 2023-10-24 06:20:46,332 [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 2023-10-24 06:20:46,332 [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 2023-10-24 06:20:46,332 [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 2023-10-24 06:20:46,332 [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 2023-10-24 06:20:46,332 [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 2023-10-24 06:20:46,332 [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 2023-10-24 06:20:46,332 [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 2023-10-24 06:20:46,333 [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 2023-10-24 06:20:46,333 [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 2023-10-24 06:20:46,333 [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 2023-10-24 06:20:46,333 [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 2023-10-24 06:20:46,333 [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 2023-10-24 06:20:46,333 [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 2023-10-24 06:20:46,333 [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 2023-10-24 06:20:46,333 [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 2023-10-24 06:20:46,333 [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 2023-10-24 06:20:46,333 [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 2023-10-24 06:20:46,334 [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 2023-10-24 06:20:46,334 [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 2023-10-24 06:20:46,334 [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 2023-10-24 06:20:46,334 [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 2023-10-24 06:20:46,334 [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 2023-10-24 06:20:46,334 [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 2023-10-24 06:20:46,334 [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 2023-10-24 06:20:46,334 [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 2023-10-24 06:20:46,334 [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 2023-10-24 06:20:46,334 [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 2023-10-24 06:20:46,334 [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 2023-10-24 06:20:46,334 [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 2023-10-24 06:20:46,334 [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 2023-10-24 06:20:46,335 [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 2023-10-24 06:20:46,335 [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 2023-10-24 06:20:46,335 [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 2023-10-24 06:20:46,335 [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 2023-10-24 06:20:46,335 [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 2023-10-24 06:20:46,335 [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 2023-10-24 06:20:46,335 [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 2023-10-24 06:20:46,335 [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 2023-10-24 06:20:46,335 [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 2023-10-24 06:20:46,335 [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 2023-10-24 06:20:46,335 [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 2023-10-24 06:20:46,335 [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 2023-10-24 06:20:46,335 [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 2023-10-24 06:20:46,336 [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 2023-10-24 06:20:46,336 [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 2023-10-24 06:20:46,336 [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 2023-10-24 06:20:46,336 [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 2023-10-24 06:20:46,336 [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 2023-10-24 06:20:46,336 [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 2023-10-24 06:20:46,336 [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 2023-10-24 06:20:46,336 [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 2023-10-24 06:20:46,336 [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 2023-10-24 06:20:46,336 [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 2023-10-24 06:20:46,336 [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 2023-10-24 06:20:46,336 [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 2023-10-24 06:20:46,336 [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 2023-10-24 06:20:46,337 [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 2023-10-24 06:20:46,337 [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 2023-10-24 06:20:46,337 [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 2023-10-24 06:20:46,337 [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 2023-10-24 06:20:46,337 [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 2023-10-24 06:20:46,337 [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 2023-10-24 06:20:46,337 [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 2023-10-24 06:20:46,337 [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 2023-10-24 06:20:46,337 [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 2023-10-24 06:20:46,337 [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 2023-10-24 06:20:46,337 [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 2023-10-24 06:20:46,337 [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 2023-10-24 06:20:46,337 [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 2023-10-24 06:20:46,337 [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 2023-10-24 06:20:46,338 [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 2023-10-24 06:20:46,338 [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 2023-10-24 06:20:46,338 [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 2023-10-24 06:20:46,338 [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 2023-10-24 06:20:46,338 [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 2023-10-24 06:20:46,338 [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 2023-10-24 06:20:46,338 [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 2023-10-24 06:20:46,338 [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 2023-10-24 06:20:46,338 [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 2023-10-24 06:20:46,338 [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 2023-10-24 06:20:46,338 [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 2023-10-24 06:20:46,338 [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 2023-10-24 06:20:46,339 [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 2023-10-24 06:20:46,339 [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 2023-10-24 06:20:46,339 [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 2023-10-24 06:20:46,339 [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 2023-10-24 06:20:46,339 [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 2023-10-24 06:20:46,339 [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 2023-10-24 06:20:46,339 [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 2023-10-24 06:20:46,339 [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 2023-10-24 06:20:46,339 [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 2023-10-24 06:20:46,339 [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 2023-10-24 06:20:46,339 [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 2023-10-24 06:20:46,340 [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 2023-10-24 06:20:46,340 [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 2023-10-24 06:20:46,340 [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 2023-10-24 06:20:46,340 [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 2023-10-24 06:20:46,340 [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 2023-10-24 06:20:46,340 [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 2023-10-24 06:20:46,340 [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 2023-10-24 06:20:46,340 [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 2023-10-24 06:20:46,340 [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 2023-10-24 06:20:46,340 [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 2023-10-24 06:20:46,340 [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 2023-10-24 06:20:46,340 [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 2023-10-24 06:20:46,340 [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 2023-10-24 06:20:46,341 [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 2023-10-24 06:20:46,341 [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 2023-10-24 06:20:46,341 [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 2023-10-24 06:20:46,341 [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 2023-10-24 06:20:46,341 [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 2023-10-24 06:20:46,341 [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 2023-10-24 06:20:46,341 [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 2023-10-24 06:20:46,341 [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 2023-10-24 06:20:46,342 [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 2023-10-24 06:20:46,342 [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 2023-10-24 06:20:46,342 [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 2023-10-24 06:20:46,342 [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 2023-10-24 06:20:46,342 [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 2023-10-24 06:20:46,342 [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 2023-10-24 06:20:46,342 [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 2023-10-24 06:20:46,342 [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 2023-10-24 06:20:46,343 [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 2023-10-24 06:20:46,343 [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 2023-10-24 06:20:46,343 [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 2023-10-24 06:20:46,343 [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 2023-10-24 06:20:46,343 [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 2023-10-24 06:20:46,343 [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 2023-10-24 06:20:46,343 [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 2023-10-24 06:20:46,343 [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 2023-10-24 06:20:46,344 [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 2023-10-24 06:20:46,344 [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 2023-10-24 06:20:46,344 [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 2023-10-24 06:20:46,344 [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 2023-10-24 06:20:46,344 [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 2023-10-24 06:20:46,344 [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 2023-10-24 06:20:46,344 [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 2023-10-24 06:20:46,344 [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 2023-10-24 06:20:46,345 [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 2023-10-24 06:20:46,345 [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 2023-10-24 06:20:46,345 [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 2023-10-24 06:20:46,345 [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 2023-10-24 06:20:46,345 [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 2023-10-24 06:20:46,345 [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 2023-10-24 06:20:46,345 [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 2023-10-24 06:20:46,345 [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 2023-10-24 06:20:46,346 [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 2023-10-24 06:20:46,346 [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 2023-10-24 06:20:46,346 [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 2023-10-24 06:20:46,346 [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 2023-10-24 06:20:46,346 [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 2023-10-24 06:20:46,346 [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 2023-10-24 06:20:46,346 [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 2023-10-24 06:20:46,346 [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 2023-10-24 06:20:46,347 [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 2023-10-24 06:20:46,347 [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 2023-10-24 06:20:46,347 [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 2023-10-24 06:20:46,347 [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 2023-10-24 06:20:46,347 [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 2023-10-24 06:20:46,347 [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 2023-10-24 06:20:46,347 [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 2023-10-24 06:20:46,348 [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 2023-10-24 06:20:46,348 [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 2023-10-24 06:20:46,348 [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 2023-10-24 06:20:46,348 [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 2023-10-24 06:20:46,348 [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 2023-10-24 06:20:46,348 [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 2023-10-24 06:20:46,348 [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 2023-10-24 06:20:46,349 [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 2023-10-24 06:20:46,349 [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 2023-10-24 06:20:46,349 [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 2023-10-24 06:20:46,349 [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 2023-10-24 06:20:46,349 [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 2023-10-24 06:20:46,349 [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 2023-10-24 06:20:46,350 [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 2023-10-24 06:20:46,350 [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 2023-10-24 06:20:46,350 [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 2023-10-24 06:20:46,350 [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 2023-10-24 06:20:46,350 [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 2023-10-24 06:20:46,350 [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 2023-10-24 06:20:46,351 [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 2023-10-24 06:20:46,351 [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 2023-10-24 06:20:46,351 [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 2023-10-24 06:20:46,351 [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 2023-10-24 06:20:46,351 [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 2023-10-24 06:20:46,351 [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 2023-10-24 06:20:46,352 [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 2023-10-24 06:20:46,352 [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 2023-10-24 06:20:46,352 [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 2023-10-24 06:20:46,352 [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 2023-10-24 06:20:46,352 [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 2023-10-24 06:20:46,353 [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 2023-10-24 06:20:46,353 [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 2023-10-24 06:20:46,353 [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 2023-10-24 06:20:46,353 [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 2023-10-24 06:20:46,353 [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 2023-10-24 06:20:46,353 [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 2023-10-24 06:20:46,354 [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 2023-10-24 06:20:46,354 [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 2023-10-24 06:20:46,354 [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 2023-10-24 06:20:46,354 [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 2023-10-24 06:20:46,354 [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 DEBUG 2023-10-24 06:20:46,356 [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 2023-10-24 06:20:46,356 [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 2023-10-24 06:20:46,357 [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 2023-10-24 06:20:46,357 [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 2023-10-24 06:20:46,358 [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 2023-10-24 06:20:46,358 [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 2023-10-24 06:20:46,360 [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 2023-10-24 06:20:46,360 [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 2023-10-24 06:20:46,361 [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 2023-10-24 06:20:46,361 [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 2023-10-24 06:20:46,362 [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 2023-10-24 06:20:46,362 [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 2023-10-24 06:20:46,364 [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 2023-10-24 06:20:46,364 [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 2023-10-24 06:20:46,365 [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 2023-10-24 06:20:46,365 [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 2023-10-24 06:20:46,366 [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 2023-10-24 06:20:46,366 [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 ERROR 2023-10-24 06:20:46,367 [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 2023-10-24 06:20:46,368 [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 2023-10-24 06:20:46,368 [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 ERROR 2023-10-24 06:20:46,368 [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 2023-10-24 06:20:46,369 [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 2023-10-24 06:20:46,369 [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 2023-10-24 06:20:46,369 [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 2023-10-24 06:20:46,370 [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 2023-10-24 06:20:46,370 [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 2023-10-24 06:20:46,370 [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 2023-10-24 06:20:46,371 [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 2023-10-24 06:20:46,371 [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 2023-10-24 06:20:46,375 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1193 lines from '/cvmfs/data.galaxyproject.org/managed/location/dbkeys_ucsc.loc' for '__dbkeys__' +galaxy.tool_util.data DEBUG 2023-10-24 06:20:46,376 [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 2023-10-24 06:20:46,409 [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 2023-10-24 06:20:46,409 [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 2023-10-24 06:20:46,410 [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 2023-10-24 06:20:46,410 [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 2023-10-24 06:20:46,411 [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 2023-10-24 06:20:46,412 [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 2023-10-24 06:20:46,412 [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 2023-10-24 06:20:46,413 [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 2023-10-24 06:20:46,413 [pN:job_handler_0,p:8,tN:MainThread] Loaded 18 lines from '/cvmfs/data.galaxyproject.org/managed/location/kraken2_databases.loc' for 'kraken2_databases' +galaxy.tool_util.data DEBUG 2023-10-24 06:20:46,414 [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 2023-10-24 06:20:46,417 [pN:job_handler_0,p:8,tN:MainThread] Loaded 237 lines from '/cvmfs/data.galaxyproject.org/byhand/location/all_fasta.loc' for 'all_fasta' +galaxy.tool_util.data DEBUG 2023-10-24 06:20:46,417 [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 ERROR 2023-10-24 06:20:46,419 [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 2023-10-24 06:20:46,420 [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 2023-10-24 06:20:46,421 [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 2023-10-24 06:20:46,422 [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 2023-10-24 06:20:46,422 [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 2023-10-24 06:20:46,423 [pN:job_handler_0,p:8,tN:MainThread] Loaded 4 lines from '/cvmfs/data.galaxyproject.org/byhand/location/blastdb.loc' for 'blastdb' +galaxy.tool_util.data DEBUG 2023-10-24 06:20:46,423 [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 2023-10-24 06:20:46,424 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/cvmfs/data.galaxyproject.org/byhand/location/blastdb_p.loc' for 'blastdb_p' +galaxy.tool_util.data DEBUG 2023-10-24 06:20:46,424 [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 2023-10-24 06:20:46,425 [pN:job_handler_0,p:8,tN:MainThread] Loaded 122 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bowtie2_indices.loc' for 'bowtie2_indexes' +galaxy.tool_util.data DEBUG 2023-10-24 06:20:46,425 [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 2023-10-24 06:20:46,427 [pN:job_handler_0,p:8,tN:MainThread] Loaded 16 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bwa_mem_index.loc' for 'bwa_mem_indexes' +galaxy.tool_util.data DEBUG 2023-10-24 06:20:46,427 [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 2023-10-24 06:20:46,429 [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 2023-10-24 06:20:46,429 [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 2023-10-24 06:20:46,430 [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 2023-10-24 06:20:46,430 [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 2023-10-24 06:20:46,432 [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 2023-10-24 06:20:46,432 [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 2023-10-24 06:20:46,435 [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 2023-10-24 06:20:46,435 [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 2023-10-24 06:20:46,436 [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 2023-10-24 06:20:46,436 [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 2023-10-24 06:20:46,437 [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 2023-10-24 06:20:46,437 [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 2023-10-24 06:20:46,441 [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 2023-10-24 06:20:46,441 [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 2023-10-24 06:20:46,443 [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 2023-10-24 06:20:46,443 [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 2023-10-24 06:20:46,444 [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 2023-10-24 06:20:46,444 [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 2023-10-24 06:20:46,445 [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 2023-10-24 06:20:46,445 [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 2023-10-24 06:20:46,447 [pN:job_handler_0,p:8,tN:MainThread] Loaded 202 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bowtie_indices.loc' for 'tophat_indexes' +galaxy.tool_util.data DEBUG 2023-10-24 06:20:46,447 [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 2023-10-24 06:20:46,448 [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 2023-10-24 06:20:46,448 [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 2023-10-24 06:20:46,449 [pN:job_handler_0,p:8,tN:MainThread] Loaded 122 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bowtie2_indices.loc' for 'tophat2_indexes' +galaxy.tool_util.data DEBUG 2023-10-24 06:20:46,449 [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 2023-10-24 06:20:46,451 [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 2023-10-24 06:20:46,451 [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 2023-10-24 06:20:46,452 [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 2023-10-24 06:20:46,452 [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 2023-10-24 06:20:46,455 [pN:job_handler_0,p:8,tN:MainThread] Loaded 202 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bowtie_indices.loc' for 'bowtie_indexes' +galaxy.tool_util.data DEBUG 2023-10-24 06:20:46,455 [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 2023-10-24 06:20:46,457 [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 2023-10-24 06:20:46,457 [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 2023-10-24 06:20:46,458 [pN:job_handler_0,p:8,tN:MainThread] Loaded 192 lines from '/cvmfs/data.galaxyproject.org/byhand/location/lastz_seqs.loc' for 'lastz_seqs' +galaxy.tool_util.data DEBUG 2023-10-24 06:20:46,458 [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 2023-10-24 06:20:46,462 [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 2023-10-24 06:20:46,462 [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 2023-10-24 06:20:46,465 [pN:job_handler_0,p:8,tN:MainThread] Loaded 177 lines from '/cvmfs/data.galaxyproject.org/byhand/location/fasta_indexes.loc' for 'fasta_indexes' +galaxy.tool_util.data DEBUG 2023-10-24 06:20:46,465 [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 2023-10-24 06:20:46,470 [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 2023-10-24 06:20:46,470 [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 2023-10-24 06:20:46,471 [pN:job_handler_0,p:8,tN:MainThread] Loaded 24 lines from '/cvmfs/data.galaxyproject.org/byhand/location/twobit.loc' for 'twobit' +galaxy.tool_util.data DEBUG 2023-10-24 06:20:46,471 [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 2023-10-24 06:20:46,473 [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 2023-10-24 06:20:46,473 [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 2023-10-24 06:20:46,473 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/cvmfs/data.galaxyproject.org/byhand/location/hisat2_indexes.loc' for 'hisat2_indexes' +galaxy.tool_util.data DEBUG 2023-10-24 06:20:46,473 [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 2023-10-24 06:20:46,474 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/cvmfs/data.galaxyproject.org/byhand/location/rnastar_index2x_versioned.loc' for 'rnastar_index2x_versioned' +galaxy.tool_util.data DEBUG 2023-10-24 06:20:46,474 [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 2023-10-24 06:20:46,475 [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 2023-10-24 06:20:46,475 [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 2023-10-24 06:20:46,476 [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 2023-10-24 06:20:46,476 [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 2023-10-24 06:20:46,477 [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 2023-10-24 06:20:46,477 [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 2023-10-24 06:20:46,477 [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 2023-10-24 06:20:46,478 [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 INFO 2023-10-24 06:20:46,478 [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 2023-10-24 06:20:46,480 [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 2023-10-24 06:20:46,480 [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 2023-10-24 06:20:46,480 [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 2023-10-24 06:20:46,480 [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 2023-10-24 06:20:46,481 [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 2023-10-24 06:20:46,481 [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 2023-10-24 06:20:46,481 [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 2023-10-24 06:20:46,481 [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 2023-10-24 06:20:46,482 [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 2023-10-24 06:20:46,482 [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 2023-10-24 06:20:46,482 [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 2023-10-24 06:20:46,482 [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 2023-10-24 06:20:46,482 [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 2023-10-24 06:20:46,482 [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 2023-10-24 06:20:46,483 [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 2023-10-24 06:20:46,483 [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 2023-10-24 06:20:46,483 [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 2023-10-24 06:20:46,484 [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 2023-10-24 06:20:46,484 [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 2023-10-24 06:20:46,484 [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 2023-10-24 06:20:46,484 [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 2023-10-24 06:20:46,484 [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 2023-10-24 06:20:46,485 [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 2023-10-24 06:20:46,485 [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 2023-10-24 06:20:46,485 [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 2023-10-24 06:20:46,486 [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 2023-10-24 06:20:46,486 [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 2023-10-24 06:20:46,487 [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 2023-10-24 06:20:46,487 [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 2023-10-24 06:20:46,487 [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 2023-10-24 06:20:46,487 [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 2023-10-24 06:20:46,488 [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 2023-10-24 06:20:46,488 [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 2023-10-24 06:20:46,488 [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 2023-10-24 06:20:46,488 [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 2023-10-24 06:20:46,489 [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 2023-10-24 06:20:46,489 [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 2023-10-24 06:20:46,489 [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 2023-10-24 06:20:46,489 [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 2023-10-24 06:20:46,490 [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 2023-10-24 06:20:46,490 [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 2023-10-24 06:20:46,490 [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 2023-10-24 06:20:46,491 [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 2023-10-24 06:20:46,491 [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 2023-10-24 06:20:46,491 [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 2023-10-24 06:20:46,491 [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 2023-10-24 06:20:46,492 [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 2023-10-24 06:20:46,493 [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 2023-10-24 06:20:46,493 [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 2023-10-24 06:20:46,493 [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 2023-10-24 06:20:46,493 [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 2023-10-24 06:20:46,494 [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 2023-10-24 06:20:46,494 [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 2023-10-24 06:20:46,494 [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. +galaxy.tool_util.data DEBUG 2023-10-24 06:20:46,607 [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-g_lqrkyn". +galaxy.tool_util.data WARNING 2023-10-24 06:20:46,613 [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 DEBUG 2023-10-24 06:20:46,614 [pN:job_handler_0,p:8,tN:MainThread] Loaded 156 lines from '/galaxy/server/database/tmp/TTDT_URL_igv_broad_genomes-g_lqrkyn' for 'igv_broad_genomes' +galaxy.tool_util.data DEBUG 2023-10-24 06:20:46,615 [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 2023-10-24 06:20:46,615 [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 2023-10-24 06:20:46,616 [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 2023-10-24 06:20:46,616 [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 2023-10-24 06:20:46,616 [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 2023-10-24 06:20:46,617 [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 2023-10-24 06:20:46,618 [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 2023-10-24 06:20:46,618 [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 2023-10-24 06:20:46,618 [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 2023-10-24 06:20:46,619 [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 2023-10-24 06:20:46,619 [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 2023-10-24 06:20:46,619 [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 2023-10-24 06:20:46,620 [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 2023-10-24 06:20:46,620 [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 2023-10-24 06:20:46,620 [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 2023-10-24 06:20:46,621 [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 2023-10-24 06:20:46,621 [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 2023-10-24 06:20:46,621 [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 2023-10-24 06:20:46,622 [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 2023-10-24 06:20:46,622 [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 2023-10-24 06:20:46,622 [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 2023-10-24 06:20:46,622 [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 2023-10-24 06:20:46,622 [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 2023-10-24 06:20:46,623 [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 2023-10-24 06:20:46,623 [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 2023-10-24 06:20:46,623 [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 2023-10-24 06:20:46,623 [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 2023-10-24 06:20:46,623 [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 2023-10-24 06:20:46,623 [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 2023-10-24 06:20:46,623 [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 2023-10-24 06:20:46,623 [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 2023-10-24 06:20:46,623 [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 2023-10-24 06:20:46,623 [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 2023-10-24 06:20:46,623 [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 2023-10-24 06:20:46,623 [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 2023-10-24 06:20:46,623 [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 2023-10-24 06:20:46,623 [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 2023-10-24 06:20:46,624 [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 2023-10-24 06:20:46,624 [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 2023-10-24 06:20:46,624 [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 2023-10-24 06:20:46,624 [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 2023-10-24 06:20:46,624 [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 2023-10-24 06:20:46,720 [pN:job_handler_0,p:8,tN:MainThread] directory not found: /galaxy/server/lib/galaxy/util/../../../config/plugins/activities +galaxy.tools WARNING 2023-10-24 06:20:46,725 [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 2023-10-24 06:20:46,726 [pN:job_handler_0,p:8,tN:MainThread] Parsing the tool configuration /galaxy/server/config/tool_conf.xml +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:46,726 [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 2023-10-24 06:20:46,771 [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 2023-10-24 06:20:46,771 [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 2023-10-24 06:20:46,911 [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 2023-10-24 06:20:46,911 [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 2023-10-24 06:20:46,912 [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 859, 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 1086, in load_tool + tool = self.create_tool( + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 512, 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 528, in _create_tool_from_source + return create_tool_from_source(self.app, tool_source, **kwds) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 322, in create_tool_from_source + tool = ToolClass(config_file, tool_source, app, **kwds) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 784, in __init__ + raise e + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 781, in __init__ + self.parse(tool_source, guid=guid, dynamic=dynamic) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1105, in parse + self.parse_inputs(self.tool_source) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1396, in parse_inputs + inputs = self.parse_input_elem(page_source, enctypes) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1591, in parse_input_elem + param = self.parse_param_elem(input_source, enctypes, context) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1604, 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 2023-10-24 06:20:46,943 [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 2023-10-24 06:20:46,943 [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 2023-10-24 06:20:46,961 [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 2023-10-24 06:20:46,965 [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 2023-10-24 06:20:46,966 [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 2023-10-24 06:20:46,981 [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 2023-10-24 06:20:46,989 [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 2023-10-24 06:20:46,997 [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 2023-10-24 06:20:47,003 [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 2023-10-24 06:20:47,009 [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 2023-10-24 06:20:47,014 [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 2023-10-24 06:20:47,019 [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 2023-10-24 06:20:47,026 [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 2023-10-24 06:20:47,034 [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 2023-10-24 06:20:47,042 [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 2023-10-24 06:20:47,048 [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 2023-10-24 06:20:47,055 [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 2023-10-24 06:20:47,059 [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 2023-10-24 06:20:47,068 [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 2023-10-24 06:20:47,077 [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 2023-10-24 06:20:47,083 [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 2023-10-24 06:20:47,088 [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 2023-10-24 06:20:47,101 [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 2023-10-24 06:20:47,108 [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 2023-10-24 06:20:47,114 [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 2023-10-24 06:20:47,123 [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 2023-10-24 06:20:47,129 [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 2023-10-24 06:20:47,137 [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 2023-10-24 06:20:47,149 [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 2023-10-24 06:20:47,158 [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 2023-10-24 06:20:47,170 [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 2023-10-24 06:20:47,177 [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 2023-10-24 06:20:47,182 [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 2023-10-24 06:20:47,188 [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 2023-10-24 06:20:47,199 [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 2023-10-24 06:20:47,208 [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 2023-10-24 06:20:47,216 [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 2023-10-24 06:20:47,223 [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 2023-10-24 06:20:47,230 [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 2023-10-24 06:20:47,236 [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 2023-10-24 06:20:47,241 [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 2023-10-24 06:20:47,247 [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 2023-10-24 06:20:47,252 [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 2023-10-24 06:20:47,256 [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 2023-10-24 06:20:47,260 [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 2023-10-24 06:20:47,264 [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 2023-10-24 06:20:47,269 [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 2023-10-24 06:20:47,274 [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 2023-10-24 06:20:47,278 [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 2023-10-24 06:20:47,286 [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 2023-10-24 06:20:47,293 [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 2023-10-24 06:20:47,297 [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 2023-10-24 06:20:47,301 [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 2023-10-24 06:20:47,305 [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 2023-10-24 06:20:47,309 [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 2023-10-24 06:20:47,313 [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 2023-10-24 06:20:47,317 [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 2023-10-24 06:20:47,321 [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 2023-10-24 06:20:47,326 [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 2023-10-24 06:20:47,330 [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 2023-10-24 06:20:47,334 [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 2023-10-24 06:20:47,339 [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 2023-10-24 06:20:47,343 [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 2023-10-24 06:20:47,347 [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 2023-10-24 06:20:47,352 [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 2023-10-24 06:20:47,355 [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 2023-10-24 06:20:47,359 [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 2023-10-24 06:20:47,362 [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 2023-10-24 06:20:47,367 [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 2023-10-24 06:20:47,532 [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 2023-10-24 06:20:47,719 [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 2023-10-24 06:20:47,724 [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 2023-10-24 06:20:47,738 [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 2023-10-24 06:20:47,744 [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 2023-10-24 06:20:47,748 [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 2023-10-24 06:20:47,755 [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 2023-10-24 06:20:47,763 [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 2023-10-24 06:20:47,771 [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 2023-10-24 06:20:47,780 [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 2023-10-24 06:20:47,787 [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 2023-10-24 06:20:47,794 [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 2023-10-24 06:20:47,799 [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 2023-10-24 06:20:47,807 [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 2023-10-24 06:20:47,813 [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 2023-10-24 06:20:47,819 [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 2023-10-24 06:20:47,826 [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 2023-10-24 06:20:47,834 [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 2023-10-24 06:20:47,843 [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 2023-10-24 06:20:47,850 [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 2023-10-24 06:20:47,859 [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 2023-10-24 06:20:47,867 [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 2023-10-24 06:20:47,883 [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 2023-10-24 06:20:47,896 [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 2023-10-24 06:20:47,903 [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 2023-10-24 06:20:47,912 [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 2023-10-24 06:20:47,925 [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 2023-10-24 06:20:47,930 [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 2023-10-24 06:20:47,940 [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 2023-10-24 06:20:47,955 [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 2023-10-24 06:20:47,967 [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 2023-10-24 06:20:47,983 [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 2023-10-24 06:20:47,994 [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 2023-10-24 06:20:48,001 [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 2023-10-24 06:20:48,023 [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 2023-10-24 06:20:48,030 [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 2023-10-24 06:20:48,047 [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 2023-10-24 06:20:48,078 [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 2023-10-24 06:20:48,151 [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 2023-10-24 06:20:48,168 [pN:job_handler_0,p:8,tN:MainThread] Invalid preset name specified: galaxy.util.mapped_chars +galaxy.tool_util.toolbox.base WARNING 2023-10-24 06:20:48,178 [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 2023-10-24 06:20:48,182 [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 2023-10-24 06:20:48,204 [pN:job_handler_0,p:8,tN:MainThread] Invalid preset name specified: galaxy.util.mapped_chars +galaxy.tool_util.toolbox.base WARNING 2023-10-24 06:20:48,217 [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 2023-10-24 06:20:48,225 [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 2023-10-24 06:20:48,231 [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 2023-10-24 06:20:48,236 [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 2023-10-24 06:20:48,241 [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 2023-10-24 06:20:48,247 [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 2023-10-24 06:20:48,252 [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 2023-10-24 06:20:48,262 [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 2023-10-24 06:20:48,283 [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 2023-10-24 06:20:48,303 [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 2023-10-24 06:20:48,307 [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 2023-10-24 06:20:48,323 [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 2023-10-24 06:20:48,337 [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 2023-10-24 06:20:48,351 [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 2023-10-24 06:20:48,362 [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 2023-10-24 06:20:48,377 [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 2023-10-24 06:20:48,399 [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 2023-10-24 06:20:48,407 [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 2023-10-24 06:20:48,413 [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 2023-10-24 06:20:48,418 [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 2023-10-24 06:20:48,425 [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 2023-10-24 06:20:48,434 [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 2023-10-24 06:20:48,439 [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 2023-10-24 06:20:48,445 [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 2023-10-24 06:20:48,452 [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 2023-10-24 06:20:48,457 [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 2023-10-24 06:20:48,466 [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 2023-10-24 06:20:48,472 [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 2023-10-24 06:20:48,480 [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 2023-10-24 06:20:48,484 [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 2023-10-24 06:20:48,488 [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 2023-10-24 06:20:48,493 [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 2023-10-24 06:20:48,500 [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 2023-10-24 06:20:48,505 [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 2023-10-24 06:20:48,509 [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 2023-10-24 06:20:48,516 [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 2023-10-24 06:20:48,523 [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 2023-10-24 06:20:48,528 [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 2023-10-24 06:20:48,533 [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 2023-10-24 06:20:48,537 [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 2023-10-24 06:20:48,541 [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 2023-10-24 06:20:48,546 [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 2023-10-24 06:20:48,550 [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 2023-10-24 06:20:48,557 [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 2023-10-24 06:20:48,561 [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 2023-10-24 06:20:48,568 [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 2023-10-24 06:20:48,577 [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 2023-10-24 06:20:48,584 [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 2023-10-24 06:20:48,597 [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 2023-10-24 06:20:48,607 [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 2023-10-24 06:20:48,615 [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 2023-10-24 06:20:48,635 [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 2023-10-24 06:20:48,649 [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 2023-10-24 06:20:48,659 [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 2023-10-24 06:20:48,666 [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 2023-10-24 06:20:48,676 [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 2023-10-24 06:20:48,692 [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 2023-10-24 06:20:48,702 [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 2023-10-24 06:20:48,717 [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 2023-10-24 06:20:48,724 [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 2023-10-24 06:20:48,732 [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 2023-10-24 06:20:48,736 [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 2023-10-24 06:20:48,743 [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 2023-10-24 06:20:48,749 [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 2023-10-24 06:20:48,758 [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 2023-10-24 06:20:48,767 [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 2023-10-24 06:20:48,776 [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 2023-10-24 06:20:48,781 [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 2023-10-24 06:20:48,880 [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 2023-10-24 06:20:48,978 [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 2023-10-24 06:20:48,983 [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 2023-10-24 06:20:48,991 [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 2023-10-24 06:20:49,003 [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 2023-10-24 06:20:49,008 [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 2023-10-24 06:20:49,014 [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 2023-10-24 06:20:49,019 [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 2023-10-24 06:20:49,024 [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 2023-10-24 06:20:49,028 [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 2023-10-24 06:20:49,032 [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 2023-10-24 06:20:49,038 [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 2023-10-24 06:20:49,043 [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 2023-10-24 06:20:49,048 [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 2023-10-24 06:20:49,053 [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 2023-10-24 06:20:49,061 [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 2023-10-24 06:20:49,066 [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 2023-10-24 06:20:49,074 [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 2023-10-24 06:20:49,078 [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 2023-10-24 06:20:49,082 [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 2023-10-24 06:20:49,087 [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 2023-10-24 06:20:49,092 [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 2023-10-24 06:20:49,097 [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 2023-10-24 06:20:49,101 [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 2023-10-24 06:20:49,106 [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 2023-10-24 06:20:49,114 [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 2023-10-24 06:20:49,120 [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 2023-10-24 06:20:49,129 [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 2023-10-24 06:20:49,135 [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 2023-10-24 06:20:49,140 [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 2023-10-24 06:20:49,144 [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 2023-10-24 06:20:49,148 [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 2023-10-24 06:20:49,151 [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 2023-10-24 06:20:49,158 [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 2023-10-24 06:20:49,162 [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 2023-10-24 06:20:49,169 [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 2023-10-24 06:20:49,175 [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 2023-10-24 06:20:49,180 [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 2023-10-24 06:20:49,188 [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 2023-10-24 06:20:49,199 [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 2023-10-24 06:20:49,210 [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 2023-10-24 06:20:49,215 [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 2023-10-24 06:20:49,220 [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 2023-10-24 06:20:49,229 [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 2023-10-24 06:20:49,241 [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 2023-10-24 06:20:49,246 [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 2023-10-24 06:20:49,253 [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 2023-10-24 06:20:49,258 [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 2023-10-24 06:20:49,263 [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 2023-10-24 06:20:49,273 [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 2023-10-24 06:20:49,288 [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 2023-10-24 06:20:49,292 [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 2023-10-24 06:20:49,297 [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 2023-10-24 06:20:49,636 [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 2023-10-24 06:20:49,641 [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 2023-10-24 06:20:49,646 [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 2023-10-24 06:20:49,650 [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 2023-10-24 06:20:49,655 [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 2023-10-24 06:20:49,661 [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 2023-10-24 06:20:49,665 [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 2023-10-24 06:20:49,670 [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 2023-10-24 06:20:49,747 [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 2023-10-24 06:20:49,758 [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 2023-10-24 06:20:49,764 [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 2023-10-24 06:20:49,771 [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 2023-10-24 06:20:49,786 [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 2023-10-24 06:20:49,863 [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 2023-10-24 06:20:49,868 [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 2023-10-24 06:20:49,873 [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 2023-10-24 06:20:49,952 [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 2023-10-24 06:20:49,956 [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 2023-10-24 06:20:49,962 [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 2023-10-24 06:20:49,972 [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 2023-10-24 06:20:49,976 [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 2023-10-24 06:20:49,981 [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 2023-10-24 06:20:49,989 [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 2023-10-24 06:20:49,994 [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 2023-10-24 06:20:50,010 [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 2023-10-24 06:20:50,014 [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 2023-10-24 06:20:50,019 [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 2023-10-24 06:20:50,046 [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 2023-10-24 06:20:50,083 [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 2023-10-24 06:20:50,089 [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 2023-10-24 06:20:50,096 [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 2023-10-24 06:20:50,102 [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 2023-10-24 06:20:50,109 [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 2023-10-24 06:20:50,121 [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 2023-10-24 06:20:50,132 [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 2023-10-24 06:20:50,149 [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 2023-10-24 06:20:50,165 [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 2023-10-24 06:20:50,197 [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 2023-10-24 06:20:50,212 [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 2023-10-24 06:20:50,217 [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 2023-10-24 06:20:50,225 [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 2023-10-24 06:20:50,231 [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 2023-10-24 06:20:50,237 [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 2023-10-24 06:20:50,242 [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 2023-10-24 06:20:50,263 [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 2023-10-24 06:20:50,270 [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 2023-10-24 06:20:50,276 [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 2023-10-24 06:20:50,283 [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 2023-10-24 06:20:50,288 [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 2023-10-24 06:20:50,295 [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 2023-10-24 06:20:50,302 [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 2023-10-24 06:20:50,311 [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 2023-10-24 06:20:50,317 [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 2023-10-24 06:20:50,324 [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 2023-10-24 06:20:50,330 [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 2023-10-24 06:20:50,332 [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 2023-10-24 06:20:50,337 [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 2023-10-24 06:20:50,348 [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 2023-10-24 06:20:50,356 [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 2023-10-24 06:20:50,364 [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 2023-10-24 06:20:50,372 [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 2023-10-24 06:20:50,381 [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 2023-10-24 06:20:50,391 [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 2023-10-24 06:20:50,396 [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 2023-10-24 06:20:50,401 [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 2023-10-24 06:20:50,406 [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 2023-10-24 06:20:50,412 [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 2023-10-24 06:20:50,418 [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 2023-10-24 06:20:50,423 [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 2023-10-24 06:20:50,428 [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 2023-10-24 06:20:50,433 [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 2023-10-24 06:20:50,439 [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 2023-10-24 06:20:50,451 [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 2023-10-24 06:20:50,462 [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 2023-10-24 06:20:50,480 [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 2023-10-24 06:20:50,489 [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 2023-10-24 06:20:50,559 [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 2023-10-24 06:20:50,592 [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 2023-10-24 06:20:50,599 [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 2023-10-24 06:20:50,605 [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 2023-10-24 06:20:50,608 [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 2023-10-24 06:20:50,614 [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 2023-10-24 06:20:50,619 [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 2023-10-24 06:20:50,622 [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 2023-10-24 06:20:50,627 [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 2023-10-24 06:20:50,633 [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 2023-10-24 06:20:50,634 [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 2023-10-24 06:20:50,639 [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 2023-10-24 06:20:50,642 [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 2023-10-24 06:20:50,644 [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 2023-10-24 06:20:50,650 [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 2023-10-24 06:20:50,660 [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 2023-10-24 06:20:50,667 [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 2023-10-24 06:20:50,673 [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 2023-10-24 06:20:50,681 [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 2023-10-24 06:20:50,689 [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 2023-10-24 06:20:50,693 [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 2023-10-24 06:20:50,699 [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 2023-10-24 06:20:50,703 [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 2023-10-24 06:20:50,707 [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 2023-10-24 06:20:50,759 [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 2023-10-24 06:20:50,784 [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 2023-10-24 06:20:50,790 [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 2023-10-24 06:20:50,794 [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 2023-10-24 06:20:50,798 [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 2023-10-24 06:20:50,799 [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 2023-10-24 06:20:50,804 [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 2023-10-24 06:20:50,811 [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 2023-10-24 06:20:50,817 [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 2023-10-24 06:20:50,823 [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 2023-10-24 06:20:50,827 [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 2023-10-24 06:20:50,829 [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 2023-10-24 06:20:50,833 [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 2023-10-24 06:20:50,834 [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 2023-10-24 06:20:50,839 [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 2023-10-24 06:20:50,844 [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 2023-10-24 06:20:50,849 [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 2023-10-24 06:20:50,853 [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 2023-10-24 06:20:50,859 [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 2023-10-24 06:20:50,865 [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 2023-10-24 06:20:50,870 [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 2023-10-24 06:20:50,875 [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 2023-10-24 06:20:50,879 [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 2023-10-24 06:20:50,885 [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 2023-10-24 06:20:50,889 [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 2023-10-24 06:20:50,895 [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 2023-10-24 06:20:50,901 [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 2023-10-24 06:20:50,907 [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 2023-10-24 06:20:50,912 [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 2023-10-24 06:20:50,918 [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 2023-10-24 06:20:50,927 [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 2023-10-24 06:20:50,934 [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 2023-10-24 06:20:50,942 [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 2023-10-24 06:20:50,948 [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 2023-10-24 06:20:50,957 [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 2023-10-24 06:20:51,029 [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 2023-10-24 06:20:51,036 [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 2023-10-24 06:20:51,042 [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 2023-10-24 06:20:51,049 [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 2023-10-24 06:20:51,057 [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 2023-10-24 06:20:51,080 [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 2023-10-24 06:20:51,087 [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 2023-10-24 06:20:51,095 [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 2023-10-24 06:20:51,102 [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 2023-10-24 06:20:51,107 [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 2023-10-24 06:20:51,112 [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 2023-10-24 06:20:51,119 [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 2023-10-24 06:20:51,125 [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 2023-10-24 06:20:51,134 [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 2023-10-24 06:20:51,142 [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 2023-10-24 06:20:51,151 [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 2023-10-24 06:20:51,157 [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 2023-10-24 06:20:51,163 [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 2023-10-24 06:20:51,186 [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 2023-10-24 06:20:51,194 [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 2023-10-24 06:20:51,203 [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 2023-10-24 06:20:51,209 [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 2023-10-24 06:20:51,237 [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 2023-10-24 06:20:51,249 [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 2023-10-24 06:20:51,257 [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 2023-10-24 06:20:51,263 [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 2023-10-24 06:20:51,269 [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 2023-10-24 06:20:51,274 [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 2023-10-24 06:20:51,280 [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 2023-10-24 06:20:51,284 [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 2023-10-24 06:20:51,289 [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 2023-10-24 06:20:51,436 [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 2023-10-24 06:20:51,588 [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 2023-10-24 06:20:51,733 [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 2023-10-24 06:20:51,740 [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 2023-10-24 06:20:51,744 [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 2023-10-24 06:20:51,748 [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 2023-10-24 06:20:51,753 [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 2023-10-24 06:20:51,758 [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 2023-10-24 06:20:51,763 [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 2023-10-24 06:20:51,768 [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 2023-10-24 06:20:51,788 [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 2023-10-24 06:20:51,795 [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 2023-10-24 06:20:51,813 [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 2023-10-24 06:20:51,854 [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 2023-10-24 06:20:51,862 [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 2023-10-24 06:20:51,866 [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 2023-10-24 06:20:51,872 [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 2023-10-24 06:20:51,875 [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 2023-10-24 06:20:51,881 [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 2023-10-24 06:20:51,886 [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 2023-10-24 06:20:51,890 [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 2023-10-24 06:20:51,895 [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 2023-10-24 06:20:51,901 [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 2023-10-24 06:20:51,906 [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 2023-10-24 06:20:51,912 [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 2023-10-24 06:20:51,916 [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 2023-10-24 06:20:51,921 [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 2023-10-24 06:20:51,925 [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 2023-10-24 06:20:51,930 [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 2023-10-24 06:20:51,934 [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 2023-10-24 06:20:51,940 [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 2023-10-24 06:20:51,943 [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 2023-10-24 06:20:51,948 [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 2023-10-24 06:20:51,951 [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 2023-10-24 06:20:51,955 [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 2023-10-24 06:20:51,962 [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 2023-10-24 06:20:51,967 [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 2023-10-24 06:20:51,973 [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 2023-10-24 06:20:51,978 [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 2023-10-24 06:20:51,983 [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 2023-10-24 06:20:51,987 [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 2023-10-24 06:20:51,992 [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 2023-10-24 06:20:51,995 [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 2023-10-24 06:20:51,999 [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 2023-10-24 06:20:52,005 [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 2023-10-24 06:20:52,010 [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 2023-10-24 06:20:52,015 [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 2023-10-24 06:20:52,020 [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 2023-10-24 06:20:52,025 [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 2023-10-24 06:20:52,029 [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 2023-10-24 06:20:52,037 [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 2023-10-24 06:20:52,043 [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 2023-10-24 06:20:52,047 [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 2023-10-24 06:20:52,054 [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 2023-10-24 06:20:52,059 [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 2023-10-24 06:20:52,064 [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 2023-10-24 06:20:52,069 [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 2023-10-24 06:20:52,074 [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 2023-10-24 06:20:52,079 [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 2023-10-24 06:20:52,082 [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 2023-10-24 06:20:52,088 [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 2023-10-24 06:20:52,094 [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 2023-10-24 06:20:52,099 [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 2023-10-24 06:20:52,103 [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 2023-10-24 06:20:52,108 [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 2023-10-24 06:20:52,112 [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 2023-10-24 06:20:52,118 [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 2023-10-24 06:20:52,123 [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 2023-10-24 06:20:52,127 [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 2023-10-24 06:20:52,132 [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 2023-10-24 06:20:52,136 [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 2023-10-24 06:20:52,140 [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 2023-10-24 06:20:52,145 [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 2023-10-24 06:20:52,150 [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 2023-10-24 06:20:52,163 [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 2023-10-24 06:20:52,168 [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 2023-10-24 06:20:52,174 [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 2023-10-24 06:20:52,180 [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 2023-10-24 06:20:52,185 [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 2023-10-24 06:20:52,192 [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 2023-10-24 06:20:52,199 [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 2023-10-24 06:20:52,204 [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 2023-10-24 06:20:52,208 [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 2023-10-24 06:20:52,213 [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 2023-10-24 06:20:52,218 [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 2023-10-24 06:20:52,222 [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 2023-10-24 06:20:52,228 [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 2023-10-24 06:20:52,232 [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 2023-10-24 06:20:52,238 [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 2023-10-24 06:20:52,242 [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 2023-10-24 06:20:52,245 [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 2023-10-24 06:20:52,250 [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 2023-10-24 06:20:52,253 [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 2023-10-24 06:20:52,258 [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 2023-10-24 06:20:52,263 [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 2023-10-24 06:20:52,267 [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 2023-10-24 06:20:52,272 [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 2023-10-24 06:20:52,278 [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 2023-10-24 06:20:52,282 [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 2023-10-24 06:20:52,287 [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 2023-10-24 06:20:52,293 [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 2023-10-24 06:20:52,299 [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 2023-10-24 06:20:52,305 [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 2023-10-24 06:20:52,310 [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 2023-10-24 06:20:52,314 [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 2023-10-24 06:20:52,319 [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 2023-10-24 06:20:52,323 [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 2023-10-24 06:20:52,329 [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 2023-10-24 06:20:52,334 [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 2023-10-24 06:20:52,339 [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 2023-10-24 06:20:52,343 [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 2023-10-24 06:20:52,347 [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 2023-10-24 06:20:52,351 [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 2023-10-24 06:20:52,358 [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 2023-10-24 06:20:52,364 [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 2023-10-24 06:20:52,369 [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 2023-10-24 06:20:52,374 [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 2023-10-24 06:20:52,380 [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 2023-10-24 06:20:52,386 [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 2023-10-24 06:20:52,393 [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 2023-10-24 06:20:52,398 [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 2023-10-24 06:20:52,405 [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 2023-10-24 06:20:52,411 [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 2023-10-24 06:20:52,417 [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 2023-10-24 06:20:52,421 [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 2023-10-24 06:20:52,427 [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 2023-10-24 06:20:52,431 [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 2023-10-24 06:20:52,435 [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 2023-10-24 06:20:52,439 [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 2023-10-24 06:20:52,731 [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 2023-10-24 06:20:52,740 [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 2023-10-24 06:20:52,745 [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 2023-10-24 06:20:52,750 [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 2023-10-24 06:20:52,755 [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 2023-10-24 06:20:52,759 [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 2023-10-24 06:20:52,764 [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 2023-10-24 06:20:52,768 [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 2023-10-24 06:20:52,773 [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 2023-10-24 06:20:52,782 [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 2023-10-24 06:20:52,787 [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 2023-10-24 06:20:52,793 [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 2023-10-24 06:20:52,798 [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 2023-10-24 06:20:52,803 [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 2023-10-24 06:20:52,808 [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 2023-10-24 06:20:52,812 [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 2023-10-24 06:20:52,816 [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 2023-10-24 06:20:52,821 [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 2023-10-24 06:20:52,826 [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 2023-10-24 06:20:52,832 [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 2023-10-24 06:20:52,837 [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 2023-10-24 06:20:52,841 [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 2023-10-24 06:20:52,846 [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 2023-10-24 06:20:52,851 [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 2023-10-24 06:20:52,857 [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 2023-10-24 06:20:52,861 [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 2023-10-24 06:20:52,867 [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 2023-10-24 06:20:52,872 [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 2023-10-24 06:20:52,877 [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 2023-10-24 06:20:52,881 [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 2023-10-24 06:20:52,886 [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 2023-10-24 06:20:52,890 [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 2023-10-24 06:20:52,896 [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 2023-10-24 06:20:52,900 [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 2023-10-24 06:20:52,907 [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 2023-10-24 06:20:52,912 [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 2023-10-24 06:20:52,916 [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 2023-10-24 06:20:52,920 [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 2023-10-24 06:20:52,924 [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 2023-10-24 06:20:52,929 [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 2023-10-24 06:20:52,934 [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 2023-10-24 06:20:52,938 [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 2023-10-24 06:20:52,943 [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.tools WARNING 2023-10-24 06:20:52,948 [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 2023-10-24 06:20:52,948 [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 2023-10-24 06:20:52,948 [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 2023-10-24 06:20:52,948 [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 2023-10-24 06:20:52,949 [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 2023-10-24 06:20:52,949 [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 2023-10-24 06:20:52,949 [pN:job_handler_0,p:8,tN:MainThread] Reading tools from config files finished (6224.148 ms) +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:52,950 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Get Data +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:52,950 [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 2023-10-24 06:20:52,950 [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 2023-10-24 06:20:52,950 [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 2023-10-24 06:20:52,950 [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 2023-10-24 06:20:52,950 [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 2023-10-24 06:20:52,950 [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 2023-10-24 06:20:52,951 [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 2023-10-24 06:20:52,951 [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 2023-10-24 06:20:52,951 [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 2023-10-24 06:20:52,951 [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 2023-10-24 06:20:52,951 [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 2023-10-24 06:20:52,951 [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 2023-10-24 06:20:52,951 [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 2023-10-24 06:20:52,951 [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 2023-10-24 06:20:52,951 [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 2023-10-24 06:20:52,951 [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 2023-10-24 06:20:52,951 [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 2023-10-24 06:20:52,951 [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 2023-10-24 06:20:52,951 [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 2023-10-24 06:20:52,951 [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 2023-10-24 06:20:52,952 [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 2023-10-24 06:20:52,952 [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 2023-10-24 06:20:52,952 [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 2023-10-24 06:20:52,952 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Send Data +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:52,952 [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 2023-10-24 06:20:52,952 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Send Data +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:52,952 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Expression Tools +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:52,952 [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 2023-10-24 06:20:52,952 [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 2023-10-24 06:20:52,952 [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 2023-10-24 06:20:52,952 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Collection Operations +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:52,952 [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 2023-10-24 06:20:52,952 [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 2023-10-24 06:20:52,952 [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 2023-10-24 06:20:52,952 [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 2023-10-24 06:20:52,953 [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 2023-10-24 06:20:52,953 [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 2023-10-24 06:20:52,953 [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 2023-10-24 06:20:52,953 [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 2023-10-24 06:20:52,953 [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 2023-10-24 06:20:52,953 [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 2023-10-24 06:20:52,953 [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 2023-10-24 06:20:52,953 [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 2023-10-24 06:20:52,953 [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 2023-10-24 06:20:52,953 [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 2023-10-24 06:20:52,953 [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 2023-10-24 06:20:52,953 [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 2023-10-24 06:20:52,953 [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 2023-10-24 06:20:52,953 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Text Manipulation +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:52,953 [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 2023-10-24 06:20:52,954 [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 2023-10-24 06:20:52,954 [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 2023-10-24 06:20:52,954 [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 2023-10-24 06:20:52,954 [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 2023-10-24 06:20:52,954 [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 2023-10-24 06:20:52,954 [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 2023-10-24 06:20:52,954 [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 2023-10-24 06:20:52,954 [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 2023-10-24 06:20:52,954 [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 2023-10-24 06:20:52,954 [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 2023-10-24 06:20:52,954 [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 2023-10-24 06:20:52,954 [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 2023-10-24 06:20:52,954 [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 2023-10-24 06:20:52,955 [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 2023-10-24 06:20:52,955 [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 2023-10-24 06:20:52,955 [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 2023-10-24 06:20:52,955 [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 2023-10-24 06:20:52,955 [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 2023-10-24 06:20:52,955 [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 2023-10-24 06:20:52,955 [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 2023-10-24 06:20:52,955 [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 2023-10-24 06:20:52,955 [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 2023-10-24 06:20:52,955 [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 2023-10-24 06:20:52,955 [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 2023-10-24 06:20:52,955 [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 2023-10-24 06:20:52,955 [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 2023-10-24 06:20:52,956 [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 2023-10-24 06:20:52,956 [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 2023-10-24 06:20:52,956 [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 2023-10-24 06:20:52,956 [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 2023-10-24 06:20:52,956 [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 2023-10-24 06:20:52,956 [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 2023-10-24 06:20:52,956 [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 2023-10-24 06:20:52,956 [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 2023-10-24 06:20:52,956 [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 2023-10-24 06:20:52,956 [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 2023-10-24 06:20:52,956 [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 2023-10-24 06:20:52,956 [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 2023-10-24 06:20:52,956 [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 2023-10-24 06:20:52,957 [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 2023-10-24 06:20:52,957 [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 2023-10-24 06:20:52,957 [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 2023-10-24 06:20:52,957 [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 2023-10-24 06:20:52,957 [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 2023-10-24 06:20:52,957 [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 2023-10-24 06:20:52,957 [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 2023-10-24 06:20:52,957 [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 2023-10-24 06:20:52,957 [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 2023-10-24 06:20:52,957 [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 2023-10-24 06:20:52,957 [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 2023-10-24 06:20:52,957 [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 2023-10-24 06:20:52,957 [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 2023-10-24 06:20:52,957 [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 2023-10-24 06:20:52,958 [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 2023-10-24 06:20:52,958 [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 2023-10-24 06:20:52,958 [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 2023-10-24 06:20:52,958 [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 2023-10-24 06:20:52,958 [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 2023-10-24 06:20:52,958 [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 2023-10-24 06:20:52,958 [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 2023-10-24 06:20:52,958 [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 2023-10-24 06:20:52,959 [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 2023-10-24 06:20:52,959 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Filter and Sort +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:52,959 [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 2023-10-24 06:20:52,959 [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 2023-10-24 06:20:52,959 [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 2023-10-24 06:20:52,959 [pN:job_handler_0,p:8,tN:MainThread] Loaded label: GFF +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:52,959 [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 2023-10-24 06:20:52,959 [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 2023-10-24 06:20:52,959 [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 2023-10-24 06:20:52,959 [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 2023-10-24 06:20:52,960 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Join, Subtract and Group +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:52,960 [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 2023-10-24 06:20:52,960 [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 2023-10-24 06:20:52,960 [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 2023-10-24 06:20:52,960 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Datamash +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:52,960 [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 2023-10-24 06:20:52,960 [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 2023-10-24 06:20:52,960 [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 2023-10-24 06:20:52,960 [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 2023-10-24 06:20:52,960 [pN:job_handler_0,p:8,tN:MainThread] Loading section: FASTA/FASTQ +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:52,960 [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 2023-10-24 06:20:52,960 [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 2023-10-24 06:20:52,960 [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 2023-10-24 06:20:52,961 [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 2023-10-24 06:20:52,961 [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 2023-10-24 06:20:52,961 [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 2023-10-24 06:20:52,961 [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 2023-10-24 06:20:52,961 [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 2023-10-24 06:20:52,961 [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 2023-10-24 06:20:52,961 [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 2023-10-24 06:20:52,961 [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 2023-10-24 06:20:52,961 [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 2023-10-24 06:20:52,961 [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 2023-10-24 06:20:52,961 [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 2023-10-24 06:20:52,962 [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 2023-10-24 06:20:52,962 [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 2023-10-24 06:20:52,962 [pN:job_handler_0,p:8,tN:MainThread] Loading section: FASTQ Quality Control +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:52,962 [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 2023-10-24 06:20:52,962 [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 2023-10-24 06:20:52,962 [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 2023-10-24 06:20:52,962 [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 2023-10-24 06:20:52,962 [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 2023-10-24 06:20:52,962 [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 2023-10-24 06:20:52,963 [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 2023-10-24 06:20:52,963 [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 2023-10-24 06:20:52,963 [pN:job_handler_0,p:8,tN:MainThread] Loading section: SAM/BAM +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:52,963 [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 2023-10-24 06:20:52,963 [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 2023-10-24 06:20:52,963 [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 2023-10-24 06:20:52,963 [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 2023-10-24 06:20:52,963 [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 2023-10-24 06:20:52,964 [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 2023-10-24 06:20:52,964 [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 2023-10-24 06:20:52,964 [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 2023-10-24 06:20:52,964 [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 2023-10-24 06:20:52,964 [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 2023-10-24 06:20:52,964 [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 2023-10-24 06:20:52,964 [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 2023-10-24 06:20:52,964 [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 2023-10-24 06:20:52,964 [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 2023-10-24 06:20:52,964 [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 2023-10-24 06:20:52,964 [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 2023-10-24 06:20:52,964 [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 2023-10-24 06:20:52,965 [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 2023-10-24 06:20:52,965 [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 2023-10-24 06:20:52,965 [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 2023-10-24 06:20:52,965 [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 2023-10-24 06:20:52,965 [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 2023-10-24 06:20:52,965 [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 2023-10-24 06:20:52,965 [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 2023-10-24 06:20:52,965 [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 2023-10-24 06:20:52,965 [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 2023-10-24 06:20:52,965 [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 2023-10-24 06:20:52,965 [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 2023-10-24 06:20:52,965 [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 2023-10-24 06:20:52,965 [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 2023-10-24 06:20:52,965 [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 2023-10-24 06:20:52,966 [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 2023-10-24 06:20:52,966 [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 2023-10-24 06:20:52,966 [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 2023-10-24 06:20:52,966 [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 2023-10-24 06:20:52,966 [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 2023-10-24 06:20:52,966 [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 2023-10-24 06:20:52,967 [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 2023-10-24 06:20:52,967 [pN:job_handler_0,p:8,tN:MainThread] Loading section: BED +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:52,967 [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 2023-10-24 06:20:52,967 [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 2023-10-24 06:20:52,967 [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 2023-10-24 06:20:52,967 [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 2023-10-24 06:20:52,967 [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 2023-10-24 06:20:52,967 [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 2023-10-24 06:20:52,967 [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 2023-10-24 06:20:52,968 [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 2023-10-24 06:20:52,968 [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 2023-10-24 06:20:52,968 [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 2023-10-24 06:20:52,968 [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 2023-10-24 06:20:52,968 [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 2023-10-24 06:20:52,968 [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 2023-10-24 06:20:52,968 [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 2023-10-24 06:20:52,968 [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 2023-10-24 06:20:52,968 [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 2023-10-24 06:20:52,968 [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 2023-10-24 06:20:52,968 [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 2023-10-24 06:20:52,968 [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 2023-10-24 06:20:52,969 [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 2023-10-24 06:20:52,969 [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 2023-10-24 06:20:52,969 [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 2023-10-24 06:20:52,969 [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 2023-10-24 06:20:52,969 [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 2023-10-24 06:20:52,969 [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 2023-10-24 06:20:52,969 [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 2023-10-24 06:20:52,969 [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 2023-10-24 06:20:52,969 [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 2023-10-24 06:20:52,969 [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 2023-10-24 06:20:52,969 [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 2023-10-24 06:20:52,969 [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 2023-10-24 06:20:52,969 [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 2023-10-24 06:20:52,970 [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 2023-10-24 06:20:52,970 [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 2023-10-24 06:20:52,970 [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 2023-10-24 06:20:52,970 [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 2023-10-24 06:20:52,970 [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 2023-10-24 06:20:52,970 [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 2023-10-24 06:20:52,970 [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 2023-10-24 06:20:52,970 [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 2023-10-24 06:20:52,970 [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 2023-10-24 06:20:52,970 [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 2023-10-24 06:20:52,970 [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 2023-10-24 06:20:52,971 [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 2023-10-24 06:20:52,971 [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 2023-10-24 06:20:52,971 [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 2023-10-24 06:20:52,971 [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 2023-10-24 06:20:52,971 [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 2023-10-24 06:20:52,971 [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 2023-10-24 06:20:52,971 [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 2023-10-24 06:20:52,971 [pN:job_handler_0,p:8,tN:MainThread] Loading section: VCF/BCF +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:52,971 [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 2023-10-24 06:20:52,971 [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 2023-10-24 06:20:52,971 [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 2023-10-24 06:20:52,971 [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 2023-10-24 06:20:52,972 [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 2023-10-24 06:20:52,972 [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 2023-10-24 06:20:52,972 [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 2023-10-24 06:20:52,972 [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 2023-10-24 06:20:52,972 [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 2023-10-24 06:20:52,972 [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 2023-10-24 06:20:52,972 [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 2023-10-24 06:20:52,972 [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 2023-10-24 06:20:52,972 [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 2023-10-24 06:20:52,972 [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 2023-10-24 06:20:52,972 [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 2023-10-24 06:20:52,972 [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 2023-10-24 06:20:52,972 [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 2023-10-24 06:20:52,973 [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 2023-10-24 06:20:52,973 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: 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+galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:52,973 [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 2023-10-24 06:20:52,973 [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 2023-10-24 06:20:52,973 [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 2023-10-24 06:20:52,973 [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 2023-10-24 06:20:52,973 [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 2023-10-24 06:20:52,974 [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 2023-10-24 06:20:52,974 [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 2023-10-24 06:20:52,974 [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 2023-10-24 06:20:52,974 [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 2023-10-24 06:20:52,974 [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 2023-10-24 06:20:52,974 [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 2023-10-24 06:20:52,974 [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 2023-10-24 06:20:52,974 [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 2023-10-24 06:20:52,974 [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 2023-10-24 06:20:52,974 [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 2023-10-24 06:20:52,974 [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 2023-10-24 06:20:52,974 [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 2023-10-24 06:20:52,974 [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 2023-10-24 06:20:52,974 [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 2023-10-24 06:20:52,975 [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 2023-10-24 06:20:52,975 [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 2023-10-24 06:20:52,975 [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 2023-10-24 06:20:52,975 [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 2023-10-24 06:20:52,975 [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 2023-10-24 06:20:52,975 [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 2023-10-24 06:20:52,975 [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 2023-10-24 06:20:52,975 [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 2023-10-24 06:20:52,975 [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 2023-10-24 06:20:52,975 [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 2023-10-24 06:20:52,975 [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 2023-10-24 06:20:52,975 [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 2023-10-24 06:20:52,975 [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 2023-10-24 06:20:52,976 [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 2023-10-24 06:20:52,976 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Nanopore +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:52,976 [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 2023-10-24 06:20:52,976 [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 2023-10-24 06:20:52,976 [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 2023-10-24 06:20:52,976 [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 2023-10-24 06:20:52,976 [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 2023-10-24 06:20:52,976 [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 2023-10-24 06:20:52,976 [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 2023-10-24 06:20:52,976 [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 2023-10-24 06:20:52,977 [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 2023-10-24 06:20:52,977 [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 2023-10-24 06:20:52,977 [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 2023-10-24 06:20:52,977 [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 2023-10-24 06:20:52,977 [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 2023-10-24 06:20:52,977 [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 2023-10-24 06:20:52,977 [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 2023-10-24 06:20:52,977 [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 2023-10-24 06:20:52,977 [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 2023-10-24 06:20:52,977 [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 2023-10-24 06:20:52,977 [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 2023-10-24 06:20:52,977 [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 2023-10-24 06:20:52,977 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Convert Formats +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:52,978 [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 2023-10-24 06:20:52,978 [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 2023-10-24 06:20:52,978 [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 2023-10-24 06:20:52,978 [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 2023-10-24 06:20:52,978 [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 2023-10-24 06:20:52,978 [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 2023-10-24 06:20:52,978 [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 2023-10-24 06:20:52,978 [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 2023-10-24 06:20:52,978 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Lift-Over +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:52,978 [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 2023-10-24 06:20:52,978 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Virology +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:52,978 [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 2023-10-24 06:20:52,978 [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 2023-10-24 06:20:52,978 [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 2023-10-24 06:20:52,979 [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 2023-10-24 06:20:52,979 [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 2023-10-24 06:20:52,979 [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 2023-10-24 06:20:52,979 [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 2023-10-24 06:20:52,979 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Operate on Genomic Intervals +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:52,979 [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 2023-10-24 06:20:52,979 [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 2023-10-24 06:20:52,979 [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 2023-10-24 06:20:52,979 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Fetch Sequences/Alignments +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:52,979 [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 2023-10-24 06:20:52,979 [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 2023-10-24 06:20:52,979 [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 2023-10-24 06:20:52,979 [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 2023-10-24 06:20:52,980 [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 2023-10-24 06:20:52,980 [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 2023-10-24 06:20:52,980 [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 2023-10-24 06:20:52,980 [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 2023-10-24 06:20:52,980 [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 2023-10-24 06:20:52,980 [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 2023-10-24 06:20:52,980 [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 2023-10-24 06:20:52,980 [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 2023-10-24 06:20:52,980 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Assembly +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:52,980 [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 2023-10-24 06:20:52,980 [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 2023-10-24 06:20:52,980 [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 2023-10-24 06:20:52,980 [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 2023-10-24 06:20:52,980 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Annotation +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:52,980 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Mapping +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:52,980 [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 2023-10-24 06:20:52,981 [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 2023-10-24 06:20:52,981 [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 2023-10-24 06:20:52,981 [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 2023-10-24 06:20:52,981 [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 2023-10-24 06:20:52,981 [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 2023-10-24 06:20:52,981 [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 2023-10-24 06:20:52,981 [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 2023-10-24 06:20:52,981 [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 2023-10-24 06:20:52,981 [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 2023-10-24 06:20:52,981 [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 2023-10-24 06:20:52,981 [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 2023-10-24 06:20:52,982 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Variant Calling +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:52,982 [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 2023-10-24 06:20:52,982 [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 2023-10-24 06:20:52,982 [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 2023-10-24 06:20:52,982 [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 2023-10-24 06:20:52,982 [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 2023-10-24 06:20:52,982 [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 2023-10-24 06:20:52,982 [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 2023-10-24 06:20:52,982 [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 2023-10-24 06:20:52,982 [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 2023-10-24 06:20:52,982 [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 2023-10-24 06:20:52,983 [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 2023-10-24 06:20:52,983 [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 2023-10-24 06:20:52,983 [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 2023-10-24 06:20:52,983 [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 2023-10-24 06:20:52,983 [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 2023-10-24 06:20:52,983 [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 2023-10-24 06:20:52,983 [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 2023-10-24 06:20:52,984 [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 2023-10-24 06:20:52,984 [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 2023-10-24 06:20:52,984 [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 2023-10-24 06:20:52,984 [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 2023-10-24 06:20:52,984 [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 2023-10-24 06:20:52,984 [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 2023-10-24 06:20:52,985 [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 2023-10-24 06:20:52,985 [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 2023-10-24 06:20:52,985 [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 2023-10-24 06:20:52,985 [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 2023-10-24 06:20:52,985 [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 2023-10-24 06:20:52,985 [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 2023-10-24 06:20:52,986 [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 2023-10-24 06:20:52,986 [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 2023-10-24 06:20:52,986 [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 2023-10-24 06:20:52,986 [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 2023-10-24 06:20:52,986 [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 2023-10-24 06:20:52,986 [pN:job_handler_0,p:8,tN:MainThread] Loading section: ChIP-seq +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:52,986 [pN:job_handler_0,p:8,tN:MainThread] Loading section: RNA-seq +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:52,986 [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 2023-10-24 06:20:52,986 [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 2023-10-24 06:20:52,986 [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 2023-10-24 06:20:52,987 [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 2023-10-24 06:20:52,987 [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 2023-10-24 06:20:52,987 [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 2023-10-24 06:20:52,987 [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 2023-10-24 06:20:52,987 [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 2023-10-24 06:20:52,987 [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 2023-10-24 06:20:52,987 [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 2023-10-24 06:20:52,987 [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 2023-10-24 06:20:52,987 [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 2023-10-24 06:20:52,987 [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 2023-10-24 06:20:52,987 [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 2023-10-24 06:20:52,988 [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 2023-10-24 06:20:52,988 [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 2023-10-24 06:20:52,988 [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 2023-10-24 06:20:52,988 [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 2023-10-24 06:20:52,988 [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 2023-10-24 06:20:52,988 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Multiple Alignments +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:52,988 [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 2023-10-24 06:20:52,988 [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 2023-10-24 06:20:52,988 [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 2023-10-24 06:20:52,989 [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 2023-10-24 06:20:52,989 [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 2023-10-24 06:20:52,989 [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 2023-10-24 06:20:52,989 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Phenotype Association +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:52,989 [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 2023-10-24 06:20:52,989 [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 2023-10-24 06:20:52,989 [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 2023-10-24 06:20:52,989 [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 2023-10-24 06:20:52,989 [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 2023-10-24 06:20:52,989 [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 2023-10-24 06:20:52,989 [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 2023-10-24 06:20:52,989 [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 2023-10-24 06:20:52,989 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Regional Variation +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:52,989 [pN:job_handler_0,p:8,tN:MainThread] Loading section: STR-FM: Microsatellite Analysis +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:52,989 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Motif +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:52,990 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Chromosome Conformation +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:52,990 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Metagenomic Analysis +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:52,990 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Mothur +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:52,990 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Picard +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:52,990 [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 2023-10-24 06:20:52,990 [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 2023-10-24 06:20:52,990 [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 2023-10-24 06:20:52,990 [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 2023-10-24 06:20:52,990 [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 2023-10-24 06:20:52,990 [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 2023-10-24 06:20:52,990 [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 2023-10-24 06:20:52,990 [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 2023-10-24 06:20:52,990 [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 2023-10-24 06:20:52,990 [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 2023-10-24 06:20:52,991 [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 2023-10-24 06:20:52,991 [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 2023-10-24 06:20:52,991 [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 2023-10-24 06:20:52,991 [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 2023-10-24 06:20:52,991 [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 2023-10-24 06:20:52,991 [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 2023-10-24 06:20:52,991 [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 2023-10-24 06:20:52,991 [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 2023-10-24 06:20:52,991 [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 2023-10-24 06:20:52,992 [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 2023-10-24 06:20:52,992 [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 2023-10-24 06:20:52,992 [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 2023-10-24 06:20:52,992 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: 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2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:52,994 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Pharmacology +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:52,994 [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 2023-10-24 06:20:52,994 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Single-Cell +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:52,994 [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 2023-10-24 06:20:52,994 [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 2023-10-24 06:20:52,995 [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 2023-10-24 06:20:52,995 [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 2023-10-24 06:20:52,995 [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 2023-10-24 06:20:52,995 [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 2023-10-24 06:20:52,995 [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 2023-10-24 06:20:52,995 [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 2023-10-24 06:20:52,996 [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 2023-10-24 06:20:52,996 [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 2023-10-24 06:20:52,996 [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 2023-10-24 06:20:52,996 [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 2023-10-24 06:20:52,996 [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 2023-10-24 06:20:52,996 [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 2023-10-24 06:20:52,997 [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 2023-10-24 06:20:52,997 [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 2023-10-24 06:20:52,997 [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 2023-10-24 06:20:52,997 [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 2023-10-24 06:20:52,997 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: 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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 2023-10-24 06:20:53,000 [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 panel.... +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:53,000 [pN:job_handler_0,p:8,tN:MainThread] 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 2023-10-24 06:20:53,000 [pN:job_handler_0,p:8,tN:MainThread] 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 2023-10-24 06:20:53,001 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: 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DEBUG 2023-10-24 06:20:53,014 [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 2023-10-24 06:20:53,014 [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 2023-10-24 06:20:53,015 [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 2023-10-24 06:20:53,015 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: 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+galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:53,031 [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 2023-10-24 06:20:53,032 [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 2023-10-24 06:20:53,032 [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 2023-10-24 06:20:53,032 [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 2023-10-24 06:20:53,032 [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 2023-10-24 06:20:53,032 [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 2023-10-24 06:20:53,032 [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 2023-10-24 06:20:53,032 [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 2023-10-24 06:20:53,033 [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 2023-10-24 06:20:53,033 [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 2023-10-24 06:20:53,033 [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 2023-10-24 06:20:53,033 [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 2023-10-24 06:20:53,033 [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 2023-10-24 06:20:53,033 [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 2023-10-24 06:20:53,033 [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 2023-10-24 06:20:53,034 [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 2023-10-24 06:20:53,034 [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 2023-10-24 06:20:53,034 [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 2023-10-24 06:20:53,034 [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 2023-10-24 06:20:53,034 [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 2023-10-24 06:20:53,034 [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 2023-10-24 06:20:53,034 [pN:job_handler_0,p:8,tN:MainThread] Loading section: MiModD +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:53,034 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Du Novo +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:53,035 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Seqtk +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:53,035 [pN:job_handler_0,p:8,tN:MainThread] Loading section: TRANSIT +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:53,035 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Statistics +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:53,035 [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 2023-10-24 06:20:53,035 [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 2023-10-24 06:20:53,035 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Graph/Display Data +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:53,035 [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 2023-10-24 06:20:53,035 [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 2023-10-24 06:20:53,036 [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 2023-10-24 06:20:53,036 [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 2023-10-24 06:20:53,036 [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 2023-10-24 06:20:53,036 [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 2023-10-24 06:20:53,036 [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 2023-10-24 06:20:53,036 [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 2023-10-24 06:20:53,036 [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 2023-10-24 06:20:53,036 [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 2023-10-24 06:20:53,037 [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 2023-10-24 06:20:53,037 [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 2023-10-24 06:20:53,037 [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 2023-10-24 06:20:53,037 [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 2023-10-24 06:20:53,037 [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 2023-10-24 06:20:53,037 [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 2023-10-24 06:20:53,038 [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 2023-10-24 06:20:53,038 [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 2023-10-24 06:20:53,038 [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 2023-10-24 06:20:53,038 [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 2023-10-24 06:20:53,038 [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 2023-10-24 06:20:53,039 [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 2023-10-24 06:20:53,039 [pN:job_handler_0,p:8,tN:MainThread] Loading section: RNA Analysis (deprecated) +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:53,039 [pN:job_handler_0,p:8,tN:MainThread] Loading section: CloudMap (deprecated) +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:53,039 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Metagenomic Analysis (deprecated) +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:53,039 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Text Manipulation +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:53,039 [pN:job_handler_0,p:8,tN:MainThread] Loading tool panel finished (89.497 ms) +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:53,044 [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 2023-10-24 06:20:53,044 [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 2023-10-24 06:20:53,044 [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 2023-10-24 06:20:53,045 [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 2023-10-24 06:20:53,045 [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 2023-10-24 06:20:53,045 [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 2023-10-24 06:20:53,045 [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 2023-10-24 06:20:53,045 [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 2023-10-24 06:20:53,045 [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 2023-10-24 06:20:53,045 [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 2023-10-24 06:20:53,046 [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 2023-10-24 06:20:53,046 [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 2023-10-24 06:20:53,046 [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 2023-10-24 06:20:53,046 [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 2023-10-24 06:20:53,046 [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 2023-10-24 06:20:53,046 [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 2023-10-24 06:20:53,046 [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 2023-10-24 06:20:53,046 [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 2023-10-24 06:20:53,046 [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 2023-10-24 06:20:53,047 [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 2023-10-24 06:20:53,047 [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 2023-10-24 06:20:53,047 [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 2023-10-24 06:20:53,047 [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 2023-10-24 06:20:53,047 [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 2023-10-24 06:20:53,047 [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 2023-10-24 06:20:53,047 [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 2023-10-24 06:20:53,047 [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 2023-10-24 06:20:53,047 [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 2023-10-24 06:20:53,047 [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 2023-10-24 06:20:53,047 [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 2023-10-24 06:20:53,047 [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 2023-10-24 06:20:53,047 [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 2023-10-24 06:20:53,047 [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 2023-10-24 06:20:53,048 [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 2023-10-24 06:20:53,048 [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 2023-10-24 06:20:53,048 [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 2023-10-24 06:20:53,048 [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 2023-10-24 06:20:53,048 [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 2023-10-24 06:20:53,048 [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 2023-10-24 06:20:53,048 [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 2023-10-24 06:20:53,048 [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 2023-10-24 06:20:53,048 [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 2023-10-24 06:20:53,048 [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 2023-10-24 06:20:53,048 [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 2023-10-24 06:20:53,048 [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 2023-10-24 06:20:53,048 [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 2023-10-24 06:20:53,048 [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 2023-10-24 06:20:53,049 [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 2023-10-24 06:20:53,049 [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 2023-10-24 06:20:53,049 [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 2023-10-24 06:20:53,049 [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 2023-10-24 06:20:53,049 [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 2023-10-24 06:20:53,049 [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 2023-10-24 06:20:53,049 [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 2023-10-24 06:20:53,049 [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 2023-10-24 06:20:53,049 [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 2023-10-24 06:20:53,049 [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 2023-10-24 06:20:53,049 [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 2023-10-24 06:20:53,049 [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 2023-10-24 06:20:53,049 [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 2023-10-24 06:20:53,049 [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 2023-10-24 06:20:53,050 [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 2023-10-24 06:20:53,050 [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 2023-10-24 06:20:53,050 [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 2023-10-24 06:20:53,050 [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 2023-10-24 06:20:53,050 [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 2023-10-24 06:20:53,050 [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 2023-10-24 06:20:53,050 [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 2023-10-24 06:20:53,050 [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 2023-10-24 06:20:53,051 [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 2023-10-24 06:20:53,051 [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 2023-10-24 06:20:53,051 [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 2023-10-24 06:20:53,051 [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 2023-10-24 06:20:53,051 [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 2023-10-24 06:20:53,051 [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 2023-10-24 06:20:53,051 [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 2023-10-24 06:20:53,051 [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 2023-10-24 06:20:53,051 [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 2023-10-24 06:20:53,051 [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 2023-10-24 06:20:53,052 [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 2023-10-24 06:20:53,052 [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 2023-10-24 06:20:53,052 [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 2023-10-24 06:20:53,052 [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 2023-10-24 06:20:53,052 [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 2023-10-24 06:20:53,052 [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 2023-10-24 06:20:53,052 [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 2023-10-24 06:20:53,052 [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 2023-10-24 06:20:53,052 [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 2023-10-24 06:20:53,052 [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 2023-10-24 06:20:53,052 [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 2023-10-24 06:20:53,052 [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 2023-10-24 06:20:53,052 [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 2023-10-24 06:20:53,053 [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 2023-10-24 06:20:53,053 [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 2023-10-24 06:20:53,053 [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 2023-10-24 06:20:53,053 [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 2023-10-24 06:20:53,053 [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 2023-10-24 06:20:53,053 [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 2023-10-24 06:20:53,053 [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 2023-10-24 06:20:53,053 [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 2023-10-24 06:20:53,053 [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 2023-10-24 06:20:53,053 [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 2023-10-24 06:20:53,053 [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 2023-10-24 06:20:53,053 [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 2023-10-24 06:20:53,053 [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 2023-10-24 06:20:53,053 [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 2023-10-24 06:20:53,054 [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 2023-10-24 06:20:53,054 [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 2023-10-24 06:20:53,054 [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 2023-10-24 06:20:53,054 [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 2023-10-24 06:20:53,054 [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 2023-10-24 06:20:53,054 [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 2023-10-24 06:20:53,054 [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 2023-10-24 06:20:53,054 [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 2023-10-24 06:20:53,054 [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 2023-10-24 06:20:53,054 [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 2023-10-24 06:20:53,054 [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 2023-10-24 06:20:53,054 [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 2023-10-24 06:20:53,054 [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 2023-10-24 06:20:53,055 [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 2023-10-24 06:20:53,055 [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 2023-10-24 06:20:53,055 [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 2023-10-24 06:20:53,055 [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 2023-10-24 06:20:53,055 [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 2023-10-24 06:20:53,055 [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 2023-10-24 06:20:53,055 [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 2023-10-24 06:20:53,055 [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 2023-10-24 06:20:53,055 [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 2023-10-24 06:20:53,055 [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 2023-10-24 06:20:53,055 [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 2023-10-24 06:20:53,055 [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 2023-10-24 06:20:53,055 [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 2023-10-24 06:20:53,055 [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 2023-10-24 06:20:53,055 [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 2023-10-24 06:20:53,055 [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 2023-10-24 06:20:53,056 [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 2023-10-24 06:20:53,056 [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 2023-10-24 06:20:53,056 [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 2023-10-24 06:20:53,056 [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 2023-10-24 06:20:53,056 [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 2023-10-24 06:20:53,056 [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 2023-10-24 06:20:53,056 [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 2023-10-24 06:20:53,056 [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 2023-10-24 06:20:53,056 [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 2023-10-24 06:20:53,056 [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 2023-10-24 06:20:53,056 [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 2023-10-24 06:20:53,057 [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 2023-10-24 06:20:53,057 [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 2023-10-24 06:20:53,057 [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 2023-10-24 06:20:53,057 [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 2023-10-24 06:20:53,057 [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 2023-10-24 06:20:53,057 [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 2023-10-24 06:20:53,057 [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 2023-10-24 06:20:53,057 [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 2023-10-24 06:20:53,057 [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 2023-10-24 06:20:53,057 [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 2023-10-24 06:20:53,057 [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 2023-10-24 06:20:53,058 [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 2023-10-24 06:20:53,058 [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 2023-10-24 06:20:53,058 [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 2023-10-24 06:20:53,058 [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 2023-10-24 06:20:53,058 [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 2023-10-24 06:20:53,058 [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 2023-10-24 06:20:53,058 [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 2023-10-24 06:20:53,058 [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 2023-10-24 06:20:53,058 [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 2023-10-24 06:20:53,058 [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 2023-10-24 06:20:53,059 [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 2023-10-24 06:20:53,059 [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 2023-10-24 06:20:53,059 [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 2023-10-24 06:20:53,059 [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 2023-10-24 06:20:53,059 [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 2023-10-24 06:20:53,059 [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 2023-10-24 06:20:53,059 [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 2023-10-24 06:20:53,059 [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 2023-10-24 06:20:53,059 [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 2023-10-24 06:20:53,060 [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 2023-10-24 06:20:53,060 [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 2023-10-24 06:20:53,060 [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 2023-10-24 06:20:53,060 [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 2023-10-24 06:20:53,060 [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 2023-10-24 06:20:53,060 [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 2023-10-24 06:20:53,060 [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 2023-10-24 06:20:53,060 [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 2023-10-24 06:20:53,060 [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 2023-10-24 06:20:53,060 [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 2023-10-24 06:20:53,060 [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 2023-10-24 06:20:53,060 [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 2023-10-24 06:20:53,060 [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 2023-10-24 06:20:53,061 [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 2023-10-24 06:20:53,061 [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 2023-10-24 06:20:53,061 [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 2023-10-24 06:20:53,061 [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 2023-10-24 06:20:53,061 [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 2023-10-24 06:20:53,061 [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 2023-10-24 06:20:53,061 [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 2023-10-24 06:20:53,061 [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 2023-10-24 06:20:53,061 [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 2023-10-24 06:20:53,061 [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 2023-10-24 06:20:53,061 [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 2023-10-24 06:20:53,061 [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 2023-10-24 06:20:53,061 [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 2023-10-24 06:20:53,061 [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 2023-10-24 06:20:53,061 [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 2023-10-24 06:20:53,062 [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 2023-10-24 06:20:53,062 [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 2023-10-24 06:20:53,062 [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 2023-10-24 06:20:53,062 [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 2023-10-24 06:20:53,062 [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 2023-10-24 06:20:53,062 [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 2023-10-24 06:20:53,062 [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 2023-10-24 06:20:53,062 [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 2023-10-24 06:20:53,062 [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 2023-10-24 06:20:53,062 [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 2023-10-24 06:20:53,063 [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 2023-10-24 06:20:53,063 [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 2023-10-24 06:20:53,063 [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 2023-10-24 06:20:53,063 [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 2023-10-24 06:20:53,063 [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 2023-10-24 06:20:53,063 [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 2023-10-24 06:20:53,063 [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 2023-10-24 06:20:53,063 [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 2023-10-24 06:20:53,063 [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 2023-10-24 06:20:53,063 [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 2023-10-24 06:20:53,063 [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 2023-10-24 06:20:53,063 [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 2023-10-24 06:20:53,064 [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 2023-10-24 06:20:53,064 [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 2023-10-24 06:20:53,064 [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 2023-10-24 06:20:53,064 [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 2023-10-24 06:20:53,064 [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 2023-10-24 06:20:53,064 [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 2023-10-24 06:20:53,064 [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 2023-10-24 06:20:53,064 [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 2023-10-24 06:20:53,064 [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 2023-10-24 06:20:53,064 [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 2023-10-24 06:20:53,064 [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 2023-10-24 06:20:53,064 [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 2023-10-24 06:20:53,064 [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 2023-10-24 06:20:53,064 [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 2023-10-24 06:20:53,065 [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 2023-10-24 06:20:53,065 [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 2023-10-24 06:20:53,065 [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 2023-10-24 06:20:53,065 [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 2023-10-24 06:20:53,065 [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 2023-10-24 06:20:53,065 [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 2023-10-24 06:20:53,065 [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 2023-10-24 06:20:53,065 [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 2023-10-24 06:20:53,065 [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 2023-10-24 06:20:53,065 [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 2023-10-24 06:20:53,065 [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 2023-10-24 06:20:53,065 [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 2023-10-24 06:20:53,065 [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 2023-10-24 06:20:53,066 [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 2023-10-24 06:20:53,066 [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 2023-10-24 06:20:53,066 [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 2023-10-24 06:20:53,066 [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 2023-10-24 06:20:53,066 [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 2023-10-24 06:20:53,066 [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 2023-10-24 06:20:53,066 [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 2023-10-24 06:20:53,066 [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 2023-10-24 06:20:53,066 [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 2023-10-24 06:20:53,066 [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 2023-10-24 06:20:53,067 [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 2023-10-24 06:20:53,067 [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 2023-10-24 06:20:53,067 [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 2023-10-24 06:20:53,067 [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 2023-10-24 06:20:53,067 [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 2023-10-24 06:20:53,067 [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 2023-10-24 06:20:53,067 [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 2023-10-24 06:20:53,067 [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 2023-10-24 06:20:53,067 [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 2023-10-24 06:20:53,067 [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 2023-10-24 06:20:53,067 [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 2023-10-24 06:20:53,067 [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 2023-10-24 06:20:53,067 [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 2023-10-24 06:20:53,067 [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 2023-10-24 06:20:53,068 [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 2023-10-24 06:20:53,068 [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 2023-10-24 06:20:53,068 [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 2023-10-24 06:20:53,068 [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 2023-10-24 06:20:53,068 [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 2023-10-24 06:20:53,068 [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 2023-10-24 06:20:53,068 [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 2023-10-24 06:20:53,068 [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 2023-10-24 06:20:53,068 [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 2023-10-24 06:20:53,068 [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 2023-10-24 06:20:53,068 [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 2023-10-24 06:20:53,068 [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 2023-10-24 06:20:53,068 [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 2023-10-24 06:20:53,068 [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 2023-10-24 06:20:53,069 [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 2023-10-24 06:20:53,069 [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 2023-10-24 06:20:53,069 [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 2023-10-24 06:20:53,069 [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 2023-10-24 06:20:53,069 [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 2023-10-24 06:20:53,069 [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 2023-10-24 06:20:53,069 [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 2023-10-24 06:20:53,069 [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 2023-10-24 06:20:53,069 [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 2023-10-24 06:20:53,069 [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 2023-10-24 06:20:53,069 [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 2023-10-24 06:20:53,069 [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 2023-10-24 06:20:53,069 [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 2023-10-24 06:20:53,069 [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 2023-10-24 06:20:53,069 [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 2023-10-24 06:20:53,070 [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 2023-10-24 06:20:53,070 [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 2023-10-24 06:20:53,070 [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 2023-10-24 06:20:53,070 [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 2023-10-24 06:20:53,070 [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 2023-10-24 06:20:53,070 [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 2023-10-24 06:20:53,070 [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 2023-10-24 06:20:53,070 [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 2023-10-24 06:20:53,070 [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 2023-10-24 06:20:53,070 [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 2023-10-24 06:20:53,070 [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 2023-10-24 06:20:53,070 [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 2023-10-24 06:20:53,070 [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 2023-10-24 06:20:53,071 [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 2023-10-24 06:20:53,071 [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 2023-10-24 06:20:53,071 [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 2023-10-24 06:20:53,071 [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 2023-10-24 06:20:53,071 [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 2023-10-24 06:20:53,071 [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 2023-10-24 06:20:53,071 [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 2023-10-24 06:20:53,071 [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 2023-10-24 06:20:53,071 [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 2023-10-24 06:20:53,071 [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 2023-10-24 06:20:53,071 [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 2023-10-24 06:20:53,071 [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 2023-10-24 06:20:53,071 [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 2023-10-24 06:20:53,071 [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 2023-10-24 06:20:53,072 [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 2023-10-24 06:20:53,072 [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 2023-10-24 06:20:53,072 [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 2023-10-24 06:20:53,072 [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 2023-10-24 06:20:53,072 [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 2023-10-24 06:20:53,072 [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 2023-10-24 06:20:53,072 [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 2023-10-24 06:20:53,072 [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 2023-10-24 06:20:53,072 [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 2023-10-24 06:20:53,072 [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 2023-10-24 06:20:53,072 [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 2023-10-24 06:20:53,072 [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 2023-10-24 06:20:53,072 [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 2023-10-24 06:20:53,072 [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 2023-10-24 06:20:53,073 [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 2023-10-24 06:20:53,073 [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 2023-10-24 06:20:53,073 [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 2023-10-24 06:20:53,073 [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 2023-10-24 06:20:53,073 [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 2023-10-24 06:20:53,073 [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 2023-10-24 06:20:53,073 [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 2023-10-24 06:20:53,073 [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 2023-10-24 06:20:53,073 [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 2023-10-24 06:20:53,073 [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 2023-10-24 06:20:53,073 [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 2023-10-24 06:20:53,073 [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 2023-10-24 06:20:53,073 [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 2023-10-24 06:20:53,073 [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 2023-10-24 06:20:53,073 [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 2023-10-24 06:20:53,074 [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 2023-10-24 06:20:53,074 [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 2023-10-24 06:20:53,074 [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 2023-10-24 06:20:53,074 [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 2023-10-24 06:20:53,074 [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 2023-10-24 06:20:53,074 [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 2023-10-24 06:20:53,074 [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 2023-10-24 06:20:53,074 [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 2023-10-24 06:20:53,074 [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 2023-10-24 06:20:53,074 [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 2023-10-24 06:20:53,074 [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 2023-10-24 06:20:53,074 [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 2023-10-24 06:20:53,074 [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 2023-10-24 06:20:53,075 [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 2023-10-24 06:20:53,075 [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 2023-10-24 06:20:53,075 [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 2023-10-24 06:20:53,075 [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 2023-10-24 06:20:53,075 [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 2023-10-24 06:20:53,075 [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 2023-10-24 06:20:53,075 [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 2023-10-24 06:20:53,076 [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 2023-10-24 06:20:53,076 [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 2023-10-24 06:20:53,076 [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 2023-10-24 06:20:53,076 [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 2023-10-24 06:20:53,076 [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 2023-10-24 06:20:53,076 [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 2023-10-24 06:20:53,076 [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 2023-10-24 06:20:53,077 [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 2023-10-24 06:20:53,077 [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 2023-10-24 06:20:53,077 [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 2023-10-24 06:20:53,077 [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 2023-10-24 06:20:53,077 [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 2023-10-24 06:20:53,077 [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 2023-10-24 06:20:53,077 [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 2023-10-24 06:20:53,078 [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 2023-10-24 06:20:53,078 [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 2023-10-24 06:20:53,078 [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 2023-10-24 06:20:53,078 [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 2023-10-24 06:20:53,078 [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 2023-10-24 06:20:53,078 [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 2023-10-24 06:20:53,078 [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 2023-10-24 06:20:53,079 [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 2023-10-24 06:20:53,079 [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 2023-10-24 06:20:53,079 [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 2023-10-24 06:20:53,079 [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 2023-10-24 06:20:53,079 [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 2023-10-24 06:20:53,080 [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 2023-10-24 06:20:53,080 [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 2023-10-24 06:20:53,080 [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 2023-10-24 06:20:53,080 [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 2023-10-24 06:20:53,080 [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 2023-10-24 06:20:53,081 [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 2023-10-24 06:20:53,081 [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 2023-10-24 06:20:53,081 [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 2023-10-24 06:20:53,081 [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 2023-10-24 06:20:53,081 [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 2023-10-24 06:20:53,081 [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 2023-10-24 06:20:53,081 [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 2023-10-24 06:20:53,082 [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 2023-10-24 06:20:53,082 [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 2023-10-24 06:20:53,082 [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 2023-10-24 06:20:53,082 [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 2023-10-24 06:20:53,082 [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 2023-10-24 06:20:53,083 [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 2023-10-24 06:20:53,083 [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 2023-10-24 06:20:53,083 [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 2023-10-24 06:20:53,083 [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 2023-10-24 06:20:53,083 [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 2023-10-24 06:20:53,083 [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 2023-10-24 06:20:53,084 [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 2023-10-24 06:20:53,084 [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 2023-10-24 06:20:53,084 [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 2023-10-24 06:20:53,084 [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 2023-10-24 06:20:53,084 [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 2023-10-24 06:20:53,084 [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 2023-10-24 06:20:53,084 [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 2023-10-24 06:20:53,084 [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 2023-10-24 06:20:53,085 [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 2023-10-24 06:20:53,085 [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 2023-10-24 06:20:53,085 [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 2023-10-24 06:20:53,085 [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 2023-10-24 06:20:53,085 [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 2023-10-24 06:20:53,085 [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 2023-10-24 06:20:53,085 [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 2023-10-24 06:20:53,086 [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 2023-10-24 06:20:53,086 [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 2023-10-24 06:20:53,086 [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 2023-10-24 06:20:53,086 [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 2023-10-24 06:20:53,086 [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 2023-10-24 06:20:53,086 [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 2023-10-24 06:20:53,086 [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 2023-10-24 06:20:53,087 [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 2023-10-24 06:20:53,087 [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 2023-10-24 06:20:53,087 [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 2023-10-24 06:20:53,087 [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 2023-10-24 06:20:53,087 [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 2023-10-24 06:20:53,087 [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 2023-10-24 06:20:53,088 [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 2023-10-24 06:20:53,088 [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 2023-10-24 06:20:53,088 [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 2023-10-24 06:20:53,088 [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 2023-10-24 06:20:53,088 [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 2023-10-24 06:20:53,088 [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 2023-10-24 06:20:53,088 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[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 2023-10-24 06:20:53,092 [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 2023-10-24 06:20:53,092 [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 2023-10-24 06:20:53,092 [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 2023-10-24 06:20:53,092 [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 2023-10-24 06:20:53,092 [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 2023-10-24 06:20:53,092 [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 2023-10-24 06:20:53,093 [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 2023-10-24 06:20:53,093 [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 2023-10-24 06:20:53,093 [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 2023-10-24 06:20:53,093 [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 2023-10-24 06:20:53,093 [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 2023-10-24 06:20:53,093 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: 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06:20:53,106 [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 2023-10-24 06:20:53,106 [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 2023-10-24 06:20:53,106 [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/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 2023-10-24 06:20:53,106 [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__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 2023-10-24 06:20:53,108 [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 2023-10-24 06:20:53,108 [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.... 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panel.... +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:53,117 [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 2023-10-24 06:20:53,117 [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 2023-10-24 06:20:53,117 [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 2023-10-24 06:20:53,117 [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 2023-10-24 06:20:53,118 [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 2023-10-24 06:20:53,118 [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 2023-10-24 06:20:53,118 [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 2023-10-24 06:20:53,118 [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 2023-10-24 06:20:53,118 [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 2023-10-24 06:20:53,118 [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 2023-10-24 06:20:53,118 [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 2023-10-24 06:20:53,118 [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 2023-10-24 06:20:53,118 [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 2023-10-24 06:20:53,118 [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 2023-10-24 06:20:53,118 [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 2023-10-24 06:20:53,118 [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 2023-10-24 06:20:53,119 [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 2023-10-24 06:20:53,119 [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 2023-10-24 06:20:53,119 [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 2023-10-24 06:20:53,119 [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 2023-10-24 06:20:53,119 [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 2023-10-24 06:20:53,119 [pN:job_handler_0,p:8,tN:MainThread] Loading EDAM tool panel finished (79.686 ms) +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:53,123 [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 2023-10-24 06:20:53,124 [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 2023-10-24 06:20:53,124 [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 2023-10-24 06:20:53,124 [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 2023-10-24 06:20:53,124 [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 2023-10-24 06:20:53,124 [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 2023-10-24 06:20:53,124 [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 2023-10-24 06:20:53,124 [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 2023-10-24 06:20:53,124 [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 2023-10-24 06:20:53,125 [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 2023-10-24 06:20:53,125 [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 2023-10-24 06:20:53,125 [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 2023-10-24 06:20:53,125 [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 2023-10-24 06:20:53,125 [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 2023-10-24 06:20:53,126 [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 2023-10-24 06:20:53,126 [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 2023-10-24 06:20:53,126 [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 2023-10-24 06:20:53,126 [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 2023-10-24 06:20:53,126 [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 2023-10-24 06:20:53,126 [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 2023-10-24 06:20:53,126 [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 2023-10-24 06:20:53,126 [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 2023-10-24 06:20:53,126 [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 2023-10-24 06:20:53,126 [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 2023-10-24 06:20:53,126 [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 2023-10-24 06:20:53,126 [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 2023-10-24 06:20:53,127 [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 2023-10-24 06:20:53,127 [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 2023-10-24 06:20:53,127 [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 2023-10-24 06:20:53,127 [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 2023-10-24 06:20:53,127 [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 2023-10-24 06:20:53,127 [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 2023-10-24 06:20:53,127 [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 2023-10-24 06:20:53,127 [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 2023-10-24 06:20:53,127 [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 2023-10-24 06:20:53,127 [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 2023-10-24 06:20:53,127 [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 2023-10-24 06:20:53,128 [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 2023-10-24 06:20:53,128 [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 2023-10-24 06:20:53,128 [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 2023-10-24 06:20:53,128 [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 2023-10-24 06:20:53,128 [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 2023-10-24 06:20:53,128 [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 2023-10-24 06:20:53,128 [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 2023-10-24 06:20:53,128 [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 2023-10-24 06:20:53,129 [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 2023-10-24 06:20:53,129 [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 2023-10-24 06:20:53,129 [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 2023-10-24 06:20:53,129 [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 2023-10-24 06:20:53,129 [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 2023-10-24 06:20:53,129 [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 2023-10-24 06:20:53,129 [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 2023-10-24 06:20:53,129 [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 2023-10-24 06:20:53,129 [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 2023-10-24 06:20:53,129 [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 2023-10-24 06:20:53,129 [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 2023-10-24 06:20:53,129 [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 2023-10-24 06:20:53,129 [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 2023-10-24 06:20:53,130 [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 2023-10-24 06:20:53,130 [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 2023-10-24 06:20:53,130 [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 2023-10-24 06:20:53,130 [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 2023-10-24 06:20:53,130 [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 2023-10-24 06:20:53,130 [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 2023-10-24 06:20:53,130 [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 2023-10-24 06:20:53,130 [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 2023-10-24 06:20:53,130 [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 2023-10-24 06:20:53,130 [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 2023-10-24 06:20:53,130 [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 2023-10-24 06:20:53,130 [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 2023-10-24 06:20:53,130 [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 2023-10-24 06:20:53,130 [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 2023-10-24 06:20:53,130 [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 2023-10-24 06:20:53,131 [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 2023-10-24 06:20:53,131 [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 2023-10-24 06:20:53,131 [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 2023-10-24 06:20:53,131 [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 2023-10-24 06:20:53,131 [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 2023-10-24 06:20:53,131 [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 2023-10-24 06:20:53,131 [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 2023-10-24 06:20:53,131 [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 2023-10-24 06:20:53,131 [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 2023-10-24 06:20:53,131 [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 2023-10-24 06:20:53,131 [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 2023-10-24 06:20:53,131 [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 2023-10-24 06:20:53,131 [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 2023-10-24 06:20:53,131 [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 2023-10-24 06:20:53,131 [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 2023-10-24 06:20:53,131 [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 2023-10-24 06:20:53,132 [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 2023-10-24 06:20:53,132 [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 2023-10-24 06:20:53,132 [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 2023-10-24 06:20:53,132 [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 2023-10-24 06:20:53,132 [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 2023-10-24 06:20:53,132 [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 2023-10-24 06:20:53,132 [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 2023-10-24 06:20:53,132 [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 2023-10-24 06:20:53,132 [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 2023-10-24 06:20:53,132 [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 2023-10-24 06:20:53,132 [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 2023-10-24 06:20:53,132 [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 2023-10-24 06:20:53,132 [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 2023-10-24 06:20:53,132 [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 2023-10-24 06:20:53,132 [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 2023-10-24 06:20:53,133 [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 2023-10-24 06:20:53,133 [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 2023-10-24 06:20:53,133 [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 2023-10-24 06:20:53,133 [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 2023-10-24 06:20:53,133 [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 2023-10-24 06:20:53,133 [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 2023-10-24 06:20:53,133 [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 2023-10-24 06:20:53,133 [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 2023-10-24 06:20:53,133 [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 2023-10-24 06:20:53,133 [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 2023-10-24 06:20:53,133 [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 2023-10-24 06:20:53,133 [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 2023-10-24 06:20:53,133 [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 2023-10-24 06:20:53,134 [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 2023-10-24 06:20:53,134 [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 2023-10-24 06:20:53,134 [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 2023-10-24 06:20:53,134 [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 2023-10-24 06:20:53,134 [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 2023-10-24 06:20:53,134 [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 2023-10-24 06:20:53,134 [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 2023-10-24 06:20:53,134 [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 2023-10-24 06:20:53,134 [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 2023-10-24 06:20:53,134 [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 2023-10-24 06:20:53,134 [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 2023-10-24 06:20:53,134 [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 2023-10-24 06:20:53,134 [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 2023-10-24 06:20:53,134 [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 2023-10-24 06:20:53,135 [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 2023-10-24 06:20:53,135 [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 2023-10-24 06:20:53,135 [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 2023-10-24 06:20:53,135 [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 2023-10-24 06:20:53,135 [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 2023-10-24 06:20:53,135 [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 2023-10-24 06:20:53,135 [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 2023-10-24 06:20:53,135 [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 2023-10-24 06:20:53,135 [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 2023-10-24 06:20:53,135 [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 2023-10-24 06:20:53,135 [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 2023-10-24 06:20:53,135 [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 2023-10-24 06:20:53,135 [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 2023-10-24 06:20:53,135 [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 2023-10-24 06:20:53,135 [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 2023-10-24 06:20:53,136 [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 2023-10-24 06:20:53,136 [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 2023-10-24 06:20:53,136 [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 2023-10-24 06:20:53,136 [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 2023-10-24 06:20:53,136 [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 2023-10-24 06:20:53,136 [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 2023-10-24 06:20:53,136 [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 2023-10-24 06:20:53,136 [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 2023-10-24 06:20:53,136 [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 2023-10-24 06:20:53,136 [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 2023-10-24 06:20:53,136 [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 2023-10-24 06:20:53,136 [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 2023-10-24 06:20:53,136 [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 2023-10-24 06:20:53,137 [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 2023-10-24 06:20:53,137 [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 2023-10-24 06:20:53,137 [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 2023-10-24 06:20:53,137 [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 2023-10-24 06:20:53,137 [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 2023-10-24 06:20:53,137 [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 2023-10-24 06:20:53,137 [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 2023-10-24 06:20:53,137 [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 2023-10-24 06:20:53,137 [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 2023-10-24 06:20:53,137 [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 2023-10-24 06:20:53,137 [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 2023-10-24 06:20:53,137 [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 2023-10-24 06:20:53,138 [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 2023-10-24 06:20:53,138 [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 2023-10-24 06:20:53,138 [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 2023-10-24 06:20:53,138 [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 2023-10-24 06:20:53,138 [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 2023-10-24 06:20:53,138 [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 2023-10-24 06:20:53,138 [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 2023-10-24 06:20:53,138 [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 2023-10-24 06:20:53,138 [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 2023-10-24 06:20:53,138 [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 2023-10-24 06:20:53,139 [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 2023-10-24 06:20:53,139 [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 2023-10-24 06:20:53,139 [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 2023-10-24 06:20:53,139 [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 2023-10-24 06:20:53,139 [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 2023-10-24 06:20:53,139 [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 2023-10-24 06:20:53,139 [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 2023-10-24 06:20:53,139 [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 2023-10-24 06:20:53,139 [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 2023-10-24 06:20:53,139 [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 2023-10-24 06:20:53,140 [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 2023-10-24 06:20:53,140 [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 2023-10-24 06:20:53,140 [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 2023-10-24 06:20:53,140 [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 2023-10-24 06:20:53,140 [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 2023-10-24 06:20:53,140 [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 2023-10-24 06:20:53,140 [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 2023-10-24 06:20:53,140 [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 2023-10-24 06:20:53,140 [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 2023-10-24 06:20:53,140 [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 2023-10-24 06:20:53,140 [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 2023-10-24 06:20:53,140 [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 2023-10-24 06:20:53,141 [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 2023-10-24 06:20:53,141 [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 2023-10-24 06:20:53,141 [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 2023-10-24 06:20:53,141 [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 2023-10-24 06:20:53,141 [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 2023-10-24 06:20:53,141 [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 2023-10-24 06:20:53,141 [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 2023-10-24 06:20:53,141 [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 2023-10-24 06:20:53,141 [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 2023-10-24 06:20:53,141 [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 2023-10-24 06:20:53,141 [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 2023-10-24 06:20:53,141 [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 2023-10-24 06:20:53,141 [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 2023-10-24 06:20:53,141 [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 2023-10-24 06:20:53,142 [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 2023-10-24 06:20:53,142 [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 2023-10-24 06:20:53,142 [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 2023-10-24 06:20:53,142 [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 2023-10-24 06:20:53,142 [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 2023-10-24 06:20:53,142 [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 2023-10-24 06:20:53,142 [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 2023-10-24 06:20:53,142 [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 2023-10-24 06:20:53,142 [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 2023-10-24 06:20:53,142 [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 2023-10-24 06:20:53,142 [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 2023-10-24 06:20:53,142 [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 2023-10-24 06:20:53,143 [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 2023-10-24 06:20:53,143 [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 2023-10-24 06:20:53,143 [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 2023-10-24 06:20:53,143 [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 2023-10-24 06:20:53,143 [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 2023-10-24 06:20:53,143 [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 2023-10-24 06:20:53,143 [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 2023-10-24 06:20:53,143 [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 2023-10-24 06:20:53,143 [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 2023-10-24 06:20:53,143 [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 2023-10-24 06:20:53,143 [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 2023-10-24 06:20:53,143 [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 2023-10-24 06:20:53,144 [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 2023-10-24 06:20:53,144 [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 2023-10-24 06:20:53,144 [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 2023-10-24 06:20:53,144 [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 2023-10-24 06:20:53,144 [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 2023-10-24 06:20:53,144 [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 2023-10-24 06:20:53,144 [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 2023-10-24 06:20:53,144 [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 2023-10-24 06:20:53,144 [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 2023-10-24 06:20:53,144 [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 2023-10-24 06:20:53,144 [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 2023-10-24 06:20:53,144 [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 2023-10-24 06:20:53,144 [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 2023-10-24 06:20:53,145 [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 2023-10-24 06:20:53,145 [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 2023-10-24 06:20:53,145 [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 2023-10-24 06:20:53,145 [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 2023-10-24 06:20:53,145 [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 2023-10-24 06:20:53,145 [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 2023-10-24 06:20:53,145 [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 2023-10-24 06:20:53,145 [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 2023-10-24 06:20:53,145 [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 2023-10-24 06:20:53,145 [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 2023-10-24 06:20:53,145 [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 2023-10-24 06:20:53,145 [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 2023-10-24 06:20:53,145 [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 2023-10-24 06:20:53,146 [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 2023-10-24 06:20:53,146 [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 2023-10-24 06:20:53,146 [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 2023-10-24 06:20:53,146 [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 2023-10-24 06:20:53,146 [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 2023-10-24 06:20:53,146 [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 2023-10-24 06:20:53,146 [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 2023-10-24 06:20:53,146 [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 2023-10-24 06:20:53,146 [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 2023-10-24 06:20:53,146 [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 2023-10-24 06:20:53,146 [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 2023-10-24 06:20:53,147 [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 2023-10-24 06:20:53,147 [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 2023-10-24 06:20:53,147 [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 2023-10-24 06:20:53,147 [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 2023-10-24 06:20:53,147 [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 2023-10-24 06:20:53,147 [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 2023-10-24 06:20:53,147 [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 2023-10-24 06:20:53,147 [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 2023-10-24 06:20:53,147 [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 2023-10-24 06:20:53,147 [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 2023-10-24 06:20:53,147 [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 2023-10-24 06:20:53,147 [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 2023-10-24 06:20:53,147 [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 2023-10-24 06:20:53,148 [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 2023-10-24 06:20:53,148 [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 2023-10-24 06:20:53,148 [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 2023-10-24 06:20:53,148 [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 2023-10-24 06:20:53,148 [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 2023-10-24 06:20:53,148 [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 2023-10-24 06:20:53,148 [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 2023-10-24 06:20:53,148 [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 2023-10-24 06:20:53,148 [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 2023-10-24 06:20:53,148 [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 2023-10-24 06:20:53,148 [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 2023-10-24 06:20:53,148 [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 2023-10-24 06:20:53,148 [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 2023-10-24 06:20:53,148 [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 2023-10-24 06:20:53,149 [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 2023-10-24 06:20:53,149 [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 2023-10-24 06:20:53,149 [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 2023-10-24 06:20:53,149 [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 2023-10-24 06:20:53,149 [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 2023-10-24 06:20:53,149 [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 2023-10-24 06:20:53,149 [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 2023-10-24 06:20:53,149 [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 2023-10-24 06:20:53,149 [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 2023-10-24 06:20:53,149 [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 2023-10-24 06:20:53,149 [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 2023-10-24 06:20:53,149 [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 2023-10-24 06:20:53,149 [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 2023-10-24 06:20:53,149 [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 2023-10-24 06:20:53,150 [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 2023-10-24 06:20:53,150 [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 2023-10-24 06:20:53,150 [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 2023-10-24 06:20:53,150 [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 2023-10-24 06:20:53,150 [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 2023-10-24 06:20:53,150 [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 2023-10-24 06:20:53,150 [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 2023-10-24 06:20:53,150 [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 2023-10-24 06:20:53,150 [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 2023-10-24 06:20:53,150 [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 2023-10-24 06:20:53,150 [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 2023-10-24 06:20:53,150 [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 2023-10-24 06:20:53,150 [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 2023-10-24 06:20:53,150 [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 2023-10-24 06:20:53,151 [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 2023-10-24 06:20:53,151 [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 2023-10-24 06:20:53,151 [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 2023-10-24 06:20:53,151 [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 2023-10-24 06:20:53,151 [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 2023-10-24 06:20:53,151 [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 2023-10-24 06:20:53,151 [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 2023-10-24 06:20:53,151 [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 2023-10-24 06:20:53,151 [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 2023-10-24 06:20:53,151 [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 2023-10-24 06:20:53,151 [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 2023-10-24 06:20:53,151 [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 2023-10-24 06:20:53,151 [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 2023-10-24 06:20:53,152 [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 2023-10-24 06:20:53,152 [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 2023-10-24 06:20:53,152 [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 2023-10-24 06:20:53,152 [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 2023-10-24 06:20:53,152 [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 2023-10-24 06:20:53,152 [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 2023-10-24 06:20:53,152 [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 2023-10-24 06:20:53,152 [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 2023-10-24 06:20:53,152 [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 2023-10-24 06:20:53,152 [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 2023-10-24 06:20:53,152 [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 2023-10-24 06:20:53,152 [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 2023-10-24 06:20:53,152 [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 2023-10-24 06:20:53,152 [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 2023-10-24 06:20:53,153 [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 2023-10-24 06:20:53,153 [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 2023-10-24 06:20:53,153 [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 2023-10-24 06:20:53,153 [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 2023-10-24 06:20:53,153 [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 2023-10-24 06:20:53,153 [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 2023-10-24 06:20:53,153 [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 2023-10-24 06:20:53,153 [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 2023-10-24 06:20:53,153 [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 2023-10-24 06:20:53,154 [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 2023-10-24 06:20:53,154 [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 2023-10-24 06:20:53,154 [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 2023-10-24 06:20:53,154 [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 2023-10-24 06:20:53,154 [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 2023-10-24 06:20:53,154 [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 2023-10-24 06:20:53,154 [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 2023-10-24 06:20:53,154 [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 2023-10-24 06:20:53,154 [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 2023-10-24 06:20:53,154 [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 2023-10-24 06:20:53,155 [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 2023-10-24 06:20:53,155 [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 2023-10-24 06:20:53,155 [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 2023-10-24 06:20:53,155 [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 2023-10-24 06:20:53,155 [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 2023-10-24 06:20:53,155 [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 2023-10-24 06:20:53,155 [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 2023-10-24 06:20:53,155 [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 2023-10-24 06:20:53,155 [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 2023-10-24 06:20:53,156 [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 2023-10-24 06:20:53,156 [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 2023-10-24 06:20:53,156 [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 2023-10-24 06:20:53,156 [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 2023-10-24 06:20:53,156 [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 2023-10-24 06:20:53,156 [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 2023-10-24 06:20:53,156 [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 2023-10-24 06:20:53,156 [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 2023-10-24 06:20:53,157 [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 2023-10-24 06:20:53,157 [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 2023-10-24 06:20:53,157 [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 2023-10-24 06:20:53,157 [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 2023-10-24 06:20:53,157 [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 2023-10-24 06:20:53,157 [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 2023-10-24 06:20:53,158 [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 2023-10-24 06:20:53,158 [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 2023-10-24 06:20:53,158 [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 2023-10-24 06:20:53,158 [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 2023-10-24 06:20:53,158 [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 2023-10-24 06:20:53,158 [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 2023-10-24 06:20:53,158 [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 2023-10-24 06:20:53,158 [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 2023-10-24 06:20:53,159 [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 2023-10-24 06:20:53,159 [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 2023-10-24 06:20:53,159 [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 2023-10-24 06:20:53,159 [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 2023-10-24 06:20:53,159 [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 2023-10-24 06:20:53,159 [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 2023-10-24 06:20:53,159 [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 2023-10-24 06:20:53,159 [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 2023-10-24 06:20:53,160 [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 2023-10-24 06:20:53,160 [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 2023-10-24 06:20:53,160 [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 2023-10-24 06:20:53,160 [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 2023-10-24 06:20:53,160 [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 2023-10-24 06:20:53,160 [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 2023-10-24 06:20:53,160 [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 2023-10-24 06:20:53,161 [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 2023-10-24 06:20:53,161 [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 2023-10-24 06:20:53,161 [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 2023-10-24 06:20:53,161 [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 2023-10-24 06:20:53,161 [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 2023-10-24 06:20:53,162 [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 2023-10-24 06:20:53,162 [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 2023-10-24 06:20:53,162 [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 2023-10-24 06:20:53,162 [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 2023-10-24 06:20:53,162 [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 2023-10-24 06:20:53,162 [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 2023-10-24 06:20:53,162 [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 2023-10-24 06:20:53,162 [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 2023-10-24 06:20:53,162 [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 2023-10-24 06:20:53,162 [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 2023-10-24 06:20:53,162 [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 2023-10-24 06:20:53,163 [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 2023-10-24 06:20:53,163 [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 2023-10-24 06:20:53,163 [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 2023-10-24 06:20:53,163 [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 2023-10-24 06:20:53,163 [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 2023-10-24 06:20:53,163 [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 2023-10-24 06:20:53,163 [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 2023-10-24 06:20:53,163 [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 2023-10-24 06:20:53,163 [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 2023-10-24 06:20:53,163 [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 2023-10-24 06:20:53,164 [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 2023-10-24 06:20:53,164 [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 2023-10-24 06:20:53,164 [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 2023-10-24 06:20:53,164 [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 2023-10-24 06:20:53,164 [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 2023-10-24 06:20:53,164 [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 2023-10-24 06:20:53,164 [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 2023-10-24 06:20:53,164 [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 2023-10-24 06:20:53,164 [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 2023-10-24 06:20:53,164 [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 2023-10-24 06:20:53,165 [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 2023-10-24 06:20:53,165 [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 2023-10-24 06:20:53,165 [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 2023-10-24 06:20:53,165 [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 2023-10-24 06:20:53,165 [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 2023-10-24 06:20:53,165 [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 2023-10-24 06:20:53,165 [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 2023-10-24 06:20:53,166 [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 2023-10-24 06:20:53,166 [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 2023-10-24 06:20:53,166 [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 2023-10-24 06:20:53,166 [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 2023-10-24 06:20:53,166 [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 2023-10-24 06:20:53,166 [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 2023-10-24 06:20:53,166 [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 2023-10-24 06:20:53,166 [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 2023-10-24 06:20:53,166 [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 2023-10-24 06:20:53,166 [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 2023-10-24 06:20:53,166 [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 2023-10-24 06:20:53,166 [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 2023-10-24 06:20:53,167 [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 2023-10-24 06:20:53,167 [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 2023-10-24 06:20:53,167 [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 2023-10-24 06:20:53,167 [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 2023-10-24 06:20:53,167 [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 2023-10-24 06:20:53,167 [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 2023-10-24 06:20:53,167 [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 2023-10-24 06:20:53,167 [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 2023-10-24 06:20:53,167 [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 2023-10-24 06:20:53,167 [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 2023-10-24 06:20:53,167 [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 2023-10-24 06:20:53,167 [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 2023-10-24 06:20:53,168 [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 2023-10-24 06:20:53,168 [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 2023-10-24 06:20:53,168 [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 2023-10-24 06:20:53,168 [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 2023-10-24 06:20:53,168 [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 2023-10-24 06:20:53,168 [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 2023-10-24 06:20:53,168 [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 2023-10-24 06:20:53,168 [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 2023-10-24 06:20:53,169 [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 2023-10-24 06:20:53,169 [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 2023-10-24 06:20:53,169 [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 2023-10-24 06:20:53,169 [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 2023-10-24 06:20:53,169 [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 2023-10-24 06:20:53,169 [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 2023-10-24 06:20:53,169 [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 2023-10-24 06:20:53,169 [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 2023-10-24 06:20:53,169 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+galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:53,177 [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 2023-10-24 06:20:53,177 [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 2023-10-24 06:20:53,177 [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 2023-10-24 06:20:53,177 [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 2023-10-24 06:20:53,177 [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 2023-10-24 06:20:53,177 [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 2023-10-24 06:20:53,177 [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 2023-10-24 06:20:53,177 [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 2023-10-24 06:20:53,178 [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 2023-10-24 06:20:53,178 [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 2023-10-24 06:20:53,178 [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 2023-10-24 06:20:53,178 [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: 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06:20:53,178 [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 2023-10-24 06:20:53,178 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__composition__tabulate/qiime2__composition__tabulate/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 2023-10-24 06:20:53,178 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__composition__ancom/qiime2__composition__ancom/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 2023-10-24 06:20:53,178 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: 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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 2023-10-24 06:20:53,180 [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 2023-10-24 06:20:53,180 [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 2023-10-24 06:20:53,180 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: 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DEBUG 2023-10-24 06:20:53,180 [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 2023-10-24 06:20:53,180 [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 2023-10-24 06:20:53,180 [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 2023-10-24 06:20:53,181 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: 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toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__vsearch__cluster_features_open_reference/qiime2__vsearch__cluster_features_open_reference/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 2023-10-24 06:20:53,190 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__vsearch__merge_pairs/qiime2__vsearch__merge_pairs/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 2023-10-24 06:20:53,190 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__vsearch__uchime_denovo/qiime2__vsearch__uchime_denovo/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 2023-10-24 06:20:53,190 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: 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+galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:53,191 [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 2023-10-24 06:20:53,191 [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 2023-10-24 06:20:53,191 [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 2023-10-24 06:20:53,191 [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 2023-10-24 06:20:53,191 [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 2023-10-24 06:20:53,191 [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 2023-10-24 06:20:53,192 [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 2023-10-24 06:20:53,192 [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 2023-10-24 06:20:53,192 [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 2023-10-24 06:20:53,192 [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 2023-10-24 06:20:53,192 [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 2023-10-24 06:20:53,192 [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 2023-10-24 06:20:53,192 [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 2023-10-24 06:20:53,192 [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/iuc/volcanoplot/volcanoplot/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:20:53,193 [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 2023-10-24 06:20:53,193 [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 2023-10-24 06:20:53,193 [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 2023-10-24 06:20:53,193 [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 2023-10-24 06:20:53,193 [pN:job_handler_0,p:8,tN:MainThread] Loading EDAM tool panel finished (73.870 ms) +galaxy.tool_util.toolbox.integrated_panel DEBUG 2023-10-24 06:20:53,193 [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 2023-10-24 06:20:53,212 [pN:job_handler_0,p:8,tN:MainThread] Conda not installed and auto-installation disabled. +galaxy.tool_util.deps.installable WARNING 2023-10-24 06:20:53,218 [pN:job_handler_0,p:8,tN:MainThread] Conda not installed and auto-installation disabled. +galaxy.tool_util.deps.containers DEBUG 2023-10-24 06:20:53,220 [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 2023-10-24 06:20:53,241 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'ucsc_bam' for datatype 'bam', inherit=False. +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,242 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'ensembl_bam' for datatype 'bam', inherit=False. +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,256 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igv_bam' for datatype 'bam', inherit=False. +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,257 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igb_bam' for datatype 'bam', inherit=False. +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,257 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'iobio_bam' for datatype 'bam', inherit=False. +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,258 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igb_bed' for datatype 'bed', inherit=False. +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,258 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igb_bedgraph' for datatype 'bedgraph', inherit=False. +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,261 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'ucsc_bigbed' for datatype 'bigbed', inherit=False. +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,261 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igb_bb' for datatype 'bigbed', inherit=False. +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,263 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'ucsc_bigwig' for datatype 'bigwig', inherit=False. +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,264 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igb_bigwig' for datatype 'bigwig', inherit=False. +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,264 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igv_bigwig' for datatype 'bigwig', inherit=False. +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,265 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'intermine_simple' for datatype 'intermine_tabular', inherit=False. +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,274 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igv_fasta' for datatype 'fasta', inherit=True. +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,276 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'ensembl_gff' for datatype 'gff', inherit=True. +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,285 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igv_gff' for datatype 'gff', inherit=True. +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,286 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igb_gtf' for datatype 'gtf', inherit=False. +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,288 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'ensembl_interval' for datatype 'interval', inherit=True. +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,290 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'gbrowse_interval_as_bed' for datatype 'interval', inherit=True. +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,291 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'rviewer_interval' for datatype 'interval', inherit=True. +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,300 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igv_interval_as_bed' for datatype 'interval', inherit=True. +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,301 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'avivator' for datatype 'ome.tiff', inherit=False. +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,301 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'q2view' for datatype 'qza', inherit=False. +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,302 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'q2view' for datatype 'qzv', inherit=False. +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,303 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'ucsc_maf_customtrack' for datatype 'mafcustomtrack', inherit=False. +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,305 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'ucsc_vcf' for datatype 'vcf', inherit=False. +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,315 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igv_vcf' for datatype 'vcf', inherit=False. +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,316 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'rviewer_vcf' for datatype 'vcf', inherit=True. +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,317 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'iobio_vcf' for datatype 'vcf', inherit=False. +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,317 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igb_wig' for datatype 'wig', inherit=False. +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,328 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igv_vcf' for datatype 'vcf_bgzip', inherit=False. +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,338 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igv_genbank' for datatype 'genbank', inherit=False. +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,339 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'biom_simple' for datatype 'biom1', inherit=False. +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,339 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'icn3d_simple' for datatype 'sdf', inherit=False. +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,340 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'icn3d_simple' for datatype 'mol2', inherit=False. +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,340 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'icn3d_simple' for datatype 'pdb', inherit=False. +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,340 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'ucsc_trackhub' for datatype 'trackhub', inherit=False. +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,341 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bed' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,341 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,341 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bed' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,341 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bed' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,341 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bedgraph' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,341 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedgraph' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,341 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bedgraph' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,341 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bedgraph' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,341 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bedstrict' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,341 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedstrict' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,341 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bedstrict' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,341 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bedstrict' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,341 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bed6' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,341 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed6' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,341 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bed6' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,341 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bed6' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,341 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bed12' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,341 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed12' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,341 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bed12' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,341 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bed12' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,341 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'probed' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,341 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'probed' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,341 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'probed' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,341 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'probed' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,342 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'chrint' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,342 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'chrint' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,342 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'chrint' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,342 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'chrint' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,342 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_fasta' to datatype 'fasta.gz' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,342 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_gff' to datatype 'gff3' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,342 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_gff' to datatype 'gff3' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,342 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_gff' to datatype 'gff3.gz' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,342 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_gff' to datatype 'gff3.gz' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,342 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_gff' to datatype 'gff3.bz2' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,342 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_gff' to datatype 'gff3.bz2' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,342 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_gff' to datatype 'gtf' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,342 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_gff' to datatype 'gtf' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,343 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'encodepeak' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,343 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'encodepeak' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,343 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'encodepeak' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,343 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'encodepeak' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,343 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_fasta' to datatype 'sequences' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,344 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'interval_tabix.gz' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,344 [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 2023-10-24 06:20:53,344 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'interval_tabix.gz' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,344 [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 2023-10-24 06:20:53,344 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'juicer_medium_tabix.gz' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,344 [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 2023-10-24 06:20:53,344 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'juicer_medium_tabix.gz' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,344 [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 2023-10-24 06:20:53,344 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bed_tabix.gz' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,344 [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 2023-10-24 06:20:53,344 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bed_tabix.gz' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,344 [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 2023-10-24 06:20:53,344 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'gff_tabix.gz' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,344 [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 2023-10-24 06:20:53,344 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'gff_tabix.gz' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,344 [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 2023-10-24 06:20:53,345 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_fasta' to datatype 'mothur.align' +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,348 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,349 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,350 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,351 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,352 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,353 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,354 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_Bam_Bai_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,356 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,357 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,358 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,359 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bam_to_coodinate_sorted_bam +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,360 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,361 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_cram_to_bam_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,362 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bed_to_gff_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,364 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,365 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,367 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,368 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bed_to_fli_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,369 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bedgraph_to_bigwig +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,370 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_len_to_linecount +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,370 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_parquet_to_csv +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,375 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: bigwigtowig +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,376 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,378 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,379 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,380 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: csv_to_tabular +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,381 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: tabular_to_csv +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,381 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_fasta_to_tabular +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,382 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_fasta_to_bowtie_base_index +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,383 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_fasta_to_bowtie_color_index +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,384 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_fasta_to_2bit +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,385 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_fasta_to_len +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,386 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_fasta_to_fai +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,387 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,388 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,389 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,390 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,391 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,392 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,394 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,395 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,396 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,397 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,398 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,399 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,400 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,401 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,402 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,404 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,405 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,405 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,406 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,408 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,408 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,410 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,411 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gff_to_bed_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,412 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gff_to_interval_index_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,413 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,414 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gff_to_fli_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,417 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,418 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,420 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,421 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,422 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,424 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gff_to_interval_index_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,425 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,426 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bed_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,427 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bedstrict_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,429 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bed6_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,430 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bed12_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,432 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,434 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,436 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,437 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_picard_interval_list_to_bed6 +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,438 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_tar_to_directory +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,440 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,441 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,443 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,444 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,445 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,447 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,448 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_maf_to_fasta_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,449 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_maf_to_interval_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,451 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,453 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,454 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,456 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,458 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,459 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_sam_to_unsorted_bam +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,460 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bam_to_coodinate_sorted_bam +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,462 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,463 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_sam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,464 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: tabular_to_dbnsfp +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,465 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: tabular_to_csv +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,467 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,468 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,469 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,470 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,472 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,473 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,475 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,476 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bcf_uncompressed_to_bcf +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,477 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bcf_uncompressed_to_bcf +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,478 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_wig_to_bigwig +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,479 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_wiggle_to_interval_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,481 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,482 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,483 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: lped2fpedconvert +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,485 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: lped2pbedconvert +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,485 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: pbed2lpedconvert +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,486 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: pbed2ldindepconvert +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,487 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,488 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,489 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_biom +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,491 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_biom +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,492 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,493 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,495 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,496 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_SMILES_to_MOL +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,497 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,498 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_smiles_to_smiles +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,500 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,501 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,503 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,504 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,505 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,507 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,508 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_inchi_to_mol +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,509 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,511 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,512 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,514 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,515 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,517 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,518 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,519 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,521 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,522 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,523 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_mol2_to_mol +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,525 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,526 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_cml_to_smiles +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,527 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,529 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,531 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,532 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_Pdb_to_Gro_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,533 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,534 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,535 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,536 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,537 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,538 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,539 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_Gro_to_Pdb_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,540 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_ref_to_seq_taxomony +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,540 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_neostorezip_to_neostore +galaxy.datatypes.registry DEBUG 2023-10-24 06:20:53,542 [pN:job_handler_0,p:8,tN:MainThread] Loaded external metadata tool: __SET_METADATA__ +galaxy.tools.special_tools DEBUG 2023-10-24 06:20:53,543 [pN:job_handler_0,p:8,tN:MainThread] Loaded history export tool: __EXPORT_HISTORY__ +galaxy.tools.special_tools DEBUG 2023-10-24 06:20:53,544 [pN:job_handler_0,p:8,tN:MainThread] Loaded history export to uri tool: __EXPORT_HISTORY_TO_URI__ +galaxy.tools.special_tools DEBUG 2023-10-24 06:20:53,545 [pN:job_handler_0,p:8,tN:MainThread] Loaded history import tool: __IMPORT_HISTORY__ +galaxy.tools.special_tools DEBUG 2023-10-24 06:20:53,546 [pN:job_handler_0,p:8,tN:MainThread] Loaded data fetch tool: __DATA_FETCH__ +sqlitedict DEBUG 2023-10-24 06:20:53,548 [pN:job_handler_0,p:8,tN:MainThread] closing SqliteDict(/cvmfs/cloud.galaxyproject.org/var/tool_cache/cache.sqlite) +sqlitedict.SqliteMultithread DEBUG 2023-10-24 06:20:53,548 [pN:job_handler_0,p:8,tN:Thread-2] received: --close--, send: --no more-- +sqlitedict DEBUG 2023-10-24 06:20:53,549 [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 2023-10-24 06:20:53,554 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: PCA_3Dplot +galaxy.visualization.plugins.registry INFO 2023-10-24 06:20:53,554 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: aequatus +galaxy.visualization.plugins.registry INFO 2023-10-24 06:20:53,555 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: annotate_image +galaxy.visualization.plugins.config_parser INFO 2023-10-24 06:20:53,556 [pN:job_handler_0,p:8,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2023-10-24 06:20:53,556 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: chiraviz +galaxy.visualization.plugins.config_parser INFO 2023-10-24 06:20:53,556 [pN:job_handler_0,p:8,tN:MainThread] Visualizations plugin disabled: Circster. Skipping... +galaxy.visualization.plugins.config_parser INFO 2023-10-24 06:20:53,557 [pN:job_handler_0,p:8,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2023-10-24 06:20:53,557 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: csg +galaxy.visualization.plugins.registry INFO 2023-10-24 06:20:53,558 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: cytoscape +galaxy.visualization.plugins.registry INFO 2023-10-24 06:20:53,559 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: drawrna +galaxy.visualization.plugins.registry INFO 2023-10-24 06:20:53,559 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: editor +galaxy.visualization.plugins.registry INFO 2023-10-24 06:20:53,560 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: example +galaxy.visualization.plugins.config_parser INFO 2023-10-24 06:20:53,561 [pN:job_handler_0,p:8,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2023-10-24 06:20:53,561 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: fits_image_viewer +galaxy.visualization.plugins.config_parser INFO 2023-10-24 06:20:53,561 [pN:job_handler_0,p:8,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2023-10-24 06:20:53,562 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: graphviz +galaxy.visualization.plugins.registry INFO 2023-10-24 06:20:53,562 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: h5web +galaxy.visualization.plugins.registry INFO 2023-10-24 06:20:53,565 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: heatmap_cluster +galaxy.visualization.plugins.registry INFO 2023-10-24 06:20:53,568 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: heatmap_default +galaxy.visualization.plugins.config_parser INFO 2023-10-24 06:20:53,569 [pN:job_handler_0,p:8,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2023-10-24 06:20:53,569 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: hivtrace +galaxy.visualization.plugins.config_parser INFO 2023-10-24 06:20:53,570 [pN:job_handler_0,p:8,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2023-10-24 06:20:53,570 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: hyphyvision +galaxy.visualization.plugins.registry INFO 2023-10-24 06:20:53,572 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_bar +galaxy.visualization.plugins.registry INFO 2023-10-24 06:20:53,574 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_box +galaxy.visualization.plugins.registry INFO 2023-10-24 06:20:53,576 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_histogram +galaxy.visualization.plugins.registry INFO 2023-10-24 06:20:53,578 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_line +galaxy.visualization.plugins.registry INFO 2023-10-24 06:20:53,580 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_scatter +galaxy.visualization.plugins.config_parser INFO 2023-10-24 06:20:53,581 [pN:job_handler_0,p:8,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2023-10-24 06:20:53,582 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: audio_player +galaxy.visualization.plugins.config_parser INFO 2023-10-24 06:20:53,582 [pN:job_handler_0,p:8,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2023-10-24 06:20:53,582 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: video_player +galaxy.visualization.plugins.registry INFO 2023-10-24 06:20:53,583 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: msa +galaxy.visualization.plugins.config_parser INFO 2023-10-24 06:20:53,583 [pN:job_handler_0,p:8,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2023-10-24 06:20:53,584 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: mvpapp +galaxy.visualization.plugins.registry INFO 2023-10-24 06:20:53,585 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: ngl +galaxy.visualization.plugins.registry INFO 2023-10-24 06:20:53,585 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nora +galaxy.visualization.plugins.registry INFO 2023-10-24 06:20:53,590 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_bar +galaxy.visualization.plugins.registry INFO 2023-10-24 06:20:53,592 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_bar_stacked +galaxy.visualization.plugins.registry INFO 2023-10-24 06:20:53,593 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_histogram +galaxy.visualization.plugins.registry INFO 2023-10-24 06:20:53,595 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_histogram_discrete +galaxy.visualization.plugins.registry INFO 2023-10-24 06:20:53,597 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_horizontal +galaxy.visualization.plugins.registry INFO 2023-10-24 06:20:53,599 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_horizontal_stacked +galaxy.visualization.plugins.registry INFO 2023-10-24 06:20:53,601 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_line +galaxy.visualization.plugins.registry INFO 2023-10-24 06:20:53,603 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_line_focus +galaxy.visualization.plugins.registry INFO 2023-10-24 06:20:53,605 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_pie +galaxy.visualization.plugins.registry INFO 2023-10-24 06:20:53,606 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_scatter +galaxy.visualization.plugins.registry INFO 2023-10-24 06:20:53,608 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_stackedarea +galaxy.visualization.plugins.registry INFO 2023-10-24 06:20:53,610 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_stackedarea_full +galaxy.visualization.plugins.registry INFO 2023-10-24 06:20:53,612 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_stackedarea_stream +galaxy.visualization.plugins.registry INFO 2023-10-24 06:20:53,613 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: openlayers +galaxy.visualization.plugins.registry INFO 2023-10-24 06:20:53,613 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: openseadragon +galaxy.visualization.plugins.registry INFO 2023-10-24 06:20:53,614 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: phylocanvas +galaxy.visualization.plugins.registry INFO 2023-10-24 06:20:53,615 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: phyloviz +galaxy.visualization.plugins.registry INFO 2023-10-24 06:20:53,616 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: pv +galaxy.visualization.plugins.registry INFO 2023-10-24 06:20:53,617 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: scatterplot +galaxy.visualization.plugins.config_parser INFO 2023-10-24 06:20:53,618 [pN:job_handler_0,p:8,tN:MainThread] Visualizations plugin disabled: Sweepster. Skipping... +galaxy.visualization.plugins.registry INFO 2023-10-24 06:20:53,619 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: trackster +galaxy.visualization.plugins.registry INFO 2023-10-24 06:20:53,619 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: ts_visjs +galaxy.visualization.plugins.config_parser INFO 2023-10-24 06:20:53,620 [pN:job_handler_0,p:8,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2023-10-24 06:20:53,620 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: unipept +galaxy.visualization.plugins.registry INFO 2023-10-24 06:20:53,621 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: venn +galaxy.tours._impl INFO 2023-10-24 06:20:53,638 [pN:job_handler_0,p:8,tN:MainThread] Loaded tour 'core.deferred' +galaxy.tours._impl INFO 2023-10-24 06:20:53,650 [pN:job_handler_0,p:8,tN:MainThread] Loaded tour 'core.history' +galaxy.tours._impl INFO 2023-10-24 06:20:53,660 [pN:job_handler_0,p:8,tN:MainThread] Loaded tour 'core.windows' +galaxy.tours._impl INFO 2023-10-24 06:20:53,682 [pN:job_handler_0,p:8,tN:MainThread] Loaded tour 'core.galaxy_ui' +galaxy.jobs.manager DEBUG 2023-10-24 06:20:53,688 [pN:job_handler_0,p:8,tN:MainThread] Initializing job handler +galaxy.jobs INFO 2023-10-24 06:20:53,688 [pN:job_handler_0,p:8,tN:MainThread] Handler 'job_handler_0' will load all configured runner plugins +galaxy.jobs.runners DEBUG 2023-10-24 06:20:53,689 [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': 'edge-23-10-24-06-08-1-galaxy', 'k8s_interactivetools_ingress_annotations': '\nnginx.ingress.kubernetes.io/auth-tls-pass-certificate-to-upstream: "true"\nnginx.ingress.kubernetes.io/auth-tls-secret: \'edge-23-10-24-06-08-1/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': 'edge-23-10-24-06-08-1', 'k8s_node_selector': 'cloud.google.com/gke-nodepool: default-pool', 'k8s_persistent_volume_claims': 'edge-23-10-24-06-08-1-galaxy-galaxy-pvc:/galaxy/server/database,edge-23-10-24-06-08-1-galaxy-refdata-gxy-pvc/data.galaxyproject.org:/cvmfs/data.galaxyproject.org,edge-23-10-24-06-08-1-galaxy-galaxy-pvc/cvmfsclone:/cvmfs/cloud.galaxyproject.org', 'k8s_pod_priority_class': 'edge-23-10-24-06-08-1-priority-class', 'k8s_pull_policy': 'IfNotPresent', 'k8s_supplemental_group_id': '101', 'k8s_use_service_account': True} +galaxy.jobs.runners.state_handler_factory DEBUG 2023-10-24 06:20:53,691 [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 2023-10-24 06:20:53,691 [pN:job_handler_0,p:8,tN:MainThread] Galaxy instance [edge-23-10-24-06-08-1-galaxy] is either too long (>20 characters) or it includes non DNS acceptable characters, ignoring it. +galaxy.jobs DEBUG 2023-10-24 06:20:53,691 [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 2023-10-24 06:20:53,692 [pN:job_handler_0,p:8,tN:MainThread] Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit +galaxy.jobs DEBUG 2023-10-24 06:20:53,693 [pN:job_handler_0,p:8,tN:MainThread] Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local' +galaxy.jobs.handler DEBUG 2023-10-24 06:20:53,693 [pN:job_handler_0,p:8,tN:MainThread] Loaded job runners plugins: k8s:local +galaxy.jobs.runners DEBUG 2023-10-24 06:20:53,698 [pN:job_handler_0,p:8,tN:MainThread] Starting 4 KubernetesRunner workers +galaxy.jobs.runners DEBUG 2023-10-24 06:20:53,700 [pN:job_handler_0,p:8,tN:MainThread] Starting 4 LocalRunner workers +galaxy.jobs.handler DEBUG 2023-10-24 06:20:53,701 [pN:job_handler_0,p:8,tN:MainThread] Handler queue starting for jobs assigned to handler: job_handler_0 +galaxy.jobs.handler INFO 2023-10-24 06:20:53,715 [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 2023-10-24 06:20:53,717 [pN:job_handler_0,p:8,tN:MainThread] job handler queue started +galaxy.jobs.handler INFO 2023-10-24 06:20:53,717 [pN:job_handler_0,p:8,tN:MainThread] job handler stop queue started +galaxy.web_stack.handlers DEBUG 2023-10-24 06:20:53,740 [pN:job_handler_0,p:8,tN:MainThread] Read definition for handler 'workflow_scheduler0' +galaxy.web_stack.handlers DEBUG 2023-10-24 06:20:53,740 [pN:job_handler_0,p:8,tN:MainThread] Read definition for handler 'workflow_scheduler0' +galaxy.web_stack.handlers DEBUG 2023-10-24 06:20:53,740 [pN:job_handler_0,p:8,tN:MainThread] default set to child with id or tag 'schedulers' +galaxy.web_stack.handlers INFO 2023-10-24 06:20:53,757 [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 2023-10-24 06:20:53,757 [pN:job_handler_0,p:8,tN:MainThread] Workflow scheduling handler assignment method(s): db-skip-locked +galaxy.workflow.scheduling_manager INFO 2023-10-24 06:20:53,758 [pN:job_handler_0,p:8,tN:MainThread] Tag [schedulers] handlers: workflow_scheduler0 +galaxy.web_stack.handlers DEBUG 2023-10-24 06:20:53,758 [pN:job_handler_0,p:8,tN:MainThread] default set to child with id or tag 'schedulers' +galaxy.queue_worker INFO 2023-10-24 06:20:53,773 [pN:job_handler_0,p:8,tN:MainThread] Binding and starting galaxy control worker for job_handler_0 +galaxy.queue_worker INFO 2023-10-24 06:20:53,778 [pN:job_handler_0,p:8,tN:MainThread] Queuing async task rebuild_toolbox_search_index for job_handler_0. +galaxy.model.database_heartbeat DEBUG 2023-10-24 06:20:53,790 [pN:job_handler_0,p:8,tN:database_heartbeart_job_handler_0.thread] job_handler_0 is config watcher +galaxy.app INFO 2023-10-24 06:20:53,822 [pN:job_handler_0,p:8,tN:MainThread] Galaxy app startup finished (13515.982 ms) +galaxy.web_stack INFO 2023-10-24 06:20:53,822 [pN:job_handler_0,p:8,tN:MainThread] Galaxy server instance 'job_handler_0' is running +galaxy.queue_worker INFO 2023-10-24 06:20:53,833 [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 2023-10-24 06:20:53,833 [pN:job_handler_0,p:8,tN:Thread-1] App is not a webapp, not building a search index +galaxy.model.database_heartbeat DEBUG 2023-10-24 06:21:53,802 [pN:job_handler_0,p:8,tN:database_heartbeart_job_handler_0.thread] job_handler_0 is not config watcher +galaxy.queue_worker INFO 2023-10-24 06:21:58,219 [pN:job_handler_0,p:8,tN:Thread-1] Instance 'job_handler_0' received 'reload_toolbox' task, executing now. +galaxy.queue_worker DEBUG 2023-10-24 06:21:58,219 [pN:job_handler_0,p:8,tN:Thread-1] Executing toolbox reload on 'job_handler_0' +galaxy.util WARNING 2023-10-24 06:21:58,246 [pN:job_handler_0,p:8,tN:Thread-1] directory not found: /galaxy/server/lib/galaxy/util/../../../config/plugins/activities +galaxy.tools WARNING 2023-10-24 06:21:58,251 [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 2023-10-24 06:21:58,252 [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 2023-10-24 06:21:58,252 [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 2023-10-24 06:21:58,253 [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 2023-10-24 06:21:58,253 [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 2023-10-24 06:21:58,255 [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 2023-10-24 06:21:58,255 [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 2023-10-24 06:21:58,257 [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 859, 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 1086, in load_tool + tool = self.create_tool( + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 512, 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 528, in _create_tool_from_source + return create_tool_from_source(self.app, tool_source, **kwds) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 322, in create_tool_from_source + tool = ToolClass(config_file, tool_source, app, **kwds) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 784, in __init__ + raise e + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 781, in __init__ + self.parse(tool_source, guid=guid, dynamic=dynamic) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1105, in parse + self.parse_inputs(self.tool_source) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1396, in parse_inputs + inputs = self.parse_input_elem(page_source, enctypes) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1591, in parse_input_elem + param = self.parse_param_elem(input_source, enctypes, context) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1604, 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 2023-10-24 06:21:58,258 [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 2023-10-24 06:21:58,258 [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 2023-10-24 06:21:58,272 [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.tools WARNING 2023-10-24 06:21:58,305 [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 2023-10-24 06:21:58,305 [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 2023-10-24 06:21:58,305 [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 2023-10-24 06:21:58,305 [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 2023-10-24 06:21:58,306 [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 2023-10-24 06:21:58,306 [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 2023-10-24 06:21:58,306 [pN:job_handler_0,p:8,tN:Thread-1] Reading tools from config files finished (54.436 ms) +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:21:58,306 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Get Data +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:21:58,306 [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 2023-10-24 06:21:58,306 [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 2023-10-24 06:21:58,306 [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 2023-10-24 06:21:58,306 [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 2023-10-24 06:21:58,307 [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 2023-10-24 06:21:58,307 [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 2023-10-24 06:21:58,307 [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 2023-10-24 06:21:58,307 [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 2023-10-24 06:21:58,307 [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 2023-10-24 06:21:58,307 [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 2023-10-24 06:21:58,307 [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 2023-10-24 06:21:58,307 [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 2023-10-24 06:21:58,307 [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 2023-10-24 06:21:58,307 [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 2023-10-24 06:21:58,307 [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 2023-10-24 06:21:58,307 [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 2023-10-24 06:21:58,307 [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 2023-10-24 06:21:58,308 [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 2023-10-24 06:21:58,308 [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 2023-10-24 06:21:58,308 [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 2023-10-24 06:21:58,308 [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 2023-10-24 06:21:58,308 [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 2023-10-24 06:21:58,308 [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 2023-10-24 06:21:58,308 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Send Data +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:21:58,308 [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 2023-10-24 06:21:58,308 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Send Data +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:21:58,308 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Expression Tools +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:21:58,308 [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 2023-10-24 06:21:58,308 [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 2023-10-24 06:21:58,308 [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 2023-10-24 06:21:58,308 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Collection Operations +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:21:58,308 [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 2023-10-24 06:21:58,308 [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 2023-10-24 06:21:58,309 [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 2023-10-24 06:21:58,309 [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 2023-10-24 06:21:58,309 [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 2023-10-24 06:21:58,309 [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 2023-10-24 06:21:58,309 [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 2023-10-24 06:21:58,309 [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 2023-10-24 06:21:58,309 [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 2023-10-24 06:21:58,309 [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 2023-10-24 06:21:58,309 [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 2023-10-24 06:21:58,309 [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 2023-10-24 06:21:58,309 [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 2023-10-24 06:21:58,309 [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 2023-10-24 06:21:58,309 [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 2023-10-24 06:21:58,309 [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 2023-10-24 06:21:58,310 [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 2023-10-24 06:21:58,310 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Text Manipulation +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:21:58,310 [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 2023-10-24 06:21:58,310 [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 2023-10-24 06:21:58,310 [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 2023-10-24 06:21:58,310 [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 2023-10-24 06:21:58,310 [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 2023-10-24 06:21:58,310 [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 2023-10-24 06:21:58,310 [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 2023-10-24 06:21:58,310 [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 2023-10-24 06:21:58,310 [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 2023-10-24 06:21:58,310 [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 2023-10-24 06:21:58,310 [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 2023-10-24 06:21:58,310 [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 2023-10-24 06:21:58,311 [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 2023-10-24 06:21:58,311 [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 2023-10-24 06:21:58,311 [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 2023-10-24 06:21:58,311 [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 2023-10-24 06:21:58,311 [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 2023-10-24 06:21:58,311 [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 2023-10-24 06:21:58,311 [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 2023-10-24 06:21:58,311 [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 2023-10-24 06:21:58,311 [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 2023-10-24 06:21:58,311 [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 2023-10-24 06:21:58,311 [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 2023-10-24 06:21:58,311 [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 2023-10-24 06:21:58,311 [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 2023-10-24 06:21:58,312 [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 2023-10-24 06:21:58,312 [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 2023-10-24 06:21:58,312 [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 2023-10-24 06:21:58,312 [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 2023-10-24 06:21:58,312 [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 2023-10-24 06:21:58,312 [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 2023-10-24 06:21:58,312 [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 2023-10-24 06:21:58,312 [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 2023-10-24 06:21:58,312 [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 2023-10-24 06:21:58,312 [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 2023-10-24 06:21:58,312 [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 2023-10-24 06:21:58,312 [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 2023-10-24 06:21:58,312 [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 2023-10-24 06:21:58,313 [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 2023-10-24 06:21:58,313 [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 2023-10-24 06:21:58,313 [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 2023-10-24 06:21:58,313 [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 2023-10-24 06:21:58,313 [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 2023-10-24 06:21:58,313 [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 2023-10-24 06:21:58,313 [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 2023-10-24 06:21:58,313 [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 2023-10-24 06:21:58,313 [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 2023-10-24 06:21:58,313 [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 2023-10-24 06:21:58,313 [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 2023-10-24 06:21:58,313 [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 2023-10-24 06:21:58,313 [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 2023-10-24 06:21:58,313 [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 2023-10-24 06:21:58,314 [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 2023-10-24 06:21:58,314 [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 2023-10-24 06:21:58,314 [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 2023-10-24 06:21:58,314 [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 2023-10-24 06:21:58,314 [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 2023-10-24 06:21:58,314 [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 2023-10-24 06:21:58,314 [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 2023-10-24 06:21:58,314 [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 2023-10-24 06:21:58,314 [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 2023-10-24 06:21:58,314 [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 2023-10-24 06:21:58,315 [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 2023-10-24 06:21:58,315 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Filter and Sort +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:21:58,315 [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 2023-10-24 06:21:58,315 [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 2023-10-24 06:21:58,315 [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 2023-10-24 06:21:58,315 [pN:job_handler_0,p:8,tN:Thread-1] Loaded label: GFF +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:21:58,315 [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 2023-10-24 06:21:58,315 [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 2023-10-24 06:21:58,315 [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 2023-10-24 06:21:58,315 [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 2023-10-24 06:21:58,315 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Join, Subtract and Group +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:21:58,315 [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 2023-10-24 06:21:58,315 [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 2023-10-24 06:21:58,316 [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 2023-10-24 06:21:58,316 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Datamash +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:21:58,316 [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 2023-10-24 06:21:58,316 [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 2023-10-24 06:21:58,316 [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 2023-10-24 06:21:58,316 [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 2023-10-24 06:21:58,316 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: FASTA/FASTQ +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:21:58,316 [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 2023-10-24 06:21:58,316 [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 2023-10-24 06:21:58,316 [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 2023-10-24 06:21:58,316 [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 2023-10-24 06:21:58,316 [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 2023-10-24 06:21:58,317 [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 2023-10-24 06:21:58,317 [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 2023-10-24 06:21:58,317 [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 2023-10-24 06:21:58,317 [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 2023-10-24 06:21:58,317 [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 2023-10-24 06:21:58,317 [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 2023-10-24 06:21:58,317 [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 2023-10-24 06:21:58,317 [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 2023-10-24 06:21:58,317 [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 2023-10-24 06:21:58,317 [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 2023-10-24 06:21:58,318 [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 2023-10-24 06:21:58,318 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: FASTQ Quality Control +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:21:58,318 [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 2023-10-24 06:21:58,318 [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 2023-10-24 06:21:58,318 [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 2023-10-24 06:21:58,318 [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 2023-10-24 06:21:58,318 [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 2023-10-24 06:21:58,318 [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 2023-10-24 06:21:58,318 [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 2023-10-24 06:21:58,319 [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 2023-10-24 06:21:58,319 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: SAM/BAM +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:21:58,319 [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 2023-10-24 06:21:58,319 [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 2023-10-24 06:21:58,319 [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 2023-10-24 06:21:58,319 [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 2023-10-24 06:21:58,319 [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 2023-10-24 06:21:58,319 [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 2023-10-24 06:21:58,319 [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 2023-10-24 06:21:58,319 [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 2023-10-24 06:21:58,319 [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 2023-10-24 06:21:58,319 [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 2023-10-24 06:21:58,320 [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 2023-10-24 06:21:58,320 [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 2023-10-24 06:21:58,320 [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 2023-10-24 06:21:58,320 [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 2023-10-24 06:21:58,320 [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 2023-10-24 06:21:58,320 [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 2023-10-24 06:21:58,320 [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 2023-10-24 06:21:58,320 [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 2023-10-24 06:21:58,320 [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 2023-10-24 06:21:58,320 [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 2023-10-24 06:21:58,320 [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 2023-10-24 06:21:58,320 [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 2023-10-24 06:21:58,320 [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 2023-10-24 06:21:58,321 [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 2023-10-24 06:21:58,321 [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 2023-10-24 06:21:58,321 [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 2023-10-24 06:21:58,321 [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 2023-10-24 06:21:58,321 [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 2023-10-24 06:21:58,321 [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 2023-10-24 06:21:58,321 [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 2023-10-24 06:21:58,321 [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 2023-10-24 06:21:58,321 [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 2023-10-24 06:21:58,321 [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 2023-10-24 06:21:58,321 [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 2023-10-24 06:21:58,321 [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 2023-10-24 06:21:58,322 [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 2023-10-24 06:21:58,322 [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 2023-10-24 06:21:58,322 [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 2023-10-24 06:21:58,322 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: BED +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:21:58,322 [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 2023-10-24 06:21:58,322 [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 2023-10-24 06:21:58,322 [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 2023-10-24 06:21:58,322 [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 2023-10-24 06:21:58,322 [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 2023-10-24 06:21:58,322 [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 2023-10-24 06:21:58,322 [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 2023-10-24 06:21:58,322 [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 2023-10-24 06:21:58,323 [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 2023-10-24 06:21:58,323 [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 2023-10-24 06:21:58,323 [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 2023-10-24 06:21:58,323 [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 2023-10-24 06:21:58,323 [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 2023-10-24 06:21:58,323 [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 2023-10-24 06:21:58,323 [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 2023-10-24 06:21:58,323 [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 2023-10-24 06:21:58,323 [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 2023-10-24 06:21:58,323 [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 2023-10-24 06:21:58,323 [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 2023-10-24 06:21:58,323 [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 2023-10-24 06:21:58,323 [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 2023-10-24 06:21:58,323 [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 2023-10-24 06:21:58,324 [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 2023-10-24 06:21:58,324 [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 2023-10-24 06:21:58,324 [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 2023-10-24 06:21:58,324 [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 2023-10-24 06:21:58,324 [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 2023-10-24 06:21:58,324 [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 2023-10-24 06:21:58,324 [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 2023-10-24 06:21:58,324 [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 2023-10-24 06:21:58,324 [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 2023-10-24 06:21:58,324 [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 2023-10-24 06:21:58,324 [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 2023-10-24 06:21:58,324 [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 2023-10-24 06:21:58,324 [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 2023-10-24 06:21:58,325 [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 2023-10-24 06:21:58,325 [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 2023-10-24 06:21:58,325 [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 2023-10-24 06:21:58,325 [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 2023-10-24 06:21:58,325 [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 2023-10-24 06:21:58,325 [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 2023-10-24 06:21:58,325 [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 2023-10-24 06:21:58,325 [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 2023-10-24 06:21:58,325 [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 2023-10-24 06:21:58,325 [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 2023-10-24 06:21:58,325 [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 2023-10-24 06:21:58,326 [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 2023-10-24 06:21:58,326 [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 2023-10-24 06:21:58,326 [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 2023-10-24 06:21:58,326 [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 2023-10-24 06:21:58,326 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: VCF/BCF +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:21:58,326 [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 2023-10-24 06:21:58,326 [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 2023-10-24 06:21:58,326 [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 2023-10-24 06:21:58,326 [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 2023-10-24 06:21:58,326 [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 2023-10-24 06:21:58,326 [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 2023-10-24 06:21:58,326 [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 2023-10-24 06:21:58,327 [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 2023-10-24 06:21:58,327 [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 2023-10-24 06:21:58,327 [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 2023-10-24 06:21:58,327 [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 2023-10-24 06:21:58,327 [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 2023-10-24 06:21:58,327 [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 2023-10-24 06:21:58,327 [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 2023-10-24 06:21:58,327 [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 2023-10-24 06:21:58,327 [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 2023-10-24 06:21:58,327 [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 2023-10-24 06:21:58,327 [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 2023-10-24 06:21:58,327 [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 2023-10-24 06:21:58,327 [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 2023-10-24 06:21:58,327 [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 2023-10-24 06:21:58,328 [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 2023-10-24 06:21:58,328 [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 2023-10-24 06:21:58,328 [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 2023-10-24 06:21:58,328 [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 2023-10-24 06:21:58,328 [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 2023-10-24 06:21:58,328 [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 2023-10-24 06:21:58,328 [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 2023-10-24 06:21:58,328 [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 2023-10-24 06:21:58,328 [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 2023-10-24 06:21:58,328 [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 2023-10-24 06:21:58,328 [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 2023-10-24 06:21:58,328 [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 2023-10-24 06:21:58,328 [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 2023-10-24 06:21:58,328 [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 2023-10-24 06:21:58,329 [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 2023-10-24 06:21:58,329 [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 2023-10-24 06:21:58,329 [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 2023-10-24 06:21:58,329 [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 2023-10-24 06:21:58,329 [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 2023-10-24 06:21:58,329 [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 2023-10-24 06:21:58,329 [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 2023-10-24 06:21:58,329 [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 2023-10-24 06:21:58,329 [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 2023-10-24 06:21:58,329 [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 2023-10-24 06:21:58,329 [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 2023-10-24 06:21:58,329 [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 2023-10-24 06:21:58,329 [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 2023-10-24 06:21:58,330 [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 2023-10-24 06:21:58,330 [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 2023-10-24 06:21:58,330 [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 2023-10-24 06:21:58,330 [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 2023-10-24 06:21:58,330 [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 2023-10-24 06:21:58,330 [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 2023-10-24 06:21:58,330 [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 2023-10-24 06:21:58,330 [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 2023-10-24 06:21:58,330 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Nanopore +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:21:58,330 [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 2023-10-24 06:21:58,330 [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 2023-10-24 06:21:58,330 [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 2023-10-24 06:21:58,330 [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 2023-10-24 06:21:58,331 [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 2023-10-24 06:21:58,331 [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 2023-10-24 06:21:58,331 [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 2023-10-24 06:21:58,331 [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 2023-10-24 06:21:58,331 [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 2023-10-24 06:21:58,331 [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 2023-10-24 06:21:58,331 [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 2023-10-24 06:21:58,331 [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 2023-10-24 06:21:58,331 [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 2023-10-24 06:21:58,331 [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 2023-10-24 06:21:58,331 [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 2023-10-24 06:21:58,331 [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 2023-10-24 06:21:58,331 [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 2023-10-24 06:21:58,331 [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 2023-10-24 06:21:58,332 [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 2023-10-24 06:21:58,332 [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 2023-10-24 06:21:58,332 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Convert Formats +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:21:58,332 [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 2023-10-24 06:21:58,332 [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 2023-10-24 06:21:58,332 [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 2023-10-24 06:21:58,332 [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 2023-10-24 06:21:58,332 [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 2023-10-24 06:21:58,332 [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 2023-10-24 06:21:58,332 [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 2023-10-24 06:21:58,332 [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 2023-10-24 06:21:58,332 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Lift-Over +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:21:58,332 [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 2023-10-24 06:21:58,332 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Virology +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:21:58,332 [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 2023-10-24 06:21:58,333 [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 2023-10-24 06:21:58,333 [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 2023-10-24 06:21:58,333 [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 2023-10-24 06:21:58,333 [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 2023-10-24 06:21:58,333 [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 2023-10-24 06:21:58,333 [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 2023-10-24 06:21:58,333 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Operate on Genomic Intervals +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:21:58,333 [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 2023-10-24 06:21:58,333 [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 2023-10-24 06:21:58,333 [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 2023-10-24 06:21:58,333 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Fetch Sequences/Alignments +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:21:58,333 [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 2023-10-24 06:21:58,333 [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 2023-10-24 06:21:58,333 [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 2023-10-24 06:21:58,333 [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 2023-10-24 06:21:58,334 [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 2023-10-24 06:21:58,334 [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 2023-10-24 06:21:58,334 [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 2023-10-24 06:21:58,334 [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 2023-10-24 06:21:58,334 [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 2023-10-24 06:21:58,334 [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 2023-10-24 06:21:58,334 [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 2023-10-24 06:21:58,334 [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 2023-10-24 06:21:58,334 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Assembly +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:21:58,334 [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 2023-10-24 06:21:58,334 [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 2023-10-24 06:21:58,334 [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 2023-10-24 06:21:58,334 [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 2023-10-24 06:21:58,334 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Annotation +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:21:58,334 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Mapping +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:21:58,334 [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 2023-10-24 06:21:58,335 [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 2023-10-24 06:21:58,335 [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 2023-10-24 06:21:58,335 [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 2023-10-24 06:21:58,335 [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 2023-10-24 06:21:58,335 [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 2023-10-24 06:21:58,335 [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 2023-10-24 06:21:58,335 [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 2023-10-24 06:21:58,335 [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 2023-10-24 06:21:58,335 [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 2023-10-24 06:21:58,335 [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 2023-10-24 06:21:58,335 [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 2023-10-24 06:21:58,335 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Variant Calling +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:21:58,336 [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 2023-10-24 06:21:58,336 [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 2023-10-24 06:21:58,336 [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 2023-10-24 06:21:58,336 [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 2023-10-24 06:21:58,336 [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 2023-10-24 06:21:58,336 [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 2023-10-24 06:21:58,336 [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 2023-10-24 06:21:58,336 [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 2023-10-24 06:21:58,336 [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 2023-10-24 06:21:58,336 [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 2023-10-24 06:21:58,336 [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 2023-10-24 06:21:58,336 [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 2023-10-24 06:21:58,337 [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 2023-10-24 06:21:58,337 [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 2023-10-24 06:21:58,337 [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 2023-10-24 06:21:58,337 [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 2023-10-24 06:21:58,337 [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 2023-10-24 06:21:58,337 [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 2023-10-24 06:21:58,337 [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 2023-10-24 06:21:58,337 [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 2023-10-24 06:21:58,337 [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 2023-10-24 06:21:58,337 [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 2023-10-24 06:21:58,337 [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 2023-10-24 06:21:58,337 [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 2023-10-24 06:21:58,337 [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 2023-10-24 06:21:58,338 [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 2023-10-24 06:21:58,338 [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 2023-10-24 06:21:58,338 [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 2023-10-24 06:21:58,338 [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 2023-10-24 06:21:58,338 [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 2023-10-24 06:21:58,338 [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 2023-10-24 06:21:58,338 [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 2023-10-24 06:21:58,338 [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 2023-10-24 06:21:58,338 [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 2023-10-24 06:21:58,338 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: ChIP-seq +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:21:58,339 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: RNA-seq +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:21:58,339 [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 2023-10-24 06:21:58,339 [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 2023-10-24 06:21:58,339 [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 2023-10-24 06:21:58,339 [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 2023-10-24 06:21:58,339 [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 2023-10-24 06:21:58,339 [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 2023-10-24 06:21:58,339 [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 2023-10-24 06:21:58,339 [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 2023-10-24 06:21:58,339 [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 2023-10-24 06:21:58,339 [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 2023-10-24 06:21:58,339 [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 2023-10-24 06:21:58,340 [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 2023-10-24 06:21:58,340 [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 2023-10-24 06:21:58,340 [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 2023-10-24 06:21:58,340 [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 2023-10-24 06:21:58,340 [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 2023-10-24 06:21:58,340 [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 2023-10-24 06:21:58,340 [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 2023-10-24 06:21:58,340 [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 2023-10-24 06:21:58,340 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Multiple Alignments +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:21:58,341 [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 2023-10-24 06:21:58,341 [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 2023-10-24 06:21:58,341 [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 2023-10-24 06:21:58,341 [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 2023-10-24 06:21:58,341 [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 2023-10-24 06:21:58,341 [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 2023-10-24 06:21:58,341 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Phenotype Association +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:21:58,341 [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 2023-10-24 06:21:58,341 [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 2023-10-24 06:21:58,341 [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 2023-10-24 06:21:58,341 [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 2023-10-24 06:21:58,341 [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 2023-10-24 06:21:58,341 [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 2023-10-24 06:21:58,341 [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 2023-10-24 06:21:58,341 [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 2023-10-24 06:21:58,342 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Regional Variation +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:21:58,342 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: STR-FM: Microsatellite Analysis +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:21:58,342 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Motif +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:21:58,342 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Chromosome Conformation +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:21:58,342 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Metagenomic Analysis +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:21:58,342 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Mothur +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:21:58,342 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Picard +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:21:58,342 [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 2023-10-24 06:21:58,342 [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 2023-10-24 06:21:58,342 [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 2023-10-24 06:21:58,342 [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 2023-10-24 06:21:58,342 [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 2023-10-24 06:21:58,342 [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 2023-10-24 06:21:58,342 [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 2023-10-24 06:21:58,342 [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 2023-10-24 06:21:58,342 [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 2023-10-24 06:21:58,343 [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 2023-10-24 06:21:58,343 [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 2023-10-24 06:21:58,343 [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 2023-10-24 06:21:58,343 [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 2023-10-24 06:21:58,343 [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 2023-10-24 06:21:58,343 [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 2023-10-24 06:21:58,343 [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 2023-10-24 06:21:58,343 [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 2023-10-24 06:21:58,343 [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 2023-10-24 06:21:58,343 [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 2023-10-24 06:21:58,343 [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 2023-10-24 06:21:58,343 [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 2023-10-24 06:21:58,343 [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 2023-10-24 06:21:58,344 [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 2023-10-24 06:21:58,344 [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 2023-10-24 06:21:58,344 [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 2023-10-24 06:21:58,344 [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 2023-10-24 06:21:58,344 [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 2023-10-24 06:21:58,344 [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 2023-10-24 06:21:58,344 [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 2023-10-24 06:21:58,344 [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 2023-10-24 06:21:58,344 [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 2023-10-24 06:21:58,345 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Pharmacology +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:21:58,345 [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 2023-10-24 06:21:58,345 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Single-Cell +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:21:58,345 [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 2023-10-24 06:21:58,345 [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 2023-10-24 06:21:58,345 [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 2023-10-24 06:21:58,345 [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 2023-10-24 06:21:58,345 [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 2023-10-24 06:21:58,345 [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 2023-10-24 06:21:58,345 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__cutadapt__trim_single/qiime2__cutadapt__trim_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 2023-10-24 06:21:58,355 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__cutadapt__trim_paired/qiime2__cutadapt__trim_paired/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 2023-10-24 06:21:58,355 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__cutadapt__demux_single/qiime2__cutadapt__demux_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 2023-10-24 06:21:58,355 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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+galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:21:58,367 [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 2023-10-24 06:21:58,367 [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 2023-10-24 06:21:58,367 [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 2023-10-24 06:21:58,367 [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 2023-10-24 06:21:58,367 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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+galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:21:58,368 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: TRANSIT +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:21:58,368 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Statistics +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:21:58,368 [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 2023-10-24 06:21:58,369 [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 2023-10-24 06:21:58,369 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Graph/Display Data +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:21:58,369 [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 2023-10-24 06:21:58,369 [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 2023-10-24 06:21:58,369 [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 2023-10-24 06:21:58,369 [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 2023-10-24 06:21:58,369 [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 2023-10-24 06:21:58,369 [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 2023-10-24 06:21:58,369 [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 2023-10-24 06:21:58,369 [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 2023-10-24 06:21:58,369 [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 2023-10-24 06:21:58,369 [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 2023-10-24 06:21:58,369 [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 2023-10-24 06:21:58,369 [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 2023-10-24 06:21:58,370 [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 2023-10-24 06:21:58,370 [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 2023-10-24 06:21:58,370 [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 2023-10-24 06:21:58,370 [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 2023-10-24 06:21:58,370 [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 2023-10-24 06:21:58,370 [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 2023-10-24 06:21:58,370 [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 2023-10-24 06:21:58,370 [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 2023-10-24 06:21:58,370 [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 2023-10-24 06:21:58,370 [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 2023-10-24 06:21:58,371 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: RNA Analysis (deprecated) +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:21:58,371 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: CloudMap (deprecated) +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:21:58,371 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Metagenomic Analysis (deprecated) +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:21:58,371 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Text Manipulation +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:21:58,371 [pN:job_handler_0,p:8,tN:Thread-1] Loading tool panel finished (64.886 ms) +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:21:58,375 [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 2023-10-24 06:21:58,375 [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 2023-10-24 06:21:58,376 [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 2023-10-24 06:21:58,376 [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 2023-10-24 06:21:58,376 [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 2023-10-24 06:21:58,376 [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 2023-10-24 06:21:58,376 [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 2023-10-24 06:21:58,376 [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 2023-10-24 06:21:58,376 [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 2023-10-24 06:21:58,376 [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 2023-10-24 06:21:58,377 [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 2023-10-24 06:21:58,377 [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 2023-10-24 06:21:58,377 [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 2023-10-24 06:21:58,377 [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 2023-10-24 06:21:58,377 [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 2023-10-24 06:21:58,377 [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 2023-10-24 06:21:58,377 [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 2023-10-24 06:21:58,377 [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 2023-10-24 06:21:58,377 [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 2023-10-24 06:21:58,378 [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 2023-10-24 06:21:58,378 [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 2023-10-24 06:21:58,378 [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 2023-10-24 06:21:58,378 [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 2023-10-24 06:21:58,378 [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 2023-10-24 06:21:58,378 [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 2023-10-24 06:21:58,378 [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 2023-10-24 06:21:58,378 [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 2023-10-24 06:21:58,378 [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 2023-10-24 06:21:58,378 [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 2023-10-24 06:21:58,378 [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 2023-10-24 06:21:58,378 [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 2023-10-24 06:21:58,378 [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 2023-10-24 06:21:58,378 [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 2023-10-24 06:21:58,378 [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 2023-10-24 06:21:58,379 [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 2023-10-24 06:21:58,379 [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 2023-10-24 06:21:58,379 [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 2023-10-24 06:21:58,379 [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 2023-10-24 06:21:58,379 [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 2023-10-24 06:21:58,379 [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 2023-10-24 06:21:58,379 [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 2023-10-24 06:21:58,379 [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 2023-10-24 06:21:58,379 [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 2023-10-24 06:21:58,379 [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 2023-10-24 06:21:58,379 [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 2023-10-24 06:21:58,379 [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 2023-10-24 06:21:58,379 [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 2023-10-24 06:21:58,379 [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 2023-10-24 06:21:58,379 [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 2023-10-24 06:21:58,380 [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 2023-10-24 06:21:58,380 [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 2023-10-24 06:21:58,380 [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 2023-10-24 06:21:58,380 [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 2023-10-24 06:21:58,380 [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 2023-10-24 06:21:58,380 [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 2023-10-24 06:21:58,380 [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 2023-10-24 06:21:58,380 [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 2023-10-24 06:21:58,380 [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 2023-10-24 06:21:58,380 [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 2023-10-24 06:21:58,380 [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 2023-10-24 06:21:58,380 [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 2023-10-24 06:21:58,381 [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 2023-10-24 06:21:58,381 [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 2023-10-24 06:21:58,381 [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 2023-10-24 06:21:58,381 [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 2023-10-24 06:21:58,381 [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 2023-10-24 06:21:58,381 [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 2023-10-24 06:21:58,381 [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 2023-10-24 06:21:58,381 [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 2023-10-24 06:21:58,382 [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 2023-10-24 06:21:58,382 [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 2023-10-24 06:21:58,382 [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 2023-10-24 06:21:58,382 [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 2023-10-24 06:21:58,382 [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 2023-10-24 06:21:58,382 [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 2023-10-24 06:21:58,382 [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 2023-10-24 06:21:58,382 [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 2023-10-24 06:21:58,383 [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 2023-10-24 06:21:58,383 [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 2023-10-24 06:21:58,383 [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 2023-10-24 06:21:58,383 [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 2023-10-24 06:21:58,383 [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 2023-10-24 06:21:58,383 [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 2023-10-24 06:21:58,383 [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 2023-10-24 06:21:58,383 [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 2023-10-24 06:21:58,383 [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 2023-10-24 06:21:58,383 [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 2023-10-24 06:21:58,383 [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 2023-10-24 06:21:58,383 [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 2023-10-24 06:21:58,383 [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 2023-10-24 06:21:58,384 [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 2023-10-24 06:21:58,384 [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 2023-10-24 06:21:58,384 [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 2023-10-24 06:21:58,384 [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 2023-10-24 06:21:58,384 [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 2023-10-24 06:21:58,384 [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 2023-10-24 06:21:58,384 [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 2023-10-24 06:21:58,384 [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 2023-10-24 06:21:58,384 [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 2023-10-24 06:21:58,384 [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 2023-10-24 06:21:58,384 [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 2023-10-24 06:21:58,384 [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 2023-10-24 06:21:58,384 [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 2023-10-24 06:21:58,385 [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 2023-10-24 06:21:58,385 [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 2023-10-24 06:21:58,385 [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 2023-10-24 06:21:58,385 [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 2023-10-24 06:21:58,385 [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 2023-10-24 06:21:58,385 [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 2023-10-24 06:21:58,385 [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 2023-10-24 06:21:58,385 [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 2023-10-24 06:21:58,385 [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 2023-10-24 06:21:58,385 [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 2023-10-24 06:21:58,386 [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 2023-10-24 06:21:58,386 [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 2023-10-24 06:21:58,386 [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 2023-10-24 06:21:58,386 [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 2023-10-24 06:21:58,386 [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 2023-10-24 06:21:58,386 [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 2023-10-24 06:21:58,386 [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 2023-10-24 06:21:58,386 [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 2023-10-24 06:21:58,386 [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 2023-10-24 06:21:58,386 [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 2023-10-24 06:21:58,386 [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 2023-10-24 06:21:58,386 [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 2023-10-24 06:21:58,386 [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 2023-10-24 06:21:58,387 [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 2023-10-24 06:21:58,387 [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 2023-10-24 06:21:58,387 [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 2023-10-24 06:21:58,387 [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 2023-10-24 06:21:58,387 [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 2023-10-24 06:21:58,387 [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 2023-10-24 06:21:58,387 [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 2023-10-24 06:21:58,387 [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 2023-10-24 06:21:58,387 [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 2023-10-24 06:21:58,387 [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 2023-10-24 06:21:58,387 [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 2023-10-24 06:21:58,387 [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 2023-10-24 06:21:58,387 [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 2023-10-24 06:21:58,387 [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 2023-10-24 06:21:58,388 [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 2023-10-24 06:21:58,388 [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 2023-10-24 06:21:58,388 [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 2023-10-24 06:21:58,388 [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 2023-10-24 06:21:58,388 [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 2023-10-24 06:21:58,388 [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 2023-10-24 06:21:58,388 [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 2023-10-24 06:21:58,388 [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 2023-10-24 06:21:58,388 [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 2023-10-24 06:21:58,388 [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 2023-10-24 06:21:58,389 [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 2023-10-24 06:21:58,389 [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 2023-10-24 06:21:58,389 [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 2023-10-24 06:21:58,389 [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 2023-10-24 06:21:58,389 [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 2023-10-24 06:21:58,389 [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 2023-10-24 06:21:58,389 [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 2023-10-24 06:21:58,389 [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 2023-10-24 06:21:58,389 [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 2023-10-24 06:21:58,389 [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 2023-10-24 06:21:58,389 [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 2023-10-24 06:21:58,389 [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 2023-10-24 06:21:58,390 [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 2023-10-24 06:21:58,390 [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 2023-10-24 06:21:58,390 [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 2023-10-24 06:21:58,390 [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 2023-10-24 06:21:58,390 [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 2023-10-24 06:21:58,390 [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 2023-10-24 06:21:58,390 [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 2023-10-24 06:21:58,390 [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 2023-10-24 06:21:58,390 [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 2023-10-24 06:21:58,391 [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 2023-10-24 06:21:58,391 [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 2023-10-24 06:21:58,391 [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 2023-10-24 06:21:58,391 [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 2023-10-24 06:21:58,391 [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 2023-10-24 06:21:58,391 [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 2023-10-24 06:21:58,391 [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 2023-10-24 06:21:58,391 [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 2023-10-24 06:21:58,391 [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 2023-10-24 06:21:58,391 [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 2023-10-24 06:21:58,392 [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 2023-10-24 06:21:58,392 [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 2023-10-24 06:21:58,392 [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 2023-10-24 06:21:58,392 [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 2023-10-24 06:21:58,392 [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 2023-10-24 06:21:58,392 [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 2023-10-24 06:21:58,392 [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 2023-10-24 06:21:58,392 [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 2023-10-24 06:21:58,392 [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 2023-10-24 06:21:58,392 [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 2023-10-24 06:21:58,392 [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 2023-10-24 06:21:58,392 [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 2023-10-24 06:21:58,392 [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 2023-10-24 06:21:58,393 [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 2023-10-24 06:21:58,393 [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 2023-10-24 06:21:58,393 [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 2023-10-24 06:21:58,393 [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 2023-10-24 06:21:58,393 [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 2023-10-24 06:21:58,393 [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 2023-10-24 06:21:58,393 [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 2023-10-24 06:21:58,393 [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 2023-10-24 06:21:58,393 [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 2023-10-24 06:21:58,393 [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 2023-10-24 06:21:58,393 [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 2023-10-24 06:21:58,393 [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 2023-10-24 06:21:58,393 [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 2023-10-24 06:21:58,394 [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 2023-10-24 06:21:58,394 [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 2023-10-24 06:21:58,394 [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 2023-10-24 06:21:58,394 [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 2023-10-24 06:21:58,394 [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 2023-10-24 06:21:58,394 [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 2023-10-24 06:21:58,394 [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 2023-10-24 06:21:58,394 [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 2023-10-24 06:21:58,394 [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 2023-10-24 06:21:58,394 [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 2023-10-24 06:21:58,394 [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 2023-10-24 06:21:58,394 [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 2023-10-24 06:21:58,395 [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 2023-10-24 06:21:58,395 [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 2023-10-24 06:21:58,395 [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 2023-10-24 06:21:58,395 [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 2023-10-24 06:21:58,395 [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 2023-10-24 06:21:58,395 [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 2023-10-24 06:21:58,395 [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 2023-10-24 06:21:58,395 [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 2023-10-24 06:21:58,395 [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 2023-10-24 06:21:58,395 [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 2023-10-24 06:21:58,395 [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 2023-10-24 06:21:58,395 [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 2023-10-24 06:21:58,395 [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 2023-10-24 06:21:58,396 [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 2023-10-24 06:21:58,396 [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 2023-10-24 06:21:58,396 [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 2023-10-24 06:21:58,396 [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 2023-10-24 06:21:58,396 [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 2023-10-24 06:21:58,396 [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 2023-10-24 06:21:58,396 [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 2023-10-24 06:21:58,396 [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 2023-10-24 06:21:58,396 [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 2023-10-24 06:21:58,396 [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 2023-10-24 06:21:58,396 [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 2023-10-24 06:21:58,396 [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 2023-10-24 06:21:58,396 [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 2023-10-24 06:21:58,396 [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 2023-10-24 06:21:58,397 [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 2023-10-24 06:21:58,397 [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 2023-10-24 06:21:58,397 [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 2023-10-24 06:21:58,397 [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 2023-10-24 06:21:58,397 [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 2023-10-24 06:21:58,397 [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 2023-10-24 06:21:58,397 [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 2023-10-24 06:21:58,397 [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 2023-10-24 06:21:58,397 [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 2023-10-24 06:21:58,397 [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 2023-10-24 06:21:58,397 [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 2023-10-24 06:21:58,398 [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 2023-10-24 06:21:58,398 [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 2023-10-24 06:21:58,398 [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 2023-10-24 06:21:58,398 [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 2023-10-24 06:21:58,398 [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 2023-10-24 06:21:58,398 [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 2023-10-24 06:21:58,398 [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 2023-10-24 06:21:58,398 [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 2023-10-24 06:21:58,398 [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 2023-10-24 06:21:58,398 [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 2023-10-24 06:21:58,398 [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 2023-10-24 06:21:58,398 [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 2023-10-24 06:21:58,399 [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 2023-10-24 06:21:58,399 [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 2023-10-24 06:21:58,399 [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 2023-10-24 06:21:58,399 [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 2023-10-24 06:21:58,399 [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 2023-10-24 06:21:58,399 [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 2023-10-24 06:21:58,399 [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 2023-10-24 06:21:58,399 [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 2023-10-24 06:21:58,399 [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 2023-10-24 06:21:58,399 [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 2023-10-24 06:21:58,399 [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 2023-10-24 06:21:58,399 [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 2023-10-24 06:21:58,399 [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 2023-10-24 06:21:58,400 [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 2023-10-24 06:21:58,400 [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 2023-10-24 06:21:58,400 [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 2023-10-24 06:21:58,400 [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 2023-10-24 06:21:58,400 [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 2023-10-24 06:21:58,400 [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 2023-10-24 06:21:58,400 [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 2023-10-24 06:21:58,400 [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 2023-10-24 06:21:58,400 [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 2023-10-24 06:21:58,400 [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 2023-10-24 06:21:58,400 [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 2023-10-24 06:21:58,400 [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 2023-10-24 06:21:58,400 [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 2023-10-24 06:21:58,400 [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 2023-10-24 06:21:58,401 [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 2023-10-24 06:21:58,401 [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 2023-10-24 06:21:58,401 [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 2023-10-24 06:21:58,401 [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 2023-10-24 06:21:58,401 [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 2023-10-24 06:21:58,401 [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 2023-10-24 06:21:58,401 [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 2023-10-24 06:21:58,401 [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 2023-10-24 06:21:58,401 [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 2023-10-24 06:21:58,401 [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 2023-10-24 06:21:58,401 [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 2023-10-24 06:21:58,401 [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 2023-10-24 06:21:58,401 [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 2023-10-24 06:21:58,402 [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 2023-10-24 06:21:58,402 [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 2023-10-24 06:21:58,402 [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 2023-10-24 06:21:58,402 [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 2023-10-24 06:21:58,402 [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 2023-10-24 06:21:58,402 [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 2023-10-24 06:21:58,402 [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 2023-10-24 06:21:58,402 [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 2023-10-24 06:21:58,402 [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 2023-10-24 06:21:58,402 [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 2023-10-24 06:21:58,402 [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 2023-10-24 06:21:58,402 [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 2023-10-24 06:21:58,403 [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 2023-10-24 06:21:58,403 [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 2023-10-24 06:21:58,403 [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 2023-10-24 06:21:58,403 [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 2023-10-24 06:21:58,403 [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 2023-10-24 06:21:58,403 [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 2023-10-24 06:21:58,403 [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 2023-10-24 06:21:58,403 [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 2023-10-24 06:21:58,403 [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 2023-10-24 06:21:58,403 [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 2023-10-24 06:21:58,403 [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 2023-10-24 06:21:58,403 [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 2023-10-24 06:21:58,403 [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 2023-10-24 06:21:58,403 [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 2023-10-24 06:21:58,404 [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 2023-10-24 06:21:58,404 [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 2023-10-24 06:21:58,404 [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 2023-10-24 06:21:58,404 [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 2023-10-24 06:21:58,404 [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 2023-10-24 06:21:58,404 [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 2023-10-24 06:21:58,404 [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 2023-10-24 06:21:58,404 [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 2023-10-24 06:21:58,404 [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 2023-10-24 06:21:58,404 [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 2023-10-24 06:21:58,404 [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 2023-10-24 06:21:58,404 [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 2023-10-24 06:21:58,404 [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 2023-10-24 06:21:58,404 [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 2023-10-24 06:21:58,405 [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 2023-10-24 06:21:58,405 [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 2023-10-24 06:21:58,405 [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 2023-10-24 06:21:58,405 [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 2023-10-24 06:21:58,405 [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 2023-10-24 06:21:58,405 [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 2023-10-24 06:21:58,405 [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 2023-10-24 06:21:58,405 [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 2023-10-24 06:21:58,405 [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 2023-10-24 06:21:58,405 [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 2023-10-24 06:21:58,405 [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 2023-10-24 06:21:58,405 [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 2023-10-24 06:21:58,405 [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 2023-10-24 06:21:58,405 [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 2023-10-24 06:21:58,405 [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 2023-10-24 06:21:58,406 [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 2023-10-24 06:21:58,406 [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 2023-10-24 06:21:58,406 [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 2023-10-24 06:21:58,406 [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 2023-10-24 06:21:58,406 [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 2023-10-24 06:21:58,406 [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 2023-10-24 06:21:58,406 [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 2023-10-24 06:21:58,406 [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 2023-10-24 06:21:58,406 [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 2023-10-24 06:21:58,406 [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 2023-10-24 06:21:58,406 [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 2023-10-24 06:21:58,406 [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 2023-10-24 06:21:58,406 [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 2023-10-24 06:21:58,407 [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 2023-10-24 06:21:58,407 [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 2023-10-24 06:21:58,407 [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 2023-10-24 06:21:58,407 [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 2023-10-24 06:21:58,407 [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 2023-10-24 06:21:58,407 [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 2023-10-24 06:21:58,407 [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 2023-10-24 06:21:58,407 [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 2023-10-24 06:21:58,407 [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 2023-10-24 06:21:58,407 [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 2023-10-24 06:21:58,407 [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 2023-10-24 06:21:58,408 [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 2023-10-24 06:21:58,408 [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 2023-10-24 06:21:58,408 [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 2023-10-24 06:21:58,408 [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 2023-10-24 06:21:58,408 [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 2023-10-24 06:21:58,408 [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 2023-10-24 06:21:58,408 [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 2023-10-24 06:21:58,408 [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 2023-10-24 06:21:58,408 [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 2023-10-24 06:21:58,408 [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 2023-10-24 06:21:58,408 [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 2023-10-24 06:21:58,408 [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 2023-10-24 06:21:58,409 [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 2023-10-24 06:21:58,409 [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 2023-10-24 06:21:58,409 [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 2023-10-24 06:21:58,409 [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 2023-10-24 06:21:58,409 [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 2023-10-24 06:21:58,409 [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 2023-10-24 06:21:58,409 [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 2023-10-24 06:21:58,409 [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 2023-10-24 06:21:58,409 [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 2023-10-24 06:21:58,410 [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 2023-10-24 06:21:58,410 [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 2023-10-24 06:21:58,410 [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 2023-10-24 06:21:58,410 [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 2023-10-24 06:21:58,410 [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 2023-10-24 06:21:58,410 [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 2023-10-24 06:21:58,410 [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 2023-10-24 06:21:58,410 [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 2023-10-24 06:21:58,410 [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 2023-10-24 06:21:58,410 [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 2023-10-24 06:21:58,410 [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 2023-10-24 06:21:58,410 [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 2023-10-24 06:21:58,411 [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 2023-10-24 06:21:58,411 [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 2023-10-24 06:21:58,411 [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 2023-10-24 06:21:58,411 [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 2023-10-24 06:21:58,411 [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 2023-10-24 06:21:58,411 [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 2023-10-24 06:21:58,411 [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 2023-10-24 06:21:58,411 [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 2023-10-24 06:21:58,411 [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 2023-10-24 06:21:58,411 [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 2023-10-24 06:21:58,412 [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 2023-10-24 06:21:58,412 [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 2023-10-24 06:21:58,412 [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 2023-10-24 06:21:58,412 [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 2023-10-24 06:21:58,412 [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 2023-10-24 06:21:58,412 [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 2023-10-24 06:21:58,412 [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 2023-10-24 06:21:58,412 [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 2023-10-24 06:21:58,412 [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 2023-10-24 06:21:58,412 [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 2023-10-24 06:21:58,412 [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 2023-10-24 06:21:58,412 [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 2023-10-24 06:21:58,412 [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 2023-10-24 06:21:58,412 [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 2023-10-24 06:21:58,413 [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 2023-10-24 06:21:58,413 [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 2023-10-24 06:21:58,413 [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 2023-10-24 06:21:58,413 [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 2023-10-24 06:21:58,413 [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 2023-10-24 06:21:58,413 [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 2023-10-24 06:21:58,413 [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 2023-10-24 06:21:58,413 [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 2023-10-24 06:21:58,413 [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 2023-10-24 06:21:58,413 [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 2023-10-24 06:21:58,413 [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 2023-10-24 06:21:58,413 [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 2023-10-24 06:21:58,414 [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 2023-10-24 06:21:58,414 [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 2023-10-24 06:21:58,414 [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 2023-10-24 06:21:58,414 [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 2023-10-24 06:21:58,414 [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 2023-10-24 06:21:58,414 [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 2023-10-24 06:21:58,414 [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 2023-10-24 06:21:58,414 [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 2023-10-24 06:21:58,414 [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 2023-10-24 06:21:58,414 [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 2023-10-24 06:21:58,414 [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 2023-10-24 06:21:58,414 [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 2023-10-24 06:21:58,414 [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 2023-10-24 06:21:58,415 [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 2023-10-24 06:21:58,415 [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 2023-10-24 06:21:58,415 [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 2023-10-24 06:21:58,415 [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 2023-10-24 06:21:58,415 [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 2023-10-24 06:21:58,415 [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 2023-10-24 06:21:58,415 [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 2023-10-24 06:21:58,415 [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 2023-10-24 06:21:58,415 [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 2023-10-24 06:21:58,416 [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 2023-10-24 06:21:58,416 [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 2023-10-24 06:21:58,416 [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 2023-10-24 06:21:58,416 [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 2023-10-24 06:21:58,416 [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 2023-10-24 06:21:58,416 [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 2023-10-24 06:21:58,416 [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 2023-10-24 06:21:58,416 [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 2023-10-24 06:21:58,416 [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 2023-10-24 06:21:58,416 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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_correlation/deeptools_plot_correlation/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:21:58,423 [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/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:21:58,423 [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/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:21:58,423 [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/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:21:58,423 [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/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:21:58,423 [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/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:21:58,423 [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/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:21:58,423 [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 2023-10-24 06:21:58,423 [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 2023-10-24 06:21:58,427 [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 2023-10-24 06:21:58,427 [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 2023-10-24 06:21:58,427 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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DEBUG 2023-10-24 06:21:58,429 [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 2023-10-24 06:21:58,430 [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 2023-10-24 06:21:58,430 [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 2023-10-24 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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 2023-10-24 06:21:58,444 [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 2023-10-24 06:21:58,444 [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 2023-10-24 06:21:58,444 [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 2023-10-24 06:21:58,444 [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 2023-10-24 06:21:58,445 [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 2023-10-24 06:21:58,445 [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 2023-10-24 06:21:58,445 [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 2023-10-24 06:21:58,445 [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 2023-10-24 06:21:58,445 [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 2023-10-24 06:21:58,446 [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 2023-10-24 06:21:58,446 [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 2023-10-24 06:21:58,447 [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 2023-10-24 06:21:58,447 [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 2023-10-24 06:21:58,447 [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 2023-10-24 06:21:58,447 [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 2023-10-24 06:21:58,447 [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 2023-10-24 06:21:58,447 [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 2023-10-24 06:21:58,447 [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 2023-10-24 06:21:58,448 [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 2023-10-24 06:21:58,448 [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 2023-10-24 06:21:58,448 [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 2023-10-24 06:21:58,448 [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 2023-10-24 06:21:58,448 [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 2023-10-24 06:21:58,448 [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 2023-10-24 06:21:58,448 [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 2023-10-24 06:21:58,448 [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 2023-10-24 06:21:58,448 [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 2023-10-24 06:21:58,448 [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 2023-10-24 06:21:58,448 [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 2023-10-24 06:21:58,449 [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 2023-10-24 06:21:58,449 [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 2023-10-24 06:21:58,449 [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 2023-10-24 06:21:58,449 [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 2023-10-24 06:21:58,449 [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 2023-10-24 06:21:58,449 [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 2023-10-24 06:21:58,449 [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 2023-10-24 06:21:58,449 [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 2023-10-24 06:21:58,449 [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 2023-10-24 06:21:58,449 [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 2023-10-24 06:21:58,449 [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 2023-10-24 06:21:58,450 [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 2023-10-24 06:21:58,450 [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 2023-10-24 06:21:58,450 [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 2023-10-24 06:21:58,450 [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 2023-10-24 06:21:58,450 [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 2023-10-24 06:21:58,450 [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 2023-10-24 06:21:58,450 [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 2023-10-24 06:21:58,450 [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 2023-10-24 06:21:58,450 [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 2023-10-24 06:21:58,451 [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 2023-10-24 06:21:58,451 [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 2023-10-24 06:21:58,451 [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 2023-10-24 06:21:58,451 [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 2023-10-24 06:21:58,451 [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 2023-10-24 06:21:58,451 [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 2023-10-24 06:21:58,451 [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 2023-10-24 06:21:58,451 [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 2023-10-24 06:21:58,451 [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 2023-10-24 06:21:58,451 [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 2023-10-24 06:21:58,451 [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 2023-10-24 06:21:58,451 [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 2023-10-24 06:21:58,452 [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 2023-10-24 06:21:58,452 [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 2023-10-24 06:21:58,452 [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 2023-10-24 06:21:58,452 [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 2023-10-24 06:21:58,452 [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 2023-10-24 06:21:58,452 [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 2023-10-24 06:21:58,452 [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 2023-10-24 06:21:58,452 [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 2023-10-24 06:21:58,452 [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 2023-10-24 06:21:58,452 [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 2023-10-24 06:21:58,452 [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 2023-10-24 06:21:58,452 [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 2023-10-24 06:21:58,452 [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 2023-10-24 06:21:58,452 [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 2023-10-24 06:21:58,452 [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 2023-10-24 06:21:58,452 [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 2023-10-24 06:21:58,453 [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 2023-10-24 06:21:58,453 [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 2023-10-24 06:21:58,453 [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 2023-10-24 06:21:58,453 [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 2023-10-24 06:21:58,453 [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 2023-10-24 06:21:58,453 [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 2023-10-24 06:21:58,453 [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 2023-10-24 06:21:58,453 [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 2023-10-24 06:21:58,453 [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 2023-10-24 06:21:58,453 [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 2023-10-24 06:21:58,453 [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 2023-10-24 06:21:58,453 [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 2023-10-24 06:21:58,453 [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 2023-10-24 06:21:58,453 [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 2023-10-24 06:21:58,453 [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 2023-10-24 06:21:58,454 [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 2023-10-24 06:21:58,454 [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 2023-10-24 06:21:58,454 [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 2023-10-24 06:21:58,454 [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 2023-10-24 06:21:58,454 [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 2023-10-24 06:21:58,454 [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 2023-10-24 06:21:58,454 [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 2023-10-24 06:21:58,454 [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 2023-10-24 06:21:58,454 [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 2023-10-24 06:21:58,454 [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 2023-10-24 06:21:58,454 [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 2023-10-24 06:21:58,454 [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 2023-10-24 06:21:58,454 [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 2023-10-24 06:21:58,454 [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 2023-10-24 06:21:58,455 [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 2023-10-24 06:21:58,455 [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 2023-10-24 06:21:58,455 [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 2023-10-24 06:21:58,455 [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 2023-10-24 06:21:58,455 [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 2023-10-24 06:21:58,455 [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 2023-10-24 06:21:58,455 [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 2023-10-24 06:21:58,455 [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 2023-10-24 06:21:58,455 [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 2023-10-24 06:21:58,455 [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 2023-10-24 06:21:58,455 [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 2023-10-24 06:21:58,455 [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 2023-10-24 06:21:58,456 [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 2023-10-24 06:21:58,456 [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 2023-10-24 06:21:58,456 [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 2023-10-24 06:21:58,456 [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 2023-10-24 06:21:58,456 [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 2023-10-24 06:21:58,456 [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 2023-10-24 06:21:58,456 [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 2023-10-24 06:21:58,456 [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 2023-10-24 06:21:58,456 [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 2023-10-24 06:21:58,456 [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 2023-10-24 06:21:58,456 [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 2023-10-24 06:21:58,456 [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 2023-10-24 06:21:58,456 [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 2023-10-24 06:21:58,456 [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 2023-10-24 06:21:58,457 [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 2023-10-24 06:21:58,457 [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 2023-10-24 06:21:58,457 [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 2023-10-24 06:21:58,457 [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 2023-10-24 06:21:58,457 [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 2023-10-24 06:21:58,457 [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 2023-10-24 06:21:58,457 [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 2023-10-24 06:21:58,457 [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 2023-10-24 06:21:58,457 [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 2023-10-24 06:21:58,457 [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 2023-10-24 06:21:58,457 [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 2023-10-24 06:21:58,457 [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 2023-10-24 06:21:58,457 [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 2023-10-24 06:21:58,457 [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 2023-10-24 06:21:58,457 [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 2023-10-24 06:21:58,458 [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 2023-10-24 06:21:58,458 [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 2023-10-24 06:21:58,458 [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 2023-10-24 06:21:58,458 [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 2023-10-24 06:21:58,458 [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 2023-10-24 06:21:58,458 [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 2023-10-24 06:21:58,458 [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 2023-10-24 06:21:58,458 [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 2023-10-24 06:21:58,458 [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 2023-10-24 06:21:58,458 [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 2023-10-24 06:21:58,458 [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 2023-10-24 06:21:58,458 [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 2023-10-24 06:21:58,459 [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 2023-10-24 06:21:58,459 [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 2023-10-24 06:21:58,459 [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 2023-10-24 06:21:58,459 [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 2023-10-24 06:21:58,459 [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 2023-10-24 06:21:58,459 [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 2023-10-24 06:21:58,459 [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 2023-10-24 06:21:58,459 [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 2023-10-24 06:21:58,459 [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 2023-10-24 06:21:58,459 [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 2023-10-24 06:21:58,459 [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 2023-10-24 06:21:58,460 [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 2023-10-24 06:21:58,460 [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 2023-10-24 06:21:58,460 [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 2023-10-24 06:21:58,460 [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 2023-10-24 06:21:58,460 [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 2023-10-24 06:21:58,460 [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 2023-10-24 06:21:58,460 [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 2023-10-24 06:21:58,460 [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 2023-10-24 06:21:58,460 [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 2023-10-24 06:21:58,460 [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 2023-10-24 06:21:58,460 [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 2023-10-24 06:21:58,461 [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 2023-10-24 06:21:58,461 [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 2023-10-24 06:21:58,461 [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 2023-10-24 06:21:58,461 [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 2023-10-24 06:21:58,461 [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 2023-10-24 06:21:58,461 [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 2023-10-24 06:21:58,461 [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 2023-10-24 06:21:58,461 [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 2023-10-24 06:21:58,461 [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 2023-10-24 06:21:58,462 [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 2023-10-24 06:21:58,462 [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 2023-10-24 06:21:58,462 [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 2023-10-24 06:21:58,462 [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 2023-10-24 06:21:58,462 [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 2023-10-24 06:21:58,462 [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 2023-10-24 06:21:58,462 [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 2023-10-24 06:21:58,462 [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 2023-10-24 06:21:58,462 [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 2023-10-24 06:21:58,462 [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 2023-10-24 06:21:58,462 [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 2023-10-24 06:21:58,462 [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 2023-10-24 06:21:58,463 [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 2023-10-24 06:21:58,463 [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 2023-10-24 06:21:58,463 [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 2023-10-24 06:21:58,463 [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 2023-10-24 06:21:58,463 [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 2023-10-24 06:21:58,463 [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 2023-10-24 06:21:58,463 [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 2023-10-24 06:21:58,463 [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 2023-10-24 06:21:58,463 [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 2023-10-24 06:21:58,463 [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 2023-10-24 06:21:58,463 [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 2023-10-24 06:21:58,463 [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 2023-10-24 06:21:58,463 [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 2023-10-24 06:21:58,464 [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 2023-10-24 06:21:58,464 [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 2023-10-24 06:21:58,464 [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 2023-10-24 06:21:58,464 [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 2023-10-24 06:21:58,464 [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 2023-10-24 06:21:58,464 [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 2023-10-24 06:21:58,464 [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 2023-10-24 06:21:58,464 [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 2023-10-24 06:21:58,464 [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 2023-10-24 06:21:58,464 [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 2023-10-24 06:21:58,464 [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 2023-10-24 06:21:58,464 [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 2023-10-24 06:21:58,465 [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 2023-10-24 06:21:58,465 [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 2023-10-24 06:21:58,465 [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 2023-10-24 06:21:58,465 [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 2023-10-24 06:21:58,465 [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 2023-10-24 06:21:58,465 [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 2023-10-24 06:21:58,465 [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 2023-10-24 06:21:58,465 [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 2023-10-24 06:21:58,465 [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 2023-10-24 06:21:58,465 [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 2023-10-24 06:21:58,465 [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 2023-10-24 06:21:58,465 [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 2023-10-24 06:21:58,466 [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 2023-10-24 06:21:58,466 [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 2023-10-24 06:21:58,466 [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 2023-10-24 06:21:58,466 [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 2023-10-24 06:21:58,466 [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 2023-10-24 06:21:58,466 [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 2023-10-24 06:21:58,466 [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 2023-10-24 06:21:58,466 [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 2023-10-24 06:21:58,466 [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 2023-10-24 06:21:58,466 [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 2023-10-24 06:21:58,466 [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 2023-10-24 06:21:58,466 [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 2023-10-24 06:21:58,466 [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 2023-10-24 06:21:58,467 [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 2023-10-24 06:21:58,467 [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 2023-10-24 06:21:58,467 [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 2023-10-24 06:21:58,467 [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 2023-10-24 06:21:58,467 [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 2023-10-24 06:21:58,467 [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 2023-10-24 06:21:58,467 [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 2023-10-24 06:21:58,467 [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 2023-10-24 06:21:58,467 [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 2023-10-24 06:21:58,467 [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 2023-10-24 06:21:58,467 [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 2023-10-24 06:21:58,467 [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 2023-10-24 06:21:58,467 [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 2023-10-24 06:21:58,467 [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 2023-10-24 06:21:58,468 [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 2023-10-24 06:21:58,468 [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 2023-10-24 06:21:58,468 [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 2023-10-24 06:21:58,468 [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 2023-10-24 06:21:58,468 [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 2023-10-24 06:21:58,468 [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 2023-10-24 06:21:58,468 [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 2023-10-24 06:21:58,468 [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 2023-10-24 06:21:58,468 [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 2023-10-24 06:21:58,468 [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 2023-10-24 06:21:58,469 [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 2023-10-24 06:21:58,469 [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 2023-10-24 06:21:58,469 [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 2023-10-24 06:21:58,469 [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 2023-10-24 06:21:58,469 [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 2023-10-24 06:21:58,469 [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 2023-10-24 06:21:58,469 [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 2023-10-24 06:21:58,469 [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 2023-10-24 06:21:58,469 [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 2023-10-24 06:21:58,469 [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 2023-10-24 06:21:58,469 [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 2023-10-24 06:21:58,469 [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 2023-10-24 06:21:58,469 [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 2023-10-24 06:21:58,470 [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 2023-10-24 06:21:58,470 [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 2023-10-24 06:21:58,470 [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 2023-10-24 06:21:58,470 [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 2023-10-24 06:21:58,470 [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 2023-10-24 06:21:58,470 [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 2023-10-24 06:21:58,470 [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 2023-10-24 06:21:58,470 [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 2023-10-24 06:21:58,470 [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 2023-10-24 06:21:58,470 [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 2023-10-24 06:21:58,470 [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 2023-10-24 06:21:58,470 [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 2023-10-24 06:21:58,470 [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 2023-10-24 06:21:58,471 [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 2023-10-24 06:21:58,471 [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 2023-10-24 06:21:58,471 [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 2023-10-24 06:21:58,471 [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 2023-10-24 06:21:58,471 [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 2023-10-24 06:21:58,471 [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 2023-10-24 06:21:58,471 [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 2023-10-24 06:21:58,471 [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 2023-10-24 06:21:58,471 [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 2023-10-24 06:21:58,471 [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 2023-10-24 06:21:58,471 [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 2023-10-24 06:21:58,471 [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 2023-10-24 06:21:58,471 [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 2023-10-24 06:21:58,471 [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 2023-10-24 06:21:58,472 [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 2023-10-24 06:21:58,472 [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 2023-10-24 06:21:58,472 [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 2023-10-24 06:21:58,472 [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 2023-10-24 06:21:58,472 [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 2023-10-24 06:21:58,472 [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 2023-10-24 06:21:58,472 [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 2023-10-24 06:21:58,472 [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 2023-10-24 06:21:58,472 [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 2023-10-24 06:21:58,472 [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 2023-10-24 06:21:58,472 [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 2023-10-24 06:21:58,472 [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 2023-10-24 06:21:58,472 [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 2023-10-24 06:21:58,472 [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 2023-10-24 06:21:58,473 [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 2023-10-24 06:21:58,473 [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 2023-10-24 06:21:58,473 [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 2023-10-24 06:21:58,473 [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 2023-10-24 06:21:58,473 [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 2023-10-24 06:21:58,473 [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 2023-10-24 06:21:58,473 [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 2023-10-24 06:21:58,473 [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 2023-10-24 06:21:58,473 [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 2023-10-24 06:21:58,473 [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 2023-10-24 06:21:58,473 [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 2023-10-24 06:21:58,473 [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 2023-10-24 06:21:58,474 [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 2023-10-24 06:21:58,474 [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 2023-10-24 06:21:58,474 [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 2023-10-24 06:21:58,474 [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 2023-10-24 06:21:58,474 [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 2023-10-24 06:21:58,474 [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 2023-10-24 06:21:58,474 [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 2023-10-24 06:21:58,474 [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 2023-10-24 06:21:58,474 [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 2023-10-24 06:21:58,474 [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 2023-10-24 06:21:58,474 [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 2023-10-24 06:21:58,474 [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 2023-10-24 06:21:58,474 [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 2023-10-24 06:21:58,474 [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 2023-10-24 06:21:58,475 [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 2023-10-24 06:21:58,475 [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 2023-10-24 06:21:58,475 [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 2023-10-24 06:21:58,475 [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 2023-10-24 06:21:58,475 [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 2023-10-24 06:21:58,475 [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 2023-10-24 06:21:58,475 [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 2023-10-24 06:21:58,475 [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 2023-10-24 06:21:58,475 [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 2023-10-24 06:21:58,475 [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 2023-10-24 06:21:58,475 [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 2023-10-24 06:21:58,475 [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 2023-10-24 06:21:58,475 [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 2023-10-24 06:21:58,475 [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 2023-10-24 06:21:58,476 [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 2023-10-24 06:21:58,476 [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 2023-10-24 06:21:58,476 [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 2023-10-24 06:21:58,476 [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 2023-10-24 06:21:58,476 [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 2023-10-24 06:21:58,476 [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 2023-10-24 06:21:58,476 [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 2023-10-24 06:21:58,476 [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 2023-10-24 06:21:58,476 [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 2023-10-24 06:21:58,476 [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 2023-10-24 06:21:58,476 [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 2023-10-24 06:21:58,476 [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 2023-10-24 06:21:58,476 [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 2023-10-24 06:21:58,476 [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 2023-10-24 06:21:58,476 [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 2023-10-24 06:21:58,476 [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 2023-10-24 06:21:58,477 [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 2023-10-24 06:21:58,477 [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 2023-10-24 06:21:58,477 [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 2023-10-24 06:21:58,477 [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 2023-10-24 06:21:58,477 [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 2023-10-24 06:21:58,477 [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 2023-10-24 06:21:58,477 [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 2023-10-24 06:21:58,477 [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 2023-10-24 06:21:58,477 [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 2023-10-24 06:21:58,477 [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 2023-10-24 06:21:58,477 [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 2023-10-24 06:21:58,477 [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 2023-10-24 06:21:58,478 [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 2023-10-24 06:21:58,478 [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 2023-10-24 06:21:58,478 [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 2023-10-24 06:21:58,478 [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 2023-10-24 06:21:58,478 [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 2023-10-24 06:21:58,478 [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 2023-10-24 06:21:58,478 [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 2023-10-24 06:21:58,478 [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 2023-10-24 06:21:58,478 [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 2023-10-24 06:21:58,478 [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 2023-10-24 06:21:58,478 [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 2023-10-24 06:21:58,478 [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 2023-10-24 06:21:58,478 [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 2023-10-24 06:21:58,479 [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 2023-10-24 06:21:58,479 [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 2023-10-24 06:21:58,479 [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 2023-10-24 06:21:58,479 [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 2023-10-24 06:21:58,479 [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 2023-10-24 06:21:58,479 [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 2023-10-24 06:21:58,479 [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 2023-10-24 06:21:58,479 [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 2023-10-24 06:21:58,479 [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 2023-10-24 06:21:58,479 [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 2023-10-24 06:21:58,479 [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 2023-10-24 06:21:58,479 [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 2023-10-24 06:21:58,480 [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 2023-10-24 06:21:58,480 [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 2023-10-24 06:21:58,480 [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 2023-10-24 06:21:58,480 [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 2023-10-24 06:21:58,480 [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 2023-10-24 06:21:58,480 [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 2023-10-24 06:21:58,480 [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 2023-10-24 06:21:58,480 [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 2023-10-24 06:21:58,480 [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 2023-10-24 06:21:58,481 [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 2023-10-24 06:21:58,481 [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 2023-10-24 06:21:58,481 [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 2023-10-24 06:21:58,481 [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 2023-10-24 06:21:58,481 [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 2023-10-24 06:21:58,481 [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 2023-10-24 06:21:58,481 [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 2023-10-24 06:21:58,481 [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 2023-10-24 06:21:58,481 [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 2023-10-24 06:21:58,481 [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 2023-10-24 06:21:58,481 [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 2023-10-24 06:21:58,482 [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 2023-10-24 06:21:58,482 [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 2023-10-24 06:21:58,482 [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 2023-10-24 06:21:58,482 [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 2023-10-24 06:21:58,482 [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 2023-10-24 06:21:58,482 [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 2023-10-24 06:21:58,482 [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 2023-10-24 06:21:58,482 [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 2023-10-24 06:21:58,482 [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 2023-10-24 06:21:58,482 [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 2023-10-24 06:21:58,482 [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 2023-10-24 06:21:58,482 [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 2023-10-24 06:21:58,483 [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 2023-10-24 06:21:58,483 [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 2023-10-24 06:21:58,483 [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 2023-10-24 06:21:58,483 [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 2023-10-24 06:21:58,483 [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 2023-10-24 06:21:58,483 [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 2023-10-24 06:21:58,483 [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 2023-10-24 06:21:58,483 [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 2023-10-24 06:21:58,483 [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 2023-10-24 06:21:58,483 [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 2023-10-24 06:21:58,483 [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 2023-10-24 06:21:58,483 [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 2023-10-24 06:21:58,483 [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 2023-10-24 06:21:58,483 [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 2023-10-24 06:21:58,484 [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 2023-10-24 06:21:58,484 [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 2023-10-24 06:21:58,484 [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 2023-10-24 06:21:58,484 [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 2023-10-24 06:21:58,484 [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 2023-10-24 06:21:58,484 [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 2023-10-24 06:21:58,484 [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 2023-10-24 06:21:58,484 [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 2023-10-24 06:21:58,484 [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 2023-10-24 06:21:58,484 [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 2023-10-24 06:21:58,484 [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 2023-10-24 06:21:58,484 [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 2023-10-24 06:21:58,484 [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 2023-10-24 06:21:58,485 [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 2023-10-24 06:21:58,485 [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 2023-10-24 06:21:58,485 [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 2023-10-24 06:21:58,485 [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 2023-10-24 06:21:58,485 [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 2023-10-24 06:21:58,485 [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 2023-10-24 06:21:58,485 [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 2023-10-24 06:21:58,485 [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 2023-10-24 06:21:58,485 [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 2023-10-24 06:21:58,485 [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 2023-10-24 06:21:58,486 [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 2023-10-24 06:21:58,486 [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 2023-10-24 06:21:58,486 [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 2023-10-24 06:21:58,486 [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 2023-10-24 06:21:58,486 [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 2023-10-24 06:21:58,486 [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 2023-10-24 06:21:58,486 [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 2023-10-24 06:21:58,486 [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 2023-10-24 06:21:58,486 [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 2023-10-24 06:21:58,486 [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 2023-10-24 06:21:58,486 [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 2023-10-24 06:21:58,487 [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 2023-10-24 06:21:58,487 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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DEBUG 2023-10-24 06:21:58,500 [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 2023-10-24 06:21:58,500 [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 2023-10-24 06:21:58,500 [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 2023-10-24 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06:21:58,507 [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 2023-10-24 06:21:58,507 [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 2023-10-24 06:21:58,507 [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 2023-10-24 06:21:58,507 [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 2023-10-24 06:21:58,507 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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panel.... +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:21:58,508 [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 2023-10-24 06:21:58,508 [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 2023-10-24 06:21:58,508 [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 2023-10-24 06:21:58,508 [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 2023-10-24 06:21:58,508 [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 2023-10-24 06:21:58,508 [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 2023-10-24 06:21:58,508 [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 2023-10-24 06:21:58,508 [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 2023-10-24 06:21:58,508 [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 2023-10-24 06:21:58,508 [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 2023-10-24 06:21:58,509 [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 2023-10-24 06:21:58,509 [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 2023-10-24 06:21:58,509 [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 2023-10-24 06:21:58,509 [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 2023-10-24 06:21:58,509 [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 2023-10-24 06:21:58,509 [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 2023-10-24 06:21:58,509 [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 2023-10-24 06:21:58,509 [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 2023-10-24 06:21:58,509 [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 2023-10-24 06:21:58,510 [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 2023-10-24 06:21:58,510 [pN:job_handler_0,p:8,tN:Thread-1] Loading EDAM tool panel finished (69.942 ms) +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,510 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,510 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,510 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,510 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,510 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,510 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,510 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_Bam_Bai_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,510 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,510 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,510 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,510 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_coodinate_sorted_bam +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,510 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,511 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_cram_to_bam_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,511 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_to_gff_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,511 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,511 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,511 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,511 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_to_fli_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,511 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bedgraph_to_bigwig +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,511 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_len_to_linecount +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,511 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_parquet_to_csv +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,511 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: bigwigtowig +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,511 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,511 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,511 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,511 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: csv_to_tabular +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,511 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: tabular_to_csv +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,511 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_tabular +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,511 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_bowtie_base_index +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,511 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_bowtie_color_index +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,511 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_2bit +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,511 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_len +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,511 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_fai +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,512 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,512 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,512 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,512 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,512 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,512 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,512 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,512 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,512 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,512 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,512 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,512 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,512 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,512 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,513 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,513 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,513 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,513 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,513 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,513 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,513 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,513 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,513 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gff_to_bed_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,513 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gff_to_interval_index_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,513 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,513 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gff_to_fli_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,513 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,513 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,513 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,513 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,514 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,514 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gff_to_interval_index_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,514 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,514 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bed_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,514 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bedstrict_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,514 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bed6_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,514 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bed12_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,514 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,514 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,514 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,514 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_picard_interval_list_to_bed6 +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,514 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_tar_to_directory +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,514 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,514 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,514 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,514 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,514 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,515 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,515 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_maf_to_fasta_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,515 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_maf_to_interval_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,515 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,515 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,515 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,515 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,515 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,515 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_sam_to_unsorted_bam +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,515 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_coodinate_sorted_bam +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,515 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,515 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_sam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,515 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: tabular_to_dbnsfp +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,515 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: tabular_to_csv +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,515 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,515 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,515 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,516 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,516 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,516 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,516 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,516 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bcf_uncompressed_to_bcf +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,516 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bcf_uncompressed_to_bcf +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,516 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_wig_to_bigwig +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,516 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_wiggle_to_interval_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,516 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,516 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,516 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: lped2fpedconvert +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,516 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: lped2pbedconvert +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,516 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: pbed2lpedconvert +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,516 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: pbed2ldindepconvert +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,516 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,516 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,516 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_biom +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,516 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_biom +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,516 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,517 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,517 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,517 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_SMILES_to_MOL +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,517 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,517 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_smiles_to_smiles +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,517 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,517 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,517 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,517 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,517 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,517 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,517 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_inchi_to_mol +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,517 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,517 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,517 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,517 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,518 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,518 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,518 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,518 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,518 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,518 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,518 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mol2_to_mol +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,518 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,518 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_cml_to_smiles +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,518 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,518 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,518 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,518 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_Pdb_to_Gro_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,518 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,518 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,518 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,518 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,519 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,519 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,519 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_Gro_to_Pdb_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,519 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_ref_to_seq_taxomony +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,519 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_neostorezip_to_neostore +galaxy.datatypes.registry DEBUG 2023-10-24 06:21:58,520 [pN:job_handler_0,p:8,tN:Thread-1] Loaded external metadata tool: __SET_METADATA__ +galaxy.tools.special_tools DEBUG 2023-10-24 06:21:58,521 [pN:job_handler_0,p:8,tN:Thread-1] Loaded history export tool: __EXPORT_HISTORY__ +galaxy.tools.special_tools DEBUG 2023-10-24 06:21:58,522 [pN:job_handler_0,p:8,tN:Thread-1] Loaded history export to uri tool: __EXPORT_HISTORY_TO_URI__ +galaxy.tools.special_tools DEBUG 2023-10-24 06:21:58,523 [pN:job_handler_0,p:8,tN:Thread-1] Loaded history import tool: __IMPORT_HISTORY__ +galaxy.tools.special_tools DEBUG 2023-10-24 06:21:58,524 [pN:job_handler_0,p:8,tN:Thread-1] Loaded data fetch tool: __DATA_FETCH__ +galaxy.queue_worker INFO 2023-10-24 06:21:58,524 [pN:job_handler_0,p:8,tN:Thread-1] Queuing async task rebuild_toolbox_search_index for job_handler_0. +galaxy.queue_worker DEBUG 2023-10-24 06:21:58,525 [pN:job_handler_0,p:8,tN:Thread-1] Toolbox reload (305.977 ms) +galaxy.queue_worker INFO 2023-10-24 06:21:58,526 [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 2023-10-24 06:21:58,526 [pN:job_handler_0,p:8,tN:Thread-1] App is not a webapp, not building a search index +galaxy.queue_worker INFO 2023-10-24 06:22:07,897 [pN:job_handler_0,p:8,tN:Thread-1] Instance 'job_handler_0' received 'reload_toolbox' task, executing now. +galaxy.queue_worker DEBUG 2023-10-24 06:22:07,898 [pN:job_handler_0,p:8,tN:Thread-1] Executing toolbox reload on 'job_handler_0' +galaxy.util WARNING 2023-10-24 06:22:07,923 [pN:job_handler_0,p:8,tN:Thread-1] directory not found: /galaxy/server/lib/galaxy/util/../../../config/plugins/activities +galaxy.tools WARNING 2023-10-24 06:22:07,929 [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 2023-10-24 06:22:07,930 [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 2023-10-24 06:22:07,930 [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 2023-10-24 06:22:07,931 [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 2023-10-24 06:22:07,931 [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 2023-10-24 06:22:07,933 [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 2023-10-24 06:22:07,933 [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 2023-10-24 06:22:07,935 [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 859, 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 1086, in load_tool + tool = self.create_tool( + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 512, 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 528, in _create_tool_from_source + return create_tool_from_source(self.app, tool_source, **kwds) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 322, in create_tool_from_source + tool = ToolClass(config_file, tool_source, app, **kwds) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 784, in __init__ + raise e + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 781, in __init__ + self.parse(tool_source, guid=guid, dynamic=dynamic) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1105, in parse + self.parse_inputs(self.tool_source) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1396, in parse_inputs + inputs = self.parse_input_elem(page_source, enctypes) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1591, in parse_input_elem + param = self.parse_param_elem(input_source, enctypes, context) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1604, 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 2023-10-24 06:22:07,936 [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 2023-10-24 06:22:07,936 [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 2023-10-24 06:22:07,950 [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.tools WARNING 2023-10-24 06:22:07,987 [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 2023-10-24 06:22:07,987 [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 2023-10-24 06:22:07,988 [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 2023-10-24 06:22:07,988 [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 2023-10-24 06:22:07,988 [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 2023-10-24 06:22:07,988 [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 2023-10-24 06:22:07,988 [pN:job_handler_0,p:8,tN:Thread-1] Reading tools from config files finished (59.006 ms) +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:07,988 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Get Data +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:07,988 [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 2023-10-24 06:22:07,988 [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 2023-10-24 06:22:07,988 [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 2023-10-24 06:22:07,989 [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 2023-10-24 06:22:07,989 [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 2023-10-24 06:22:07,989 [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 2023-10-24 06:22:07,989 [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 2023-10-24 06:22:07,989 [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 2023-10-24 06:22:07,989 [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 2023-10-24 06:22:07,989 [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 2023-10-24 06:22:07,989 [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 2023-10-24 06:22:07,989 [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 2023-10-24 06:22:07,989 [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 2023-10-24 06:22:07,989 [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 2023-10-24 06:22:07,989 [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 2023-10-24 06:22:07,989 [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 2023-10-24 06:22:07,990 [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 2023-10-24 06:22:07,990 [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 2023-10-24 06:22:07,990 [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 2023-10-24 06:22:07,990 [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 2023-10-24 06:22:07,990 [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 2023-10-24 06:22:07,990 [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 2023-10-24 06:22:07,990 [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 2023-10-24 06:22:07,990 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Send Data +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:07,990 [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 2023-10-24 06:22:07,991 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Send Data +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:07,991 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Expression Tools +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:07,991 [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 2023-10-24 06:22:07,991 [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 2023-10-24 06:22:07,991 [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 2023-10-24 06:22:07,991 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Collection Operations +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:07,991 [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 2023-10-24 06:22:07,991 [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 2023-10-24 06:22:07,991 [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 2023-10-24 06:22:07,991 [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 2023-10-24 06:22:07,992 [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 2023-10-24 06:22:07,992 [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 2023-10-24 06:22:07,992 [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 2023-10-24 06:22:07,992 [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 2023-10-24 06:22:07,992 [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 2023-10-24 06:22:07,992 [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 2023-10-24 06:22:07,992 [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 2023-10-24 06:22:07,992 [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 2023-10-24 06:22:07,992 [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 2023-10-24 06:22:07,992 [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 2023-10-24 06:22:07,993 [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 2023-10-24 06:22:07,993 [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 2023-10-24 06:22:07,993 [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 2023-10-24 06:22:07,993 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Text Manipulation +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:07,993 [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 2023-10-24 06:22:07,993 [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 2023-10-24 06:22:07,993 [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 2023-10-24 06:22:07,993 [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 2023-10-24 06:22:07,993 [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 2023-10-24 06:22:07,993 [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 2023-10-24 06:22:07,993 [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 2023-10-24 06:22:07,993 [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 2023-10-24 06:22:07,993 [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 2023-10-24 06:22:07,994 [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 2023-10-24 06:22:07,994 [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 2023-10-24 06:22:07,994 [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 2023-10-24 06:22:07,994 [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 2023-10-24 06:22:07,994 [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 2023-10-24 06:22:07,994 [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 2023-10-24 06:22:07,994 [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 2023-10-24 06:22:07,994 [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 2023-10-24 06:22:07,994 [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 2023-10-24 06:22:07,994 [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 2023-10-24 06:22:07,994 [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 2023-10-24 06:22:07,994 [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 2023-10-24 06:22:07,995 [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 2023-10-24 06:22:07,995 [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 2023-10-24 06:22:07,995 [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 2023-10-24 06:22:07,995 [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 2023-10-24 06:22:07,995 [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 2023-10-24 06:22:07,995 [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 2023-10-24 06:22:07,995 [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 2023-10-24 06:22:07,995 [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 2023-10-24 06:22:07,995 [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 2023-10-24 06:22:07,995 [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 2023-10-24 06:22:07,995 [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 2023-10-24 06:22:07,995 [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 2023-10-24 06:22:07,995 [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 2023-10-24 06:22:07,996 [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 2023-10-24 06:22:07,996 [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 2023-10-24 06:22:07,996 [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 2023-10-24 06:22:07,996 [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 2023-10-24 06:22:07,996 [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 2023-10-24 06:22:07,996 [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 2023-10-24 06:22:07,996 [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 2023-10-24 06:22:07,996 [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 2023-10-24 06:22:07,996 [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 2023-10-24 06:22:07,996 [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 2023-10-24 06:22:07,996 [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 2023-10-24 06:22:07,996 [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 2023-10-24 06:22:07,996 [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 2023-10-24 06:22:07,996 [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 2023-10-24 06:22:07,997 [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 2023-10-24 06:22:07,997 [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 2023-10-24 06:22:07,997 [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 2023-10-24 06:22:07,997 [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 2023-10-24 06:22:07,997 [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 2023-10-24 06:22:07,997 [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 2023-10-24 06:22:07,997 [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 2023-10-24 06:22:07,997 [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 2023-10-24 06:22:07,997 [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 2023-10-24 06:22:07,997 [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 2023-10-24 06:22:07,998 [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 2023-10-24 06:22:07,998 [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 2023-10-24 06:22:07,998 [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 2023-10-24 06:22:07,998 [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 2023-10-24 06:22:07,998 [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 2023-10-24 06:22:07,998 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Filter and Sort +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:07,998 [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 2023-10-24 06:22:07,998 [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 2023-10-24 06:22:07,998 [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 2023-10-24 06:22:07,998 [pN:job_handler_0,p:8,tN:Thread-1] Loaded label: GFF +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:07,999 [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 2023-10-24 06:22:07,999 [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 2023-10-24 06:22:07,999 [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 2023-10-24 06:22:07,999 [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 2023-10-24 06:22:07,999 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Join, Subtract and Group +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:07,999 [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 2023-10-24 06:22:07,999 [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 2023-10-24 06:22:07,999 [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 2023-10-24 06:22:07,999 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Datamash +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:07,999 [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 2023-10-24 06:22:07,999 [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 2023-10-24 06:22:07,999 [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 2023-10-24 06:22:07,999 [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 2023-10-24 06:22:08,000 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: FASTA/FASTQ +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,000 [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 2023-10-24 06:22:08,000 [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 2023-10-24 06:22:08,000 [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 2023-10-24 06:22:08,000 [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 2023-10-24 06:22:08,000 [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 2023-10-24 06:22:08,000 [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 2023-10-24 06:22:08,000 [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 2023-10-24 06:22:08,000 [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 2023-10-24 06:22:08,000 [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 2023-10-24 06:22:08,000 [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 2023-10-24 06:22:08,000 [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 2023-10-24 06:22:08,001 [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 2023-10-24 06:22:08,001 [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 2023-10-24 06:22:08,001 [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 2023-10-24 06:22:08,001 [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 2023-10-24 06:22:08,001 [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 2023-10-24 06:22:08,001 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: FASTQ Quality Control +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,002 [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 2023-10-24 06:22:08,002 [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 2023-10-24 06:22:08,002 [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 2023-10-24 06:22:08,002 [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 2023-10-24 06:22:08,002 [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 2023-10-24 06:22:08,004 [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 2023-10-24 06:22:08,005 [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 2023-10-24 06:22:08,005 [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 2023-10-24 06:22:08,005 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: SAM/BAM +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,005 [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 2023-10-24 06:22:08,005 [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 2023-10-24 06:22:08,005 [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 2023-10-24 06:22:08,005 [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 2023-10-24 06:22:08,005 [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 2023-10-24 06:22:08,005 [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 2023-10-24 06:22:08,006 [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 2023-10-24 06:22:08,006 [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 2023-10-24 06:22:08,006 [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 2023-10-24 06:22:08,006 [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 2023-10-24 06:22:08,006 [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 2023-10-24 06:22:08,006 [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 2023-10-24 06:22:08,006 [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 2023-10-24 06:22:08,006 [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 2023-10-24 06:22:08,006 [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 2023-10-24 06:22:08,006 [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 2023-10-24 06:22:08,007 [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 2023-10-24 06:22:08,007 [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 2023-10-24 06:22:08,007 [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 2023-10-24 06:22:08,007 [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 2023-10-24 06:22:08,008 [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 2023-10-24 06:22:08,008 [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 2023-10-24 06:22:08,008 [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 2023-10-24 06:22:08,008 [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 2023-10-24 06:22:08,008 [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 2023-10-24 06:22:08,008 [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 2023-10-24 06:22:08,008 [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 2023-10-24 06:22:08,008 [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 2023-10-24 06:22:08,008 [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 2023-10-24 06:22:08,008 [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 2023-10-24 06:22:08,009 [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 2023-10-24 06:22:08,009 [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 2023-10-24 06:22:08,009 [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 2023-10-24 06:22:08,009 [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 2023-10-24 06:22:08,009 [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 2023-10-24 06:22:08,009 [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 2023-10-24 06:22:08,009 [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 2023-10-24 06:22:08,009 [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 2023-10-24 06:22:08,010 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: BED +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,010 [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 2023-10-24 06:22:08,010 [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 2023-10-24 06:22:08,010 [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 2023-10-24 06:22:08,010 [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 2023-10-24 06:22:08,010 [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 2023-10-24 06:22:08,010 [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 2023-10-24 06:22:08,010 [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 2023-10-24 06:22:08,010 [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 2023-10-24 06:22:08,010 [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 2023-10-24 06:22:08,010 [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 2023-10-24 06:22:08,010 [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 2023-10-24 06:22:08,010 [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 2023-10-24 06:22:08,011 [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 2023-10-24 06:22:08,011 [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 2023-10-24 06:22:08,011 [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 2023-10-24 06:22:08,011 [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 2023-10-24 06:22:08,011 [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 2023-10-24 06:22:08,011 [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 2023-10-24 06:22:08,011 [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 2023-10-24 06:22:08,011 [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 2023-10-24 06:22:08,011 [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 2023-10-24 06:22:08,011 [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 2023-10-24 06:22:08,011 [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 2023-10-24 06:22:08,011 [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 2023-10-24 06:22:08,012 [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 2023-10-24 06:22:08,012 [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 2023-10-24 06:22:08,012 [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 2023-10-24 06:22:08,012 [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 2023-10-24 06:22:08,012 [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 2023-10-24 06:22:08,012 [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 2023-10-24 06:22:08,012 [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 2023-10-24 06:22:08,012 [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 2023-10-24 06:22:08,012 [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 2023-10-24 06:22:08,012 [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 2023-10-24 06:22:08,012 [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 2023-10-24 06:22:08,012 [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 2023-10-24 06:22:08,013 [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 2023-10-24 06:22:08,013 [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 2023-10-24 06:22:08,013 [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 2023-10-24 06:22:08,013 [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 2023-10-24 06:22:08,013 [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 2023-10-24 06:22:08,013 [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 2023-10-24 06:22:08,013 [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 2023-10-24 06:22:08,013 [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 2023-10-24 06:22:08,013 [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 2023-10-24 06:22:08,013 [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 2023-10-24 06:22:08,014 [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 2023-10-24 06:22:08,014 [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 2023-10-24 06:22:08,014 [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 2023-10-24 06:22:08,014 [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 2023-10-24 06:22:08,014 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: VCF/BCF +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,014 [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 2023-10-24 06:22:08,014 [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 2023-10-24 06:22:08,014 [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 2023-10-24 06:22:08,014 [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 2023-10-24 06:22:08,014 [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 2023-10-24 06:22:08,014 [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 2023-10-24 06:22:08,014 [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 2023-10-24 06:22:08,015 [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 2023-10-24 06:22:08,015 [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 2023-10-24 06:22:08,015 [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 2023-10-24 06:22:08,015 [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 2023-10-24 06:22:08,015 [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 2023-10-24 06:22:08,015 [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 2023-10-24 06:22:08,015 [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 2023-10-24 06:22:08,015 [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 2023-10-24 06:22:08,015 [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 2023-10-24 06:22:08,015 [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 2023-10-24 06:22:08,015 [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 2023-10-24 06:22:08,015 [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 2023-10-24 06:22:08,015 [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 2023-10-24 06:22:08,015 [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 2023-10-24 06:22:08,016 [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 2023-10-24 06:22:08,016 [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 2023-10-24 06:22:08,016 [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 2023-10-24 06:22:08,016 [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 2023-10-24 06:22:08,016 [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 2023-10-24 06:22:08,016 [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 2023-10-24 06:22:08,016 [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 2023-10-24 06:22:08,016 [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 2023-10-24 06:22:08,016 [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 2023-10-24 06:22:08,016 [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 2023-10-24 06:22:08,016 [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 2023-10-24 06:22:08,016 [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 2023-10-24 06:22:08,017 [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 2023-10-24 06:22:08,017 [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 2023-10-24 06:22:08,017 [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 2023-10-24 06:22:08,017 [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 2023-10-24 06:22:08,017 [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 2023-10-24 06:22:08,017 [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 2023-10-24 06:22:08,017 [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 2023-10-24 06:22:08,017 [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 2023-10-24 06:22:08,017 [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 2023-10-24 06:22:08,017 [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 2023-10-24 06:22:08,017 [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 2023-10-24 06:22:08,017 [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 2023-10-24 06:22:08,017 [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 2023-10-24 06:22:08,018 [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 2023-10-24 06:22:08,018 [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 2023-10-24 06:22:08,018 [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 2023-10-24 06:22:08,018 [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 2023-10-24 06:22:08,018 [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 2023-10-24 06:22:08,018 [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 2023-10-24 06:22:08,018 [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 2023-10-24 06:22:08,018 [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 2023-10-24 06:22:08,018 [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 2023-10-24 06:22:08,018 [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 2023-10-24 06:22:08,018 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Nanopore +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,018 [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 2023-10-24 06:22:08,019 [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 2023-10-24 06:22:08,019 [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 2023-10-24 06:22:08,019 [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 2023-10-24 06:22:08,019 [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 2023-10-24 06:22:08,019 [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 2023-10-24 06:22:08,019 [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 2023-10-24 06:22:08,019 [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 2023-10-24 06:22:08,019 [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 2023-10-24 06:22:08,019 [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 2023-10-24 06:22:08,019 [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 2023-10-24 06:22:08,019 [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 2023-10-24 06:22:08,019 [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 2023-10-24 06:22:08,019 [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 2023-10-24 06:22:08,019 [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 2023-10-24 06:22:08,020 [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 2023-10-24 06:22:08,020 [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 2023-10-24 06:22:08,020 [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 2023-10-24 06:22:08,020 [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 2023-10-24 06:22:08,020 [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 2023-10-24 06:22:08,020 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Convert Formats +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,020 [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 2023-10-24 06:22:08,020 [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 2023-10-24 06:22:08,020 [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 2023-10-24 06:22:08,020 [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 2023-10-24 06:22:08,020 [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 2023-10-24 06:22:08,020 [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 2023-10-24 06:22:08,020 [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 2023-10-24 06:22:08,020 [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 2023-10-24 06:22:08,021 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Lift-Over +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,021 [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 2023-10-24 06:22:08,021 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Virology +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,021 [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 2023-10-24 06:22:08,021 [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 2023-10-24 06:22:08,021 [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 2023-10-24 06:22:08,021 [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 2023-10-24 06:22:08,021 [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 2023-10-24 06:22:08,021 [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 2023-10-24 06:22:08,022 [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 2023-10-24 06:22:08,022 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Operate on Genomic Intervals +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,022 [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 2023-10-24 06:22:08,022 [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 2023-10-24 06:22:08,022 [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 2023-10-24 06:22:08,022 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Fetch Sequences/Alignments +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,022 [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 2023-10-24 06:22:08,022 [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 2023-10-24 06:22:08,022 [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 2023-10-24 06:22:08,022 [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 2023-10-24 06:22:08,022 [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 2023-10-24 06:22:08,022 [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 2023-10-24 06:22:08,023 [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 2023-10-24 06:22:08,023 [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 2023-10-24 06:22:08,023 [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 2023-10-24 06:22:08,023 [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 2023-10-24 06:22:08,023 [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 2023-10-24 06:22:08,023 [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 2023-10-24 06:22:08,023 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Assembly +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,023 [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 2023-10-24 06:22:08,023 [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 2023-10-24 06:22:08,024 [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 2023-10-24 06:22:08,024 [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 2023-10-24 06:22:08,024 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Annotation +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,024 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Mapping +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,024 [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 2023-10-24 06:22:08,024 [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 2023-10-24 06:22:08,024 [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 2023-10-24 06:22:08,025 [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 2023-10-24 06:22:08,025 [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 2023-10-24 06:22:08,025 [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 2023-10-24 06:22:08,025 [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 2023-10-24 06:22:08,025 [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 2023-10-24 06:22:08,025 [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 2023-10-24 06:22:08,025 [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 2023-10-24 06:22:08,026 [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 2023-10-24 06:22:08,026 [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 2023-10-24 06:22:08,026 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Variant Calling +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,026 [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 2023-10-24 06:22:08,026 [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 2023-10-24 06:22:08,026 [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 2023-10-24 06:22:08,027 [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 2023-10-24 06:22:08,027 [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 2023-10-24 06:22:08,027 [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 2023-10-24 06:22:08,027 [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 2023-10-24 06:22:08,027 [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 2023-10-24 06:22:08,027 [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 2023-10-24 06:22:08,027 [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 2023-10-24 06:22:08,028 [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 2023-10-24 06:22:08,028 [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 2023-10-24 06:22:08,028 [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 2023-10-24 06:22:08,028 [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 2023-10-24 06:22:08,028 [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 2023-10-24 06:22:08,028 [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 2023-10-24 06:22:08,028 [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 2023-10-24 06:22:08,028 [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 2023-10-24 06:22:08,028 [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 2023-10-24 06:22:08,029 [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 2023-10-24 06:22:08,029 [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 2023-10-24 06:22:08,029 [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 2023-10-24 06:22:08,029 [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 2023-10-24 06:22:08,029 [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 2023-10-24 06:22:08,029 [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 2023-10-24 06:22:08,029 [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 2023-10-24 06:22:08,029 [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 2023-10-24 06:22:08,029 [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 2023-10-24 06:22:08,029 [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 2023-10-24 06:22:08,030 [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 2023-10-24 06:22:08,030 [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 2023-10-24 06:22:08,030 [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 2023-10-24 06:22:08,030 [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 2023-10-24 06:22:08,030 [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 2023-10-24 06:22:08,030 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: ChIP-seq +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,030 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: RNA-seq +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,030 [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 2023-10-24 06:22:08,030 [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 2023-10-24 06:22:08,030 [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 2023-10-24 06:22:08,031 [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 2023-10-24 06:22:08,031 [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 2023-10-24 06:22:08,031 [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 2023-10-24 06:22:08,031 [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 2023-10-24 06:22:08,031 [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 2023-10-24 06:22:08,031 [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 2023-10-24 06:22:08,031 [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 2023-10-24 06:22:08,031 [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 2023-10-24 06:22:08,031 [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 2023-10-24 06:22:08,031 [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 2023-10-24 06:22:08,031 [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 2023-10-24 06:22:08,032 [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 2023-10-24 06:22:08,032 [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 2023-10-24 06:22:08,032 [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 2023-10-24 06:22:08,032 [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 2023-10-24 06:22:08,032 [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 2023-10-24 06:22:08,032 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Multiple Alignments +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,032 [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 2023-10-24 06:22:08,032 [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 2023-10-24 06:22:08,032 [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 2023-10-24 06:22:08,032 [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 2023-10-24 06:22:08,032 [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 2023-10-24 06:22:08,033 [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 2023-10-24 06:22:08,033 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Phenotype Association +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,033 [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 2023-10-24 06:22:08,033 [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 2023-10-24 06:22:08,033 [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 2023-10-24 06:22:08,033 [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 2023-10-24 06:22:08,033 [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 2023-10-24 06:22:08,033 [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 2023-10-24 06:22:08,033 [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 2023-10-24 06:22:08,033 [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 2023-10-24 06:22:08,033 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Regional Variation +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,033 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: STR-FM: Microsatellite Analysis +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,033 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Motif +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,033 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Chromosome Conformation +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,033 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Metagenomic Analysis +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,033 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Mothur +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,033 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Picard +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,033 [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 2023-10-24 06:22:08,034 [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 2023-10-24 06:22:08,034 [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 2023-10-24 06:22:08,034 [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 2023-10-24 06:22:08,034 [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 2023-10-24 06:22:08,034 [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 2023-10-24 06:22:08,034 [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 2023-10-24 06:22:08,034 [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 2023-10-24 06:22:08,034 [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 2023-10-24 06:22:08,034 [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 2023-10-24 06:22:08,034 [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 2023-10-24 06:22:08,034 [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 2023-10-24 06:22:08,034 [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 2023-10-24 06:22:08,034 [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 2023-10-24 06:22:08,035 [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 2023-10-24 06:22:08,035 [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 2023-10-24 06:22:08,035 [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 2023-10-24 06:22:08,035 [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 2023-10-24 06:22:08,035 [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 2023-10-24 06:22:08,035 [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 2023-10-24 06:22:08,035 [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 2023-10-24 06:22:08,035 [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 2023-10-24 06:22:08,035 [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 2023-10-24 06:22:08,035 [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 2023-10-24 06:22:08,035 [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 2023-10-24 06:22:08,035 [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 2023-10-24 06:22:08,035 [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 2023-10-24 06:22:08,036 [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 2023-10-24 06:22:08,036 [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 2023-10-24 06:22:08,036 [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 2023-10-24 06:22:08,036 [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 2023-10-24 06:22:08,036 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Pharmacology +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,036 [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 2023-10-24 06:22:08,036 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Single-Cell +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,036 [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 2023-10-24 06:22:08,036 [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 2023-10-24 06:22:08,037 [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 2023-10-24 06:22:08,037 [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 2023-10-24 06:22:08,037 [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 2023-10-24 06:22:08,037 [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 2023-10-24 06:22:08,037 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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+galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,044 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/deeptools_bam_pe_fragmentsize/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,044 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,044 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,044 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/deeptools_correct_gc_bias/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,044 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,044 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,044 [pN:job_handler_0,p:8,tN:Thread-1] 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 2023-10-24 06:22:08,045 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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+galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,059 [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 2023-10-24 06:22:08,059 [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 2023-10-24 06:22:08,059 [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 2023-10-24 06:22:08,059 [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 2023-10-24 06:22:08,060 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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+galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,060 [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 2023-10-24 06:22:08,060 [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 2023-10-24 06:22:08,060 [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 2023-10-24 06:22:08,060 [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 2023-10-24 06:22:08,060 [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 2023-10-24 06:22:08,060 [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 2023-10-24 06:22:08,060 [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 2023-10-24 06:22:08,060 [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 2023-10-24 06:22:08,061 [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 2023-10-24 06:22:08,061 [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 2023-10-24 06:22:08,061 [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 2023-10-24 06:22:08,061 [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 2023-10-24 06:22:08,061 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: MiModD +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,061 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Du Novo +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,061 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Seqtk +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,061 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: TRANSIT +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,061 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Statistics +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,061 [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 2023-10-24 06:22:08,061 [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 2023-10-24 06:22:08,061 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Graph/Display Data +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,061 [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 2023-10-24 06:22:08,061 [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 2023-10-24 06:22:08,061 [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 2023-10-24 06:22:08,062 [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 2023-10-24 06:22:08,062 [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 2023-10-24 06:22:08,062 [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 2023-10-24 06:22:08,062 [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 2023-10-24 06:22:08,062 [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 2023-10-24 06:22:08,062 [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 2023-10-24 06:22:08,062 [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 2023-10-24 06:22:08,062 [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 2023-10-24 06:22:08,062 [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 2023-10-24 06:22:08,062 [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 2023-10-24 06:22:08,062 [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 2023-10-24 06:22:08,062 [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 2023-10-24 06:22:08,062 [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 2023-10-24 06:22:08,063 [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 2023-10-24 06:22:08,063 [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 2023-10-24 06:22:08,063 [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 2023-10-24 06:22:08,063 [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 2023-10-24 06:22:08,063 [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 2023-10-24 06:22:08,063 [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 2023-10-24 06:22:08,063 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: RNA Analysis (deprecated) +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,063 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: CloudMap (deprecated) +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,063 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Metagenomic Analysis (deprecated) +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,063 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Text Manipulation +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,063 [pN:job_handler_0,p:8,tN:Thread-1] Loading tool panel finished (75.374 ms) +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,068 [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 2023-10-24 06:22:08,068 [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 2023-10-24 06:22:08,068 [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 2023-10-24 06:22:08,068 [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 2023-10-24 06:22:08,068 [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 2023-10-24 06:22:08,068 [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 2023-10-24 06:22:08,069 [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 2023-10-24 06:22:08,069 [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 2023-10-24 06:22:08,069 [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 2023-10-24 06:22:08,069 [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 2023-10-24 06:22:08,070 [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 2023-10-24 06:22:08,070 [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 2023-10-24 06:22:08,070 [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 2023-10-24 06:22:08,070 [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 2023-10-24 06:22:08,070 [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 2023-10-24 06:22:08,070 [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 2023-10-24 06:22:08,071 [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 2023-10-24 06:22:08,071 [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 2023-10-24 06:22:08,071 [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 2023-10-24 06:22:08,071 [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 2023-10-24 06:22:08,071 [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 2023-10-24 06:22:08,071 [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 2023-10-24 06:22:08,071 [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 2023-10-24 06:22:08,071 [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 2023-10-24 06:22:08,071 [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 2023-10-24 06:22:08,071 [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 2023-10-24 06:22:08,071 [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 2023-10-24 06:22:08,071 [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 2023-10-24 06:22:08,071 [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 2023-10-24 06:22:08,071 [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 2023-10-24 06:22:08,071 [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 2023-10-24 06:22:08,072 [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 2023-10-24 06:22:08,072 [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 2023-10-24 06:22:08,072 [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 2023-10-24 06:22:08,072 [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 2023-10-24 06:22:08,072 [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 2023-10-24 06:22:08,072 [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 2023-10-24 06:22:08,072 [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 2023-10-24 06:22:08,072 [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 2023-10-24 06:22:08,072 [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 2023-10-24 06:22:08,072 [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 2023-10-24 06:22:08,072 [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 2023-10-24 06:22:08,072 [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 2023-10-24 06:22:08,072 [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 2023-10-24 06:22:08,072 [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 2023-10-24 06:22:08,072 [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 2023-10-24 06:22:08,073 [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 2023-10-24 06:22:08,073 [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 2023-10-24 06:22:08,073 [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 2023-10-24 06:22:08,073 [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 2023-10-24 06:22:08,073 [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 2023-10-24 06:22:08,073 [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 2023-10-24 06:22:08,073 [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 2023-10-24 06:22:08,073 [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 2023-10-24 06:22:08,073 [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 2023-10-24 06:22:08,073 [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 2023-10-24 06:22:08,073 [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 2023-10-24 06:22:08,073 [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 2023-10-24 06:22:08,073 [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 2023-10-24 06:22:08,073 [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 2023-10-24 06:22:08,073 [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 2023-10-24 06:22:08,074 [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 2023-10-24 06:22:08,074 [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 2023-10-24 06:22:08,074 [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 2023-10-24 06:22:08,074 [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 2023-10-24 06:22:08,074 [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 2023-10-24 06:22:08,074 [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 2023-10-24 06:22:08,074 [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 2023-10-24 06:22:08,074 [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 2023-10-24 06:22:08,075 [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 2023-10-24 06:22:08,075 [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 2023-10-24 06:22:08,075 [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 2023-10-24 06:22:08,075 [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 2023-10-24 06:22:08,075 [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 2023-10-24 06:22:08,075 [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 2023-10-24 06:22:08,075 [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 2023-10-24 06:22:08,075 [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 2023-10-24 06:22:08,075 [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 2023-10-24 06:22:08,075 [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 2023-10-24 06:22:08,076 [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 2023-10-24 06:22:08,076 [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 2023-10-24 06:22:08,076 [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 2023-10-24 06:22:08,076 [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 2023-10-24 06:22:08,076 [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 2023-10-24 06:22:08,076 [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 2023-10-24 06:22:08,076 [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 2023-10-24 06:22:08,076 [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 2023-10-24 06:22:08,076 [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 2023-10-24 06:22:08,076 [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 2023-10-24 06:22:08,076 [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 2023-10-24 06:22:08,076 [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 2023-10-24 06:22:08,076 [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 2023-10-24 06:22:08,077 [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 2023-10-24 06:22:08,077 [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 2023-10-24 06:22:08,077 [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 2023-10-24 06:22:08,077 [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 2023-10-24 06:22:08,077 [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 2023-10-24 06:22:08,077 [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 2023-10-24 06:22:08,077 [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 2023-10-24 06:22:08,077 [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 2023-10-24 06:22:08,077 [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 2023-10-24 06:22:08,077 [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 2023-10-24 06:22:08,077 [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 2023-10-24 06:22:08,077 [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 2023-10-24 06:22:08,077 [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 2023-10-24 06:22:08,078 [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 2023-10-24 06:22:08,078 [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 2023-10-24 06:22:08,078 [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 2023-10-24 06:22:08,078 [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 2023-10-24 06:22:08,078 [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 2023-10-24 06:22:08,078 [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 2023-10-24 06:22:08,078 [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 2023-10-24 06:22:08,078 [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 2023-10-24 06:22:08,078 [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 2023-10-24 06:22:08,078 [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 2023-10-24 06:22:08,078 [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 2023-10-24 06:22:08,078 [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 2023-10-24 06:22:08,078 [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 2023-10-24 06:22:08,078 [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 2023-10-24 06:22:08,079 [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 2023-10-24 06:22:08,079 [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 2023-10-24 06:22:08,079 [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 2023-10-24 06:22:08,079 [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 2023-10-24 06:22:08,079 [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 2023-10-24 06:22:08,079 [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 2023-10-24 06:22:08,079 [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 2023-10-24 06:22:08,079 [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 2023-10-24 06:22:08,079 [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 2023-10-24 06:22:08,079 [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 2023-10-24 06:22:08,079 [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 2023-10-24 06:22:08,079 [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 2023-10-24 06:22:08,079 [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 2023-10-24 06:22:08,079 [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 2023-10-24 06:22:08,079 [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 2023-10-24 06:22:08,080 [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 2023-10-24 06:22:08,080 [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 2023-10-24 06:22:08,080 [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 2023-10-24 06:22:08,080 [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 2023-10-24 06:22:08,080 [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 2023-10-24 06:22:08,080 [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 2023-10-24 06:22:08,080 [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 2023-10-24 06:22:08,080 [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 2023-10-24 06:22:08,080 [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 2023-10-24 06:22:08,080 [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 2023-10-24 06:22:08,080 [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 2023-10-24 06:22:08,081 [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 2023-10-24 06:22:08,081 [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 2023-10-24 06:22:08,081 [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 2023-10-24 06:22:08,081 [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 2023-10-24 06:22:08,081 [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 2023-10-24 06:22:08,081 [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 2023-10-24 06:22:08,081 [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 2023-10-24 06:22:08,081 [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 2023-10-24 06:22:08,081 [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 2023-10-24 06:22:08,081 [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 2023-10-24 06:22:08,081 [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 2023-10-24 06:22:08,082 [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 2023-10-24 06:22:08,082 [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 2023-10-24 06:22:08,082 [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 2023-10-24 06:22:08,082 [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 2023-10-24 06:22:08,082 [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 2023-10-24 06:22:08,082 [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 2023-10-24 06:22:08,082 [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 2023-10-24 06:22:08,082 [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 2023-10-24 06:22:08,082 [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 2023-10-24 06:22:08,082 [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 2023-10-24 06:22:08,083 [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 2023-10-24 06:22:08,083 [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 2023-10-24 06:22:08,083 [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 2023-10-24 06:22:08,083 [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 2023-10-24 06:22:08,083 [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 2023-10-24 06:22:08,083 [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 2023-10-24 06:22:08,083 [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 2023-10-24 06:22:08,083 [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 2023-10-24 06:22:08,083 [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 2023-10-24 06:22:08,084 [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 2023-10-24 06:22:08,084 [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 2023-10-24 06:22:08,084 [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 2023-10-24 06:22:08,084 [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 2023-10-24 06:22:08,084 [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 2023-10-24 06:22:08,084 [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 2023-10-24 06:22:08,084 [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 2023-10-24 06:22:08,084 [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 2023-10-24 06:22:08,084 [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 2023-10-24 06:22:08,084 [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 2023-10-24 06:22:08,084 [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 2023-10-24 06:22:08,084 [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 2023-10-24 06:22:08,085 [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 2023-10-24 06:22:08,085 [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 2023-10-24 06:22:08,085 [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 2023-10-24 06:22:08,085 [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 2023-10-24 06:22:08,085 [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 2023-10-24 06:22:08,085 [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 2023-10-24 06:22:08,085 [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 2023-10-24 06:22:08,085 [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 2023-10-24 06:22:08,085 [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 2023-10-24 06:22:08,085 [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 2023-10-24 06:22:08,085 [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 2023-10-24 06:22:08,085 [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 2023-10-24 06:22:08,085 [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 2023-10-24 06:22:08,086 [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 2023-10-24 06:22:08,086 [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 2023-10-24 06:22:08,086 [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 2023-10-24 06:22:08,086 [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 2023-10-24 06:22:08,086 [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 2023-10-24 06:22:08,086 [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 2023-10-24 06:22:08,086 [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 2023-10-24 06:22:08,086 [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 2023-10-24 06:22:08,086 [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 2023-10-24 06:22:08,086 [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 2023-10-24 06:22:08,086 [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 2023-10-24 06:22:08,087 [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 2023-10-24 06:22:08,087 [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 2023-10-24 06:22:08,087 [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 2023-10-24 06:22:08,087 [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 2023-10-24 06:22:08,087 [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 2023-10-24 06:22:08,087 [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 2023-10-24 06:22:08,087 [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 2023-10-24 06:22:08,087 [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 2023-10-24 06:22:08,087 [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 2023-10-24 06:22:08,087 [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 2023-10-24 06:22:08,087 [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 2023-10-24 06:22:08,087 [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 2023-10-24 06:22:08,088 [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 2023-10-24 06:22:08,088 [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 2023-10-24 06:22:08,088 [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 2023-10-24 06:22:08,088 [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 2023-10-24 06:22:08,088 [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 2023-10-24 06:22:08,088 [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 2023-10-24 06:22:08,088 [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 2023-10-24 06:22:08,088 [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 2023-10-24 06:22:08,088 [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 2023-10-24 06:22:08,088 [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 2023-10-24 06:22:08,088 [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 2023-10-24 06:22:08,088 [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 2023-10-24 06:22:08,088 [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 2023-10-24 06:22:08,089 [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 2023-10-24 06:22:08,089 [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 2023-10-24 06:22:08,089 [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 2023-10-24 06:22:08,089 [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 2023-10-24 06:22:08,089 [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 2023-10-24 06:22:08,089 [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 2023-10-24 06:22:08,089 [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 2023-10-24 06:22:08,089 [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 2023-10-24 06:22:08,089 [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 2023-10-24 06:22:08,089 [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 2023-10-24 06:22:08,089 [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 2023-10-24 06:22:08,089 [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 2023-10-24 06:22:08,089 [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 2023-10-24 06:22:08,090 [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 2023-10-24 06:22:08,090 [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 2023-10-24 06:22:08,090 [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 2023-10-24 06:22:08,090 [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 2023-10-24 06:22:08,090 [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 2023-10-24 06:22:08,090 [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 2023-10-24 06:22:08,090 [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 2023-10-24 06:22:08,090 [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 2023-10-24 06:22:08,090 [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 2023-10-24 06:22:08,090 [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 2023-10-24 06:22:08,090 [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 2023-10-24 06:22:08,091 [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 2023-10-24 06:22:08,091 [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 2023-10-24 06:22:08,091 [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 2023-10-24 06:22:08,091 [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 2023-10-24 06:22:08,091 [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 2023-10-24 06:22:08,091 [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 2023-10-24 06:22:08,091 [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 2023-10-24 06:22:08,091 [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 2023-10-24 06:22:08,091 [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 2023-10-24 06:22:08,091 [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 2023-10-24 06:22:08,091 [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 2023-10-24 06:22:08,091 [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 2023-10-24 06:22:08,091 [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 2023-10-24 06:22:08,092 [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 2023-10-24 06:22:08,092 [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 2023-10-24 06:22:08,092 [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 2023-10-24 06:22:08,092 [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 2023-10-24 06:22:08,092 [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 2023-10-24 06:22:08,092 [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 2023-10-24 06:22:08,092 [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 2023-10-24 06:22:08,092 [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 2023-10-24 06:22:08,092 [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 2023-10-24 06:22:08,092 [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 2023-10-24 06:22:08,092 [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 2023-10-24 06:22:08,092 [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 2023-10-24 06:22:08,092 [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 2023-10-24 06:22:08,092 [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 2023-10-24 06:22:08,093 [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 2023-10-24 06:22:08,093 [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 2023-10-24 06:22:08,093 [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 2023-10-24 06:22:08,093 [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 2023-10-24 06:22:08,093 [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 2023-10-24 06:22:08,093 [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 2023-10-24 06:22:08,093 [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 2023-10-24 06:22:08,093 [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 2023-10-24 06:22:08,093 [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 2023-10-24 06:22:08,093 [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 2023-10-24 06:22:08,093 [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 2023-10-24 06:22:08,093 [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 2023-10-24 06:22:08,093 [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 2023-10-24 06:22:08,094 [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 2023-10-24 06:22:08,094 [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 2023-10-24 06:22:08,094 [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 2023-10-24 06:22:08,094 [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 2023-10-24 06:22:08,094 [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 2023-10-24 06:22:08,094 [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 2023-10-24 06:22:08,094 [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 2023-10-24 06:22:08,094 [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 2023-10-24 06:22:08,094 [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 2023-10-24 06:22:08,094 [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 2023-10-24 06:22:08,094 [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 2023-10-24 06:22:08,094 [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 2023-10-24 06:22:08,094 [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 2023-10-24 06:22:08,095 [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 2023-10-24 06:22:08,095 [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 2023-10-24 06:22:08,095 [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 2023-10-24 06:22:08,095 [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 2023-10-24 06:22:08,095 [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 2023-10-24 06:22:08,095 [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 2023-10-24 06:22:08,095 [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 2023-10-24 06:22:08,095 [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 2023-10-24 06:22:08,095 [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 2023-10-24 06:22:08,095 [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 2023-10-24 06:22:08,095 [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 2023-10-24 06:22:08,095 [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 2023-10-24 06:22:08,096 [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 2023-10-24 06:22:08,096 [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 2023-10-24 06:22:08,096 [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 2023-10-24 06:22:08,096 [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 2023-10-24 06:22:08,096 [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 2023-10-24 06:22:08,096 [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 2023-10-24 06:22:08,096 [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 2023-10-24 06:22:08,096 [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 2023-10-24 06:22:08,096 [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 2023-10-24 06:22:08,096 [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 2023-10-24 06:22:08,096 [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 2023-10-24 06:22:08,096 [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 2023-10-24 06:22:08,096 [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 2023-10-24 06:22:08,097 [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 2023-10-24 06:22:08,097 [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 2023-10-24 06:22:08,097 [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 2023-10-24 06:22:08,097 [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 2023-10-24 06:22:08,097 [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 2023-10-24 06:22:08,097 [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 2023-10-24 06:22:08,097 [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 2023-10-24 06:22:08,097 [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 2023-10-24 06:22:08,097 [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 2023-10-24 06:22:08,097 [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 2023-10-24 06:22:08,097 [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 2023-10-24 06:22:08,098 [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 2023-10-24 06:22:08,098 [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 2023-10-24 06:22:08,098 [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 2023-10-24 06:22:08,098 [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 2023-10-24 06:22:08,098 [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 2023-10-24 06:22:08,098 [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 2023-10-24 06:22:08,098 [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 2023-10-24 06:22:08,098 [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 2023-10-24 06:22:08,098 [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 2023-10-24 06:22:08,098 [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 2023-10-24 06:22:08,098 [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 2023-10-24 06:22:08,098 [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 2023-10-24 06:22:08,098 [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 2023-10-24 06:22:08,098 [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 2023-10-24 06:22:08,099 [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 2023-10-24 06:22:08,099 [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 2023-10-24 06:22:08,099 [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 2023-10-24 06:22:08,099 [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 2023-10-24 06:22:08,099 [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 2023-10-24 06:22:08,099 [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 2023-10-24 06:22:08,099 [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 2023-10-24 06:22:08,099 [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 2023-10-24 06:22:08,099 [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 2023-10-24 06:22:08,099 [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 2023-10-24 06:22:08,099 [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 2023-10-24 06:22:08,099 [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 2023-10-24 06:22:08,099 [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 2023-10-24 06:22:08,099 [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 2023-10-24 06:22:08,100 [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 2023-10-24 06:22:08,100 [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 2023-10-24 06:22:08,100 [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 2023-10-24 06:22:08,100 [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 2023-10-24 06:22:08,100 [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 2023-10-24 06:22:08,100 [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 2023-10-24 06:22:08,100 [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 2023-10-24 06:22:08,100 [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 2023-10-24 06:22:08,100 [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 2023-10-24 06:22:08,101 [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 2023-10-24 06:22:08,101 [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 2023-10-24 06:22:08,101 [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 2023-10-24 06:22:08,101 [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 2023-10-24 06:22:08,101 [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 2023-10-24 06:22:08,101 [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 2023-10-24 06:22:08,101 [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 2023-10-24 06:22:08,101 [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 2023-10-24 06:22:08,101 [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 2023-10-24 06:22:08,101 [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 2023-10-24 06:22:08,101 [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 2023-10-24 06:22:08,101 [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 2023-10-24 06:22:08,101 [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 2023-10-24 06:22:08,102 [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 2023-10-24 06:22:08,102 [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 2023-10-24 06:22:08,102 [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 2023-10-24 06:22:08,102 [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 2023-10-24 06:22:08,102 [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 2023-10-24 06:22:08,102 [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 2023-10-24 06:22:08,102 [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 2023-10-24 06:22:08,102 [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 2023-10-24 06:22:08,102 [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 2023-10-24 06:22:08,102 [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 2023-10-24 06:22:08,103 [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 2023-10-24 06:22:08,103 [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 2023-10-24 06:22:08,103 [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 2023-10-24 06:22:08,103 [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 2023-10-24 06:22:08,103 [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 2023-10-24 06:22:08,103 [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 2023-10-24 06:22:08,103 [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 2023-10-24 06:22:08,103 [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 2023-10-24 06:22:08,103 [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 2023-10-24 06:22:08,103 [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 2023-10-24 06:22:08,103 [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 2023-10-24 06:22:08,104 [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 2023-10-24 06:22:08,104 [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 2023-10-24 06:22:08,104 [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 2023-10-24 06:22:08,104 [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 2023-10-24 06:22:08,104 [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 2023-10-24 06:22:08,104 [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 2023-10-24 06:22:08,104 [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 2023-10-24 06:22:08,104 [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 2023-10-24 06:22:08,104 [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 2023-10-24 06:22:08,104 [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 2023-10-24 06:22:08,104 [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 2023-10-24 06:22:08,105 [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 2023-10-24 06:22:08,105 [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 2023-10-24 06:22:08,105 [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 2023-10-24 06:22:08,105 [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 2023-10-24 06:22:08,105 [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 2023-10-24 06:22:08,105 [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 2023-10-24 06:22:08,105 [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 2023-10-24 06:22:08,105 [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 2023-10-24 06:22:08,105 [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 2023-10-24 06:22:08,105 [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 2023-10-24 06:22:08,105 [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 2023-10-24 06:22:08,105 [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 2023-10-24 06:22:08,105 [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 2023-10-24 06:22:08,105 [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 2023-10-24 06:22:08,106 [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 2023-10-24 06:22:08,106 [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 2023-10-24 06:22:08,106 [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 2023-10-24 06:22:08,106 [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 2023-10-24 06:22:08,106 [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 2023-10-24 06:22:08,106 [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 2023-10-24 06:22:08,106 [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 2023-10-24 06:22:08,106 [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 2023-10-24 06:22:08,106 [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 2023-10-24 06:22:08,106 [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 2023-10-24 06:22:08,106 [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 2023-10-24 06:22:08,106 [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 2023-10-24 06:22:08,106 [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 2023-10-24 06:22:08,107 [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 2023-10-24 06:22:08,107 [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 2023-10-24 06:22:08,107 [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 2023-10-24 06:22:08,107 [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 2023-10-24 06:22:08,107 [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 2023-10-24 06:22:08,107 [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 2023-10-24 06:22:08,107 [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 2023-10-24 06:22:08,107 [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 2023-10-24 06:22:08,107 [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 2023-10-24 06:22:08,107 [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 2023-10-24 06:22:08,107 [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 2023-10-24 06:22:08,107 [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 2023-10-24 06:22:08,107 [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 2023-10-24 06:22:08,108 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,108 [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 2023-10-24 06:22:08,108 [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 2023-10-24 06:22:08,108 [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 2023-10-24 06:22:08,108 [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 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id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,115 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/deeptools_correct_gc_bias/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,115 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,115 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,116 [pN:job_handler_0,p:8,tN:Thread-1] 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 2023-10-24 06:22:08,116 [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/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,116 [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/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,116 [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/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,116 [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/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,116 [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/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,116 [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/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,116 [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 2023-10-24 06:22:08,116 [pN:job_handler_0,p:8,tN:Thread-1] 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 2023-10-24 06:22:08,116 [pN:job_handler_0,p:8,tN:Thread-1] 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 2023-10-24 06:22:08,116 [pN:job_handler_0,p:8,tN:Thread-1] 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 2023-10-24 06:22:08,117 [pN:job_handler_0,p:8,tN:Thread-1] 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 2023-10-24 06:22:08,117 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,117 [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/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 2023-10-24 06:22:08,117 [pN:job_handler_0,p:8,tN:Thread-1] 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 2023-10-24 06:22:08,117 [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/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 2023-10-24 06:22:08,117 [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/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 2023-10-24 06:22:08,117 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__cutadapt__trim_single/qiime2__cutadapt__trim_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 2023-10-24 06:22:08,117 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__cutadapt__trim_paired/qiime2__cutadapt__trim_paired/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 2023-10-24 06:22:08,117 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__cutadapt__demux_single/qiime2__cutadapt__demux_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 2023-10-24 06:22:08,118 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__cutadapt__demux_paired/qiime2__cutadapt__demux_paired/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 2023-10-24 06:22:08,118 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__dada2__denoise_pyro/qiime2__dada2__denoise_pyro/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 2023-10-24 06:22:08,118 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__dada2__denoise_ccs/qiime2__dada2__denoise_ccs/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 2023-10-24 06:22:08,118 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__dada2__denoise_single/qiime2__dada2__denoise_single/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 2023-10-24 06:22:08,118 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__dada2__denoise_paired/qiime2__dada2__denoise_paired/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 2023-10-24 06:22:08,118 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,119 [pN:job_handler_0,p:8,tN:Thread-1] 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 2023-10-24 06:22:08,119 [pN:job_handler_0,p:8,tN:Thread-1] 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 2023-10-24 06:22:08,119 [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/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 2023-10-24 06:22:08,119 [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 2023-10-24 06:22:08,119 [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 2023-10-24 06:22:08,119 [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 2023-10-24 06:22:08,119 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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DEBUG 2023-10-24 06:22:08,122 [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 2023-10-24 06:22:08,122 [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 2023-10-24 06:22:08,122 [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 2023-10-24 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panel.. +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,131 [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 2023-10-24 06:22:08,131 [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 2023-10-24 06:22:08,131 [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 2023-10-24 06:22:08,131 [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 2023-10-24 06:22:08,132 [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 2023-10-24 06:22:08,132 [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 2023-10-24 06:22:08,132 [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 2023-10-24 06:22:08,132 [pN:job_handler_0,p:8,tN:Thread-1] Loading EDAM tool panel finished (68.227 ms) +galaxy.tool_util.toolbox.base DEBUG 2023-10-24 06:22:08,137 [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 2023-10-24 06:22:08,137 [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 2023-10-24 06:22:08,137 [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 2023-10-24 06:22:08,137 [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 2023-10-24 06:22:08,137 [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 2023-10-24 06:22:08,137 [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 2023-10-24 06:22:08,137 [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 2023-10-24 06:22:08,138 [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 2023-10-24 06:22:08,138 [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 2023-10-24 06:22:08,138 [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 2023-10-24 06:22:08,138 [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 2023-10-24 06:22:08,138 [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 2023-10-24 06:22:08,138 [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 2023-10-24 06:22:08,138 [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 2023-10-24 06:22:08,139 [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 2023-10-24 06:22:08,139 [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 2023-10-24 06:22:08,139 [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 2023-10-24 06:22:08,139 [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 2023-10-24 06:22:08,139 [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 2023-10-24 06:22:08,139 [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 2023-10-24 06:22:08,139 [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 2023-10-24 06:22:08,139 [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 2023-10-24 06:22:08,139 [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 2023-10-24 06:22:08,139 [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 2023-10-24 06:22:08,139 [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 2023-10-24 06:22:08,139 [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 2023-10-24 06:22:08,139 [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 2023-10-24 06:22:08,140 [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 2023-10-24 06:22:08,140 [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 2023-10-24 06:22:08,140 [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 2023-10-24 06:22:08,140 [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 2023-10-24 06:22:08,140 [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 2023-10-24 06:22:08,140 [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 2023-10-24 06:22:08,140 [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 2023-10-24 06:22:08,140 [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 2023-10-24 06:22:08,140 [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 2023-10-24 06:22:08,140 [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 2023-10-24 06:22:08,141 [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 2023-10-24 06:22:08,141 [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 2023-10-24 06:22:08,141 [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 2023-10-24 06:22:08,141 [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 2023-10-24 06:22:08,141 [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 2023-10-24 06:22:08,141 [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 2023-10-24 06:22:08,141 [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 2023-10-24 06:22:08,141 [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 2023-10-24 06:22:08,142 [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 2023-10-24 06:22:08,142 [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 2023-10-24 06:22:08,142 [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 2023-10-24 06:22:08,142 [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 2023-10-24 06:22:08,142 [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 2023-10-24 06:22:08,142 [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 2023-10-24 06:22:08,142 [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 2023-10-24 06:22:08,142 [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 2023-10-24 06:22:08,142 [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 2023-10-24 06:22:08,142 [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 2023-10-24 06:22:08,142 [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 2023-10-24 06:22:08,142 [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 2023-10-24 06:22:08,142 [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 2023-10-24 06:22:08,143 [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 2023-10-24 06:22:08,143 [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 2023-10-24 06:22:08,143 [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 2023-10-24 06:22:08,143 [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 2023-10-24 06:22:08,143 [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 2023-10-24 06:22:08,143 [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 2023-10-24 06:22:08,143 [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 2023-10-24 06:22:08,143 [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 2023-10-24 06:22:08,143 [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 2023-10-24 06:22:08,143 [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 2023-10-24 06:22:08,143 [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 2023-10-24 06:22:08,143 [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 2023-10-24 06:22:08,143 [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 2023-10-24 06:22:08,143 [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 2023-10-24 06:22:08,143 [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 2023-10-24 06:22:08,144 [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 2023-10-24 06:22:08,144 [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 2023-10-24 06:22:08,144 [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 2023-10-24 06:22:08,144 [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 2023-10-24 06:22:08,144 [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 2023-10-24 06:22:08,144 [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 2023-10-24 06:22:08,144 [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 2023-10-24 06:22:08,144 [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 2023-10-24 06:22:08,144 [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 2023-10-24 06:22:08,144 [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 2023-10-24 06:22:08,144 [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 2023-10-24 06:22:08,144 [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 2023-10-24 06:22:08,144 [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 2023-10-24 06:22:08,144 [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 2023-10-24 06:22:08,144 [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 2023-10-24 06:22:08,144 [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 2023-10-24 06:22:08,145 [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 2023-10-24 06:22:08,145 [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 2023-10-24 06:22:08,145 [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 2023-10-24 06:22:08,145 [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 2023-10-24 06:22:08,145 [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 2023-10-24 06:22:08,145 [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 2023-10-24 06:22:08,145 [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 2023-10-24 06:22:08,145 [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 2023-10-24 06:22:08,145 [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 2023-10-24 06:22:08,145 [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 2023-10-24 06:22:08,145 [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 2023-10-24 06:22:08,145 [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 2023-10-24 06:22:08,145 [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 2023-10-24 06:22:08,145 [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 2023-10-24 06:22:08,145 [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 2023-10-24 06:22:08,146 [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 2023-10-24 06:22:08,146 [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 2023-10-24 06:22:08,146 [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 2023-10-24 06:22:08,146 [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 2023-10-24 06:22:08,146 [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 2023-10-24 06:22:08,146 [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 2023-10-24 06:22:08,146 [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 2023-10-24 06:22:08,146 [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 2023-10-24 06:22:08,146 [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 2023-10-24 06:22:08,146 [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 2023-10-24 06:22:08,146 [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 2023-10-24 06:22:08,146 [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 2023-10-24 06:22:08,146 [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 2023-10-24 06:22:08,147 [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 2023-10-24 06:22:08,147 [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 2023-10-24 06:22:08,147 [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 2023-10-24 06:22:08,147 [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 2023-10-24 06:22:08,147 [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 2023-10-24 06:22:08,147 [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 2023-10-24 06:22:08,147 [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 2023-10-24 06:22:08,147 [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 2023-10-24 06:22:08,147 [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 2023-10-24 06:22:08,147 [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 2023-10-24 06:22:08,147 [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 2023-10-24 06:22:08,147 [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 2023-10-24 06:22:08,147 [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 2023-10-24 06:22:08,147 [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 2023-10-24 06:22:08,148 [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 2023-10-24 06:22:08,148 [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 2023-10-24 06:22:08,148 [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 2023-10-24 06:22:08,148 [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 2023-10-24 06:22:08,148 [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 2023-10-24 06:22:08,148 [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 2023-10-24 06:22:08,148 [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 2023-10-24 06:22:08,148 [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 2023-10-24 06:22:08,148 [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 2023-10-24 06:22:08,148 [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 2023-10-24 06:22:08,148 [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 2023-10-24 06:22:08,148 [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 2023-10-24 06:22:08,148 [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 2023-10-24 06:22:08,148 [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 2023-10-24 06:22:08,148 [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 2023-10-24 06:22:08,149 [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 2023-10-24 06:22:08,149 [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 2023-10-24 06:22:08,149 [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 2023-10-24 06:22:08,149 [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 2023-10-24 06:22:08,149 [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 2023-10-24 06:22:08,149 [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 2023-10-24 06:22:08,149 [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 2023-10-24 06:22:08,149 [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 2023-10-24 06:22:08,149 [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 2023-10-24 06:22:08,149 [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 2023-10-24 06:22:08,149 [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 2023-10-24 06:22:08,149 [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 2023-10-24 06:22:08,149 [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 2023-10-24 06:22:08,150 [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 2023-10-24 06:22:08,150 [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 2023-10-24 06:22:08,150 [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 2023-10-24 06:22:08,150 [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 2023-10-24 06:22:08,150 [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 2023-10-24 06:22:08,150 [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 2023-10-24 06:22:08,150 [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 2023-10-24 06:22:08,150 [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 2023-10-24 06:22:08,150 [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 2023-10-24 06:22:08,150 [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 2023-10-24 06:22:08,150 [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 2023-10-24 06:22:08,151 [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 2023-10-24 06:22:08,151 [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 2023-10-24 06:22:08,151 [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 2023-10-24 06:22:08,151 [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 2023-10-24 06:22:08,151 [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 2023-10-24 06:22:08,151 [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 2023-10-24 06:22:08,151 [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 2023-10-24 06:22:08,151 [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 2023-10-24 06:22:08,151 [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 2023-10-24 06:22:08,151 [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 2023-10-24 06:22:08,151 [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 2023-10-24 06:22:08,152 [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 2023-10-24 06:22:08,152 [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 2023-10-24 06:22:08,152 [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 2023-10-24 06:22:08,152 [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 2023-10-24 06:22:08,152 [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 2023-10-24 06:22:08,152 [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 2023-10-24 06:22:08,152 [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 2023-10-24 06:22:08,152 [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 2023-10-24 06:22:08,152 [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 2023-10-24 06:22:08,152 [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 2023-10-24 06:22:08,153 [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 2023-10-24 06:22:08,153 [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 2023-10-24 06:22:08,153 [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 2023-10-24 06:22:08,153 [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 2023-10-24 06:22:08,153 [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 2023-10-24 06:22:08,153 [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 2023-10-24 06:22:08,153 [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 2023-10-24 06:22:08,153 [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 2023-10-24 06:22:08,153 [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 2023-10-24 06:22:08,153 [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 2023-10-24 06:22:08,153 [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 2023-10-24 06:22:08,154 [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 2023-10-24 06:22:08,154 [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 2023-10-24 06:22:08,154 [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 2023-10-24 06:22:08,154 [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 2023-10-24 06:22:08,154 [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 2023-10-24 06:22:08,154 [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 2023-10-24 06:22:08,154 [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 2023-10-24 06:22:08,154 [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 2023-10-24 06:22:08,154 [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 2023-10-24 06:22:08,154 [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 2023-10-24 06:22:08,154 [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 2023-10-24 06:22:08,154 [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 2023-10-24 06:22:08,154 [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 2023-10-24 06:22:08,155 [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 2023-10-24 06:22:08,155 [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 2023-10-24 06:22:08,155 [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 2023-10-24 06:22:08,155 [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 2023-10-24 06:22:08,155 [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 2023-10-24 06:22:08,155 [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 2023-10-24 06:22:08,155 [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 2023-10-24 06:22:08,155 [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 2023-10-24 06:22:08,155 [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 2023-10-24 06:22:08,155 [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 2023-10-24 06:22:08,155 [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 2023-10-24 06:22:08,155 [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 2023-10-24 06:22:08,156 [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 2023-10-24 06:22:08,156 [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 2023-10-24 06:22:08,156 [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 2023-10-24 06:22:08,156 [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 2023-10-24 06:22:08,156 [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 2023-10-24 06:22:08,156 [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 2023-10-24 06:22:08,156 [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 2023-10-24 06:22:08,156 [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 2023-10-24 06:22:08,156 [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 2023-10-24 06:22:08,156 [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 2023-10-24 06:22:08,156 [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 2023-10-24 06:22:08,157 [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 2023-10-24 06:22:08,157 [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 2023-10-24 06:22:08,157 [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 2023-10-24 06:22:08,157 [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 2023-10-24 06:22:08,157 [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 2023-10-24 06:22:08,157 [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 2023-10-24 06:22:08,157 [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 2023-10-24 06:22:08,157 [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 2023-10-24 06:22:08,157 [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 2023-10-24 06:22:08,157 [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 2023-10-24 06:22:08,157 [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 2023-10-24 06:22:08,157 [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 2023-10-24 06:22:08,157 [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 2023-10-24 06:22:08,157 [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 2023-10-24 06:22:08,158 [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 2023-10-24 06:22:08,158 [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 2023-10-24 06:22:08,158 [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 2023-10-24 06:22:08,158 [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 2023-10-24 06:22:08,158 [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 2023-10-24 06:22:08,158 [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 2023-10-24 06:22:08,158 [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 2023-10-24 06:22:08,158 [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 2023-10-24 06:22:08,158 [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 2023-10-24 06:22:08,158 [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 2023-10-24 06:22:08,158 [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 2023-10-24 06:22:08,158 [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 2023-10-24 06:22:08,158 [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 2023-10-24 06:22:08,158 [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 2023-10-24 06:22:08,159 [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 2023-10-24 06:22:08,159 [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 2023-10-24 06:22:08,159 [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 2023-10-24 06:22:08,159 [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 2023-10-24 06:22:08,159 [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 2023-10-24 06:22:08,159 [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 2023-10-24 06:22:08,159 [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 2023-10-24 06:22:08,159 [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 2023-10-24 06:22:08,159 [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 2023-10-24 06:22:08,159 [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 2023-10-24 06:22:08,160 [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 2023-10-24 06:22:08,160 [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 2023-10-24 06:22:08,160 [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 2023-10-24 06:22:08,160 [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 2023-10-24 06:22:08,160 [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 2023-10-24 06:22:08,160 [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 2023-10-24 06:22:08,160 [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 2023-10-24 06:22:08,160 [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 2023-10-24 06:22:08,160 [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 2023-10-24 06:22:08,160 [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 2023-10-24 06:22:08,160 [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 2023-10-24 06:22:08,161 [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 2023-10-24 06:22:08,161 [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 2023-10-24 06:22:08,161 [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 2023-10-24 06:22:08,161 [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 2023-10-24 06:22:08,161 [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 2023-10-24 06:22:08,161 [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 2023-10-24 06:22:08,161 [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 2023-10-24 06:22:08,161 [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 2023-10-24 06:22:08,161 [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 2023-10-24 06:22:08,161 [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 2023-10-24 06:22:08,161 [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 2023-10-24 06:22:08,161 [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 2023-10-24 06:22:08,161 [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 2023-10-24 06:22:08,162 [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 2023-10-24 06:22:08,162 [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 2023-10-24 06:22:08,162 [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 2023-10-24 06:22:08,162 [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 2023-10-24 06:22:08,162 [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 2023-10-24 06:22:08,162 [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 2023-10-24 06:22:08,162 [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 2023-10-24 06:22:08,162 [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 2023-10-24 06:22:08,162 [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 2023-10-24 06:22:08,162 [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 2023-10-24 06:22:08,162 [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 2023-10-24 06:22:08,162 [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 2023-10-24 06:22:08,162 [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 2023-10-24 06:22:08,163 [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 2023-10-24 06:22:08,163 [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 2023-10-24 06:22:08,163 [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 2023-10-24 06:22:08,163 [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 2023-10-24 06:22:08,163 [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 2023-10-24 06:22:08,163 [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 2023-10-24 06:22:08,163 [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 2023-10-24 06:22:08,163 [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 2023-10-24 06:22:08,163 [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 2023-10-24 06:22:08,163 [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 2023-10-24 06:22:08,163 [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 2023-10-24 06:22:08,163 [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 2023-10-24 06:22:08,163 [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 2023-10-24 06:22:08,164 [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 2023-10-24 06:22:08,164 [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 2023-10-24 06:22:08,164 [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 2023-10-24 06:22:08,164 [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 2023-10-24 06:22:08,164 [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 2023-10-24 06:22:08,164 [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 2023-10-24 06:22:08,164 [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 2023-10-24 06:22:08,164 [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 2023-10-24 06:22:08,164 [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 2023-10-24 06:22:08,164 [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 2023-10-24 06:22:08,164 [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 2023-10-24 06:22:08,164 [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 2023-10-24 06:22:08,164 [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 2023-10-24 06:22:08,165 [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 2023-10-24 06:22:08,165 [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 2023-10-24 06:22:08,165 [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 2023-10-24 06:22:08,165 [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 2023-10-24 06:22:08,165 [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 2023-10-24 06:22:08,165 [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 2023-10-24 06:22:08,165 [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 2023-10-24 06:22:08,165 [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 2023-10-24 06:22:08,165 [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 2023-10-24 06:22:08,165 [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 2023-10-24 06:22:08,165 [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 2023-10-24 06:22:08,165 [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 2023-10-24 06:22:08,165 [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 2023-10-24 06:22:08,165 [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 2023-10-24 06:22:08,166 [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 2023-10-24 06:22:08,166 [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 2023-10-24 06:22:08,166 [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 2023-10-24 06:22:08,166 [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 2023-10-24 06:22:08,166 [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 2023-10-24 06:22:08,166 [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 2023-10-24 06:22:08,166 [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 2023-10-24 06:22:08,166 [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 2023-10-24 06:22:08,166 [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 2023-10-24 06:22:08,166 [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 2023-10-24 06:22:08,166 [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 2023-10-24 06:22:08,166 [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 2023-10-24 06:22:08,166 [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 2023-10-24 06:22:08,166 [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 2023-10-24 06:22:08,167 [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 2023-10-24 06:22:08,167 [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 2023-10-24 06:22:08,167 [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 2023-10-24 06:22:08,167 [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 2023-10-24 06:22:08,167 [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 2023-10-24 06:22:08,167 [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 2023-10-24 06:22:08,167 [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 2023-10-24 06:22:08,167 [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 2023-10-24 06:22:08,167 [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 2023-10-24 06:22:08,167 [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 2023-10-24 06:22:08,167 [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 2023-10-24 06:22:08,167 [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 2023-10-24 06:22:08,167 [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 2023-10-24 06:22:08,167 [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 2023-10-24 06:22:08,167 [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 2023-10-24 06:22:08,168 [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 2023-10-24 06:22:08,168 [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 2023-10-24 06:22:08,168 [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 2023-10-24 06:22:08,168 [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 2023-10-24 06:22:08,168 [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 2023-10-24 06:22:08,168 [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 2023-10-24 06:22:08,168 [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 2023-10-24 06:22:08,168 [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 2023-10-24 06:22:08,168 [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 2023-10-24 06:22:08,168 [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 2023-10-24 06:22:08,168 [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 2023-10-24 06:22:08,168 [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 2023-10-24 06:22:08,168 [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 2023-10-24 06:22:08,168 [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 2023-10-24 06:22:08,169 [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 2023-10-24 06:22:08,169 [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 2023-10-24 06:22:08,169 [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 2023-10-24 06:22:08,169 [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 2023-10-24 06:22:08,169 [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 2023-10-24 06:22:08,169 [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 2023-10-24 06:22:08,169 [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 2023-10-24 06:22:08,169 [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 2023-10-24 06:22:08,169 [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 2023-10-24 06:22:08,169 [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 2023-10-24 06:22:08,169 [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 2023-10-24 06:22:08,169 [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 2023-10-24 06:22:08,170 [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 2023-10-24 06:22:08,170 [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 2023-10-24 06:22:08,170 [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 2023-10-24 06:22:08,170 [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 2023-10-24 06:22:08,170 [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 2023-10-24 06:22:08,170 [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 2023-10-24 06:22:08,170 [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 2023-10-24 06:22:08,170 [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 2023-10-24 06:22:08,170 [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 2023-10-24 06:22:08,170 [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 2023-10-24 06:22:08,170 [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 2023-10-24 06:22:08,171 [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 2023-10-24 06:22:08,171 [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 2023-10-24 06:22:08,171 [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 2023-10-24 06:22:08,171 [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 2023-10-24 06:22:08,171 [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 2023-10-24 06:22:08,171 [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 2023-10-24 06:22:08,171 [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 2023-10-24 06:22:08,171 [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 2023-10-24 06:22:08,171 [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 2023-10-24 06:22:08,171 [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 2023-10-24 06:22:08,172 [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 2023-10-24 06:22:08,172 [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 2023-10-24 06:22:08,172 [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 2023-10-24 06:22:08,172 [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 2023-10-24 06:22:08,172 [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 2023-10-24 06:22:08,172 [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 2023-10-24 06:22:08,172 [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 2023-10-24 06:22:08,172 [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 2023-10-24 06:22:08,172 [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 2023-10-24 06:22:08,172 [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 2023-10-24 06:22:08,172 [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 2023-10-24 06:22:08,173 [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 2023-10-24 06:22:08,173 [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 2023-10-24 06:22:08,173 [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 2023-10-24 06:22:08,173 [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 2023-10-24 06:22:08,173 [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 2023-10-24 06:22:08,173 [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 2023-10-24 06:22:08,173 [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 2023-10-24 06:22:08,173 [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 2023-10-24 06:22:08,173 [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 2023-10-24 06:22:08,173 [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 2023-10-24 06:22:08,174 [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 2023-10-24 06:22:08,174 [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 2023-10-24 06:22:08,174 [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 2023-10-24 06:22:08,174 [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 2023-10-24 06:22:08,174 [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 2023-10-24 06:22:08,174 [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 2023-10-24 06:22:08,174 [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 2023-10-24 06:22:08,174 [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 2023-10-24 06:22:08,174 [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 2023-10-24 06:22:08,174 [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 2023-10-24 06:22:08,174 [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 2023-10-24 06:22:08,174 [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 2023-10-24 06:22:08,174 [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 2023-10-24 06:22:08,174 [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 2023-10-24 06:22:08,175 [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 2023-10-24 06:22:08,175 [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 2023-10-24 06:22:08,175 [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 2023-10-24 06:22:08,175 [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 2023-10-24 06:22:08,175 [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 2023-10-24 06:22:08,175 [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 2023-10-24 06:22:08,175 [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 2023-10-24 06:22:08,175 [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 2023-10-24 06:22:08,175 [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 2023-10-24 06:22:08,175 [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 2023-10-24 06:22:08,175 [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 2023-10-24 06:22:08,175 [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 2023-10-24 06:22:08,175 [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 2023-10-24 06:22:08,176 [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 2023-10-24 06:22:08,176 [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 2023-10-24 06:22:08,176 [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 2023-10-24 06:22:08,176 [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 2023-10-24 06:22:08,176 [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 2023-10-24 06:22:08,176 [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 2023-10-24 06:22:08,176 [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 2023-10-24 06:22:08,176 [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 2023-10-24 06:22:08,176 [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 2023-10-24 06:22:08,176 [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 2023-10-24 06:22:08,176 [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 2023-10-24 06:22:08,176 [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 2023-10-24 06:22:08,177 [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 2023-10-24 06:22:08,177 [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 2023-10-24 06:22:08,177 [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 2023-10-24 06:22:08,177 [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 2023-10-24 06:22:08,177 [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 2023-10-24 06:22:08,177 [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 2023-10-24 06:22:08,177 [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 2023-10-24 06:22:08,177 [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 2023-10-24 06:22:08,177 [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 2023-10-24 06:22:08,177 [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 2023-10-24 06:22:08,178 [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 2023-10-24 06:22:08,178 [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 2023-10-24 06:22:08,178 [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 2023-10-24 06:22:08,178 [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 2023-10-24 06:22:08,178 [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 2023-10-24 06:22:08,178 [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 2023-10-24 06:22:08,178 [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 2023-10-24 06:22:08,178 [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/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 2023-10-24 06:22:08,189 [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 2023-10-24 06:22:08,189 [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 2023-10-24 06:22:08,189 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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DEBUG 2023-10-24 06:22:08,192 [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 2023-10-24 06:22:08,192 [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 2023-10-24 06:22:08,192 [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 2023-10-24 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toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__taxa__filter_table/qiime2__taxa__filter_table/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 2023-10-24 06:22:08,199 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__taxa__barplot/qiime2__taxa__barplot/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 2023-10-24 06:22:08,199 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__taxa__filter_seqs/qiime2__taxa__filter_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 2023-10-24 06:22:08,199 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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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 2023-10-24 06:22:08,199 [pN:job_handler_0,p:8,tN:Thread-1] 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 2023-10-24 06:22:08,200 [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 2023-10-24 06:22:08,200 [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 2023-10-24 06:22:08,200 [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 2023-10-24 06:22:08,200 [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 2023-10-24 06:22:08,200 [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 2023-10-24 06:22:08,200 [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 2023-10-24 06:22:08,200 [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 2023-10-24 06:22:08,200 [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 2023-10-24 06:22:08,200 [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 2023-10-24 06:22:08,200 [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 2023-10-24 06:22:08,200 [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 2023-10-24 06:22:08,200 [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 2023-10-24 06:22:08,200 [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 2023-10-24 06:22:08,201 [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 2023-10-24 06:22:08,201 [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 2023-10-24 06:22:08,201 [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 2023-10-24 06:22:08,201 [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 2023-10-24 06:22:08,201 [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 2023-10-24 06:22:08,201 [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 2023-10-24 06:22:08,201 [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 2023-10-24 06:22:08,201 [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 2023-10-24 06:22:08,201 [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 2023-10-24 06:22:08,201 [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 2023-10-24 06:22:08,202 [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 2023-10-24 06:22:08,202 [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 2023-10-24 06:22:08,202 [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 2023-10-24 06:22:08,202 [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 2023-10-24 06:22:08,202 [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 2023-10-24 06:22:08,203 [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 2023-10-24 06:22:08,203 [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 2023-10-24 06:22:08,203 [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 2023-10-24 06:22:08,203 [pN:job_handler_0,p:8,tN:Thread-1] Loading EDAM tool panel finished (71.057 ms) +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,203 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,203 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,204 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,204 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,204 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,204 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,204 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_Bam_Bai_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,204 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,204 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,204 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,205 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_coodinate_sorted_bam +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,205 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,205 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_cram_to_bam_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,205 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_to_gff_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,205 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,205 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,205 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,205 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_to_fli_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,205 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bedgraph_to_bigwig +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,205 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_len_to_linecount +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,205 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_parquet_to_csv +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,205 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: bigwigtowig +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,205 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,205 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,206 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,206 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: csv_to_tabular +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,206 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: tabular_to_csv +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,206 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_tabular +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,206 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_bowtie_base_index +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,206 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_bowtie_color_index +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,206 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_2bit +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,206 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_len +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,206 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_fai +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,206 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,206 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,207 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,207 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,207 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,207 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,207 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,207 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,207 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,208 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,208 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,208 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,208 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,208 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,208 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,208 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,208 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,208 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,209 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,209 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,209 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,209 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,209 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gff_to_bed_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,209 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gff_to_interval_index_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,209 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,209 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gff_to_fli_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,209 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,209 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,209 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,209 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,209 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,209 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gff_to_interval_index_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,209 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,209 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bed_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,210 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bedstrict_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,210 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bed6_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,210 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bed12_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,210 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,210 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,210 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,210 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_picard_interval_list_to_bed6 +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,210 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_tar_to_directory +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,210 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,210 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,210 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,210 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,210 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,210 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,210 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_maf_to_fasta_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,211 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_maf_to_interval_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,211 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,211 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,211 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,211 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,211 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,211 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_sam_to_unsorted_bam +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,211 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_coodinate_sorted_bam +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,211 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,212 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_sam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,212 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: tabular_to_dbnsfp +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,212 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: tabular_to_csv +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,212 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,212 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,212 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,212 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,212 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,212 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,213 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,213 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bcf_uncompressed_to_bcf +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,213 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bcf_uncompressed_to_bcf +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,213 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_wig_to_bigwig +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,213 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_wiggle_to_interval_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,213 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,213 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,213 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: lped2fpedconvert +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,213 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: lped2pbedconvert +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,213 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: pbed2lpedconvert +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,213 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: pbed2ldindepconvert +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,213 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,214 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,214 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_biom +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,214 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_biom +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,214 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,214 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,214 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,214 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_SMILES_to_MOL +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,214 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,214 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_smiles_to_smiles +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,215 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,215 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,215 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,215 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,215 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,215 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,215 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_inchi_to_mol +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,215 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,215 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,216 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,216 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,216 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,216 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,216 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,216 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,216 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,216 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,216 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mol2_to_mol +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,216 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,217 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_cml_to_smiles +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,217 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,217 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,217 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,217 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_Pdb_to_Gro_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,217 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,217 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,217 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,217 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,217 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,217 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,217 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_Gro_to_Pdb_0 +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,218 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_ref_to_seq_taxomony +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,218 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_neostorezip_to_neostore +galaxy.datatypes.registry DEBUG 2023-10-24 06:22:08,219 [pN:job_handler_0,p:8,tN:Thread-1] Loaded external metadata tool: __SET_METADATA__ +galaxy.tools.special_tools DEBUG 2023-10-24 06:22:08,221 [pN:job_handler_0,p:8,tN:Thread-1] Loaded history export tool: __EXPORT_HISTORY__ +galaxy.tools.special_tools DEBUG 2023-10-24 06:22:08,222 [pN:job_handler_0,p:8,tN:Thread-1] Loaded history export to uri tool: __EXPORT_HISTORY_TO_URI__ +galaxy.tools.special_tools DEBUG 2023-10-24 06:22:08,224 [pN:job_handler_0,p:8,tN:Thread-1] Loaded history import tool: __IMPORT_HISTORY__ +galaxy.tools.special_tools DEBUG 2023-10-24 06:22:08,226 [pN:job_handler_0,p:8,tN:Thread-1] Loaded data fetch tool: __DATA_FETCH__ +galaxy.queue_worker INFO 2023-10-24 06:22:08,226 [pN:job_handler_0,p:8,tN:Thread-1] Queuing async task rebuild_toolbox_search_index for job_handler_0. +galaxy.queue_worker DEBUG 2023-10-24 06:22:08,228 [pN:job_handler_0,p:8,tN:Thread-1] Toolbox reload (330.402 ms) +galaxy.queue_worker INFO 2023-10-24 06:22:08,229 [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 2023-10-24 06:22:08,229 [pN:job_handler_0,p:8,tN:Thread-1] App is not a webapp, not building a search index +galaxy.jobs.handler DEBUG 2023-10-24 06:24:05,985 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 1 +tpv.rules.gateway INFO 2023-10-24 06:24:06,027 [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 2023-10-24 06:24:06,473 [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 2023-10-24 06:24:06,601 [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={'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=None, 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 2023-10-24 06:24:06,602 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (1) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:24:06,620 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (1) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:24:06,645 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (1) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:24:06,684 [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 2023-10-24 06:24:06,694 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [1] queued (73.772 ms) +galaxy.jobs.handler INFO 2023-10-24 06:24:06,700 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (1) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:24:06,705 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 1 +galaxy.jobs DEBUG 2023-10-24 06:24:06,856 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [1] prepared (133.673 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:24:06,877 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] 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/9/6/b/dataset_96bf6207-9ec4-46ab-91b3-c5d3b12b4a5a_files:/galaxy/server/database/objects/9/6/b/dataset_96bf6207-9ec4-46ab-91b3-c5d3b12b4a5a.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:24:06,896 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (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.handler DEBUG 2023-10-24 06:24:07,703 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 2 +tpv.core.entities DEBUG 2023-10-24 06:24:07,739 [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={'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=None, 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 2023-10-24 06:24:07,739 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (2) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:24:07,743 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (2) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:24:07,758 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (2) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:24:07,778 [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 2023-10-24 06:24:07,788 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [2] queued (43.964 ms) +galaxy.jobs.handler INFO 2023-10-24 06:24:07,792 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (2) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:24:07,794 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 2 +galaxy.jobs DEBUG 2023-10-24 06:24:07,896 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [2] prepared (84.275 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:24:07,915 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/2/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/2/registry.xml' '/galaxy/server/database/jobs_directory/000/2/upload_params.json' '2:/galaxy/server/database/objects/d/a/8/dataset_da87cc5f-3019-40ec-b718-dad37a80f901_files:/galaxy/server/database/objects/d/a/8/dataset_da87cc5f-3019-40ec-b718-dad37a80f901.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:24:07,927 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (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 $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 06:24:42,226 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 1: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:24:42,244 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] 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 2023-10-24 06:24:48,439 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 1 finished +galaxy.model.metadata DEBUG 2023-10-24 06:24:48,486 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 1 +galaxy.jobs INFO 2023-10-24 06:24:48,533 [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 2023-10-24 06:24:48,570 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 1 executed (115.026 ms) +galaxy.jobs.runners DEBUG 2023-10-24 06:24:48,869 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 2 finished +galaxy.model.metadata DEBUG 2023-10-24 06:24:48,910 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 2 +galaxy.jobs INFO 2023-10-24 06:24:48,944 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 2 in /galaxy/server/database/jobs_directory/000/2 +galaxy.jobs DEBUG 2023-10-24 06:24:48,977 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 2 executed (94.935 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:24:49,843 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 3 +tpv.core.entities DEBUG 2023-10-24 06:24:49,886 [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={'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/miniasm/miniasm/.*, abstract=False, cores=1, mem=32, gpus=None, 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 2023-10-24 06:24:49,887 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (3) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:24:49,891 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (3) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:24:49,904 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (3) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:24:49,919 [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 2023-10-24 06:24:49,927 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [3] queued (35.872 ms) +galaxy.jobs.handler INFO 2023-10-24 06:24:49,932 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (3) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:24:49,934 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 3 +galaxy.jobs DEBUG 2023-10-24 06:24:50,009 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [3] prepared (60.623 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 06:24:50,010 [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 2023-10-24 06:24:50,010 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3+galaxy0: miniasm:0.3 +galaxy.tool_util.deps.mulled.util DEBUG 2023-10-24 06:24:50,012 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Querying https://quay.io/api/v1/repository for repos within biocontainers +galaxy.tool_util.deps.containers INFO 2023-10-24 06:25:46,455 [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/miniasm:0.3--he4a0461_2,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 06:25:46,483 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/3/tool_script.sh] for tool command [miniasm -V > /galaxy/server/database/jobs_directory/000/3/outputs/COMMAND_VERSION 2>&1; +miniasm -f '/galaxy/server/database/objects/9/6/b/dataset_96bf6207-9ec4-46ab-91b3-c5d3b12b4a5a.dat' -m '100' -i '0.05' -s '1000' -c '3' -o '1000' -h '1000' -I '0.08' -g '1000' -d '50000' -e '4' -n '3' -F '0.8' '/galaxy/server/database/objects/d/a/8/dataset_da87cc5f-3019-40ec-b718-dad37a80f901.dat' > '/galaxy/server/database/objects/b/d/a/dataset_bda10934-e73b-4721-8bcd-12e513151db6.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:25:46,495 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (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 $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 06:25:46,512 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 06:25:46,512 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3+galaxy0: miniasm:0.3 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:25:46,530 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/miniasm:0.3--he4a0461_2,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 06:25:54,520 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 3: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:26:00,692 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 3 finished +galaxy.model.metadata DEBUG 2023-10-24 06:26:00,739 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 3 +galaxy.jobs INFO 2023-10-24 06:26:00,800 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 3 in /galaxy/server/database/jobs_directory/000/3 +galaxy.jobs DEBUG 2023-10-24 06:26:00,839 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 3 executed (130.190 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:26:03,667 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 4 +tpv.core.entities DEBUG 2023-10-24 06:26:03,703 [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={'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=None, 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 2023-10-24 06:26:03,703 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (4) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:26:03,708 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (4) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:26:03,721 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (4) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:26:03,736 [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 2023-10-24 06:26:03,743 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [4] queued (34.987 ms) +galaxy.jobs.handler INFO 2023-10-24 06:26:03,746 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (4) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:26:03,750 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 4 +galaxy.jobs DEBUG 2023-10-24 06:26:03,843 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [4] prepared (77.581 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:26:03,862 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/4/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/4/registry.xml' '/galaxy/server/database/jobs_directory/000/4/upload_params.json' '4:/galaxy/server/database/objects/1/9/c/dataset_19c452e5-5cbf-4d01-9715-7a67e96dc63f_files:/galaxy/server/database/objects/1/9/c/dataset_19c452e5-5cbf-4d01-9715-7a67e96dc63f.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:26:03,875 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (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.jobs.handler DEBUG 2023-10-24 06:26:05,774 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 5 +tpv.core.entities DEBUG 2023-10-24 06:26:05,813 [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={'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=None, 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 2023-10-24 06:26:05,813 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (5) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:26:05,818 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (5) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:26:05,838 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (5) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:26:05,854 [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 2023-10-24 06:26:05,861 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [5] queued (42.448 ms) +galaxy.jobs.handler INFO 2023-10-24 06:26:05,864 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (5) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:26:05,869 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 5 +galaxy.jobs DEBUG 2023-10-24 06:26:05,971 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [5] prepared (85.598 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:26:05,993 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] 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/4/3/9/dataset_439051bb-ee13-4445-ba66-22f93ba24532_files:/galaxy/server/database/objects/4/3/9/dataset_439051bb-ee13-4445-ba66-22f93ba24532.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:26:06,008 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (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 $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 06:26:14,904 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 4: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:26:15,936 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] 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 2023-10-24 06:26:21,268 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 4 finished +galaxy.model.metadata DEBUG 2023-10-24 06:26:21,318 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 4 +galaxy.jobs INFO 2023-10-24 06:26:21,358 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 4 in /galaxy/server/database/jobs_directory/000/4 +galaxy.jobs DEBUG 2023-10-24 06:26:21,397 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 4 executed (109.711 ms) +galaxy.jobs.runners DEBUG 2023-10-24 06:26:22,323 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 5 finished +galaxy.model.metadata DEBUG 2023-10-24 06:26:22,369 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 5 +galaxy.jobs INFO 2023-10-24 06:26:22,403 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 5 in /galaxy/server/database/jobs_directory/000/5 +galaxy.jobs DEBUG 2023-10-24 06:26:22,438 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 5 executed (100.321 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:26:23,316 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 6 +tpv.core.entities DEBUG 2023-10-24 06:26:23,357 [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={'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/miniasm/miniasm/.*, abstract=False, cores=1, mem=32, gpus=None, 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 2023-10-24 06:26:23,358 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (6) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:26:23,363 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (6) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:26:23,377 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (6) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:26:23,393 [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 2023-10-24 06:26:23,401 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [6] queued (38.031 ms) +galaxy.jobs.handler INFO 2023-10-24 06:26:23,404 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (6) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:26:23,409 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 6 +galaxy.jobs DEBUG 2023-10-24 06:26:23,490 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [6] prepared (61.497 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 06:26:23,491 [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 2023-10-24 06:26:23,491 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3+galaxy0: miniasm:0.3 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:26:23,511 [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/miniasm:0.3--he4a0461_2,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 06:26:23,532 [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 [miniasm -V > /galaxy/server/database/jobs_directory/000/6/outputs/COMMAND_VERSION 2>&1; +miniasm -f '/galaxy/server/database/objects/1/9/c/dataset_19c452e5-5cbf-4d01-9715-7a67e96dc63f.dat' -m '99' -i '0.04' -s '999' -c '2' -o '999' -h '999' -I '0.7' -g '999' -d '45000' -e '3' -n '2' -F '0.7' '/galaxy/server/database/objects/4/3/9/dataset_439051bb-ee13-4445-ba66-22f93ba24532.dat' > '/galaxy/server/database/objects/2/8/3/dataset_28398346-6e29-471c-b18b-e451dfbc5ed4.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:26:23,544 [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 $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 06:26:23,555 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 06:26:23,555 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3+galaxy0: miniasm:0.3 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:26:23,572 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/miniasm:0.3--he4a0461_2,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 06:26:29,092 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 6: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:26:35,239 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 6 finished +galaxy.model.metadata DEBUG 2023-10-24 06:26:35,322 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 6 +galaxy.jobs INFO 2023-10-24 06:26:35,474 [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.jobs DEBUG 2023-10-24 06:26:35,513 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 6 executed (257.055 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:26:39,770 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 7 +tpv.core.entities DEBUG 2023-10-24 06:26:39,804 [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={'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=None, 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 2023-10-24 06:26:39,805 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (7) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:26:39,810 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (7) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:26:39,823 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (7) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:26:39,837 [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 2023-10-24 06:26:39,844 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [7] queued (33.885 ms) +galaxy.jobs.handler INFO 2023-10-24 06:26:39,847 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (7) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:26:39,851 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 7 +galaxy.jobs DEBUG 2023-10-24 06:26:39,948 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [7] prepared (79.895 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:26:39,969 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] 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/4/7/2/dataset_472dff6b-09b1-42fc-bc84-bddeaffd01d7_files:/galaxy/server/database/objects/4/7/2/dataset_472dff6b-09b1-42fc-bc84-bddeaffd01d7.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:26:39,982 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (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 $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 06:26:50,311 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 7: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:26:56,442 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 7 finished +galaxy.model.metadata DEBUG 2023-10-24 06:26:56,490 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 7 +galaxy.jobs INFO 2023-10-24 06:26:56,522 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 7 in /galaxy/server/database/jobs_directory/000/7 +galaxy.jobs DEBUG 2023-10-24 06:26:56,573 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 7 executed (115.935 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:26:57,257 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 8 +tpv.core.entities DEBUG 2023-10-24 06:26:57,298 [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={'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_bigwig_compare/deeptools_bigwig_compare/.*, abstract=False, cores=10, mem=24, gpus=None, 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 2023-10-24 06:26:57,299 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (8) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:26:57,303 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (8) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:26:57,317 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (8) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:26:57,333 [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 2023-10-24 06:26:57,343 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [8] queued (39.212 ms) +galaxy.jobs.handler INFO 2023-10-24 06:26:57,348 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (8) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:26:57,349 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 8 +galaxy.jobs DEBUG 2023-10-24 06:26:57,426 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [8] prepared (60.735 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 06:26:57,426 [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 2023-10-24 06:26:57,427 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/3.3.2.0.0: mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:336148be6fa4ca2fe5a75db2297a83862c17e65c +galaxy.tool_util.deps.containers INFO 2023-10-24 06:26:57,688 [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-eb9e7907c7a753917c1e4d7a64384c047429618a:336148be6fa4ca2fe5a75db2297a83862c17e65c-0,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 06:26:57,706 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/8/tool_script.sh] for tool command [bigwigCompare --version > /galaxy/server/database/jobs_directory/000/8/outputs/COMMAND_VERSION 2>&1; +bigwigCompare --numberOfProcessors "${GALAXY_SLOTS:-4}" --bigwig1 '/galaxy/server/database/objects/4/7/2/dataset_472dff6b-09b1-42fc-bc84-bddeaffd01d7.dat' --bigwig2 '/galaxy/server/database/objects/4/7/2/dataset_472dff6b-09b1-42fc-bc84-bddeaffd01d7.dat' --outFileName '/galaxy/server/database/objects/1/6/f/dataset_16f915b4-2906-49e3-a927-34ae8bb2136b.dat' --outFileFormat 'bigwig' --operation ratio --pseudocount 1 1] +galaxy.jobs.runners DEBUG 2023-10-24 06:26:57,719 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (8) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 06:26:57,728 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 06:26:57,728 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/3.3.2.0.0: mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:336148be6fa4ca2fe5a75db2297a83862c17e65c +galaxy.tool_util.deps.containers INFO 2023-10-24 06:26:57,751 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:336148be6fa4ca2fe5a75db2297a83862c17e65c-0,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 06:27:36,066 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 8: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:27:41,797 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 8 finished +galaxy.model.metadata DEBUG 2023-10-24 06:27:41,841 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 8 +galaxy.util WARNING 2023-10-24 06:27:41,845 [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/1/6/f/dataset_16f915b4-2906-49e3-a927-34ae8bb2136b.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/1/6/f/dataset_16f915b4-2906-49e3-a927-34ae8bb2136b.dat' +galaxy.jobs INFO 2023-10-24 06:27:41,873 [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.jobs DEBUG 2023-10-24 06:27:41,905 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 8 executed (91.361 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:27:44,561 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 9 +tpv.core.entities DEBUG 2023-10-24 06:27:44,596 [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={'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=None, 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 2023-10-24 06:27:44,596 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (9) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:27:44,601 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (9) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:27:44,614 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (9) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:27:44,629 [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 2023-10-24 06:27:44,636 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [9] queued (35.022 ms) +galaxy.jobs.handler INFO 2023-10-24 06:27:44,640 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (9) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:27:44,644 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 9 +galaxy.jobs DEBUG 2023-10-24 06:27:44,745 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [9] prepared (83.062 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:27:44,763 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] 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/c/6/d/dataset_c6d3bf47-747a-4ff2-980c-4e0ce164af9a_files:/galaxy/server/database/objects/c/6/d/dataset_c6d3bf47-747a-4ff2-980c-4e0ce164af9a.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:27:44,775 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (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.kubernetes ERROR 2023-10-24 06:27:54,237 [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://10.112.0.1:443/apis/batch/v1/namespaces/edge-23-10-24-06-08-1/jobs/gxy-lm94v + +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-lm94v": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:27:54,281 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (9/gxy-lm94v) Terminated at user's request +galaxy.jobs.handler DEBUG 2023-10-24 06:27:56,901 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 10 +tpv.core.entities DEBUG 2023-10-24 06:27:56,932 [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={'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=None, 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 2023-10-24 06:27:56,933 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (10) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:27:56,937 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (10) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:27:56,950 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (10) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:27:56,962 [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 2023-10-24 06:27:56,968 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [10] queued (31.803 ms) +galaxy.jobs.handler INFO 2023-10-24 06:27:56,972 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (10) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:27:56,976 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 10 +galaxy.jobs DEBUG 2023-10-24 06:27:57,069 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [10] prepared (77.667 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:27:57,087 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/10/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/10/registry.xml' '/galaxy/server/database/jobs_directory/000/10/upload_params.json' '10:/galaxy/server/database/objects/9/f/7/dataset_9f77a251-c0ee-4d0f-90d6-efc6897bc77b_files:/galaxy/server/database/objects/9/f/7/dataset_9f77a251-c0ee-4d0f-90d6-efc6897bc77b.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:27:57,099 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (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 $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 06:28:07,612 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 10: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:28:13,334 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 10 finished +galaxy.model.metadata DEBUG 2023-10-24 06:28:13,384 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 10 +galaxy.jobs INFO 2023-10-24 06:28:13,417 [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.jobs DEBUG 2023-10-24 06:28:13,454 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 10 executed (99.194 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:28:14,364 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 11 +tpv.core.entities DEBUG 2023-10-24 06:28:14,401 [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={'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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, gpus=None, 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 2023-10-24 06:28:14,401 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (11) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:28:14,406 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (11) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:28:14,419 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (11) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:28:14,434 [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 2023-10-24 06:28:14,443 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [11] queued (37.340 ms) +galaxy.jobs.handler INFO 2023-10-24 06:28:14,447 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (11) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:28:14,451 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 11 +galaxy.jobs DEBUG 2023-10-24 06:28:14,524 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [11] prepared (57.131 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 06:28:14,524 [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 2023-10-24 06:28:14,525 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:28:14,746 [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--py_0,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 06:28:14,765 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/11/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/9/f/7/dataset_9f77a251-c0ee-4d0f-90d6-efc6897bc77b.dat' sanger '/galaxy/server/database/objects/9/3/0/dataset_93034d75-d8f3-436a-b4ca-b0ed8185cc74.dat' sanger ascii summarize_input] +galaxy.jobs.runners DEBUG 2023-10-24 06:28:14,777 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (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 $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 06:28:14,787 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 06:28:14,787 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:28:14,805 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--py_0,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 06:28:26,869 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 11: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:28:32,491 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 11 finished +galaxy.model.metadata DEBUG 2023-10-24 06:28:32,535 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 11 +galaxy.jobs INFO 2023-10-24 06:28:32,566 [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 2023-10-24 06:28:32,593 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 11 executed (85.832 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:28:34,903 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 12 +tpv.core.entities DEBUG 2023-10-24 06:28:34,937 [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={'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=None, 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 2023-10-24 06:28:34,938 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (12) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:28:34,943 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (12) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:28:34,956 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (12) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:28:34,971 [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 2023-10-24 06:28:34,978 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [12] queued (34.290 ms) +galaxy.jobs.handler INFO 2023-10-24 06:28:34,981 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (12) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:28:34,985 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 12 +galaxy.jobs DEBUG 2023-10-24 06:28:35,113 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [12] prepared (101.656 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:28:35,132 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/12/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/12/registry.xml' '/galaxy/server/database/jobs_directory/000/12/upload_params.json' '12:/galaxy/server/database/objects/f/1/2/dataset_f1281d22-311a-4e82-901e-6bfcf8e36534_files:/galaxy/server/database/objects/f/1/2/dataset_f1281d22-311a-4e82-901e-6bfcf8e36534.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:28:35,144 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (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 $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 06:28:45,070 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 12: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:28:50,814 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 12 finished +galaxy.model.metadata DEBUG 2023-10-24 06:28:50,865 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 12 +galaxy.jobs INFO 2023-10-24 06:28:50,897 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 12 in /galaxy/server/database/jobs_directory/000/12 +galaxy.jobs DEBUG 2023-10-24 06:28:50,928 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 12 executed (93.181 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:28:52,393 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 13 +tpv.core.entities DEBUG 2023-10-24 06:28:52,430 [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={'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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, gpus=None, 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 2023-10-24 06:28:52,430 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (13) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:28:52,435 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (13) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:28:52,455 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (13) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:28:52,472 [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 2023-10-24 06:28:52,479 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [13] queued (44.277 ms) +galaxy.jobs.handler INFO 2023-10-24 06:28:52,483 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (13) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:28:52,486 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 13 +galaxy.jobs DEBUG 2023-10-24 06:28:52,554 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [13] prepared (52.369 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 06:28:52,555 [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 2023-10-24 06:28:52,555 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:28:52,575 [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--py_0,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 06:28:52,594 [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 [gx-fastq-groomer '/galaxy/server/database/objects/f/1/2/dataset_f1281d22-311a-4e82-901e-6bfcf8e36534.dat' sanger '/galaxy/server/database/objects/3/e/2/dataset_3e29aca0-3ec5-498f-bc9c-f99f49129e79.dat' sanger ascii summarize_input --fix-id] +galaxy.jobs.runners DEBUG 2023-10-24 06:28:52,607 [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 $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 06:28:52,617 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 06:28:52,617 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:28:52,634 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--py_0,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 06:28:58,212 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 13: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:29:03,927 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 13 finished +galaxy.model.metadata DEBUG 2023-10-24 06:29:03,979 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 13 +galaxy.jobs INFO 2023-10-24 06:29:04,020 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 13 in /galaxy/server/database/jobs_directory/000/13 +galaxy.jobs DEBUG 2023-10-24 06:29:04,053 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 13 executed (109.412 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:29:05,776 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 14 +tpv.core.entities DEBUG 2023-10-24 06:29:05,810 [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={'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=None, 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 2023-10-24 06:29:05,811 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (14) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:29:05,815 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (14) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:29:05,829 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (14) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:29:05,846 [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 2023-10-24 06:29:05,853 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [14] queued (38.069 ms) +galaxy.jobs.handler INFO 2023-10-24 06:29:05,859 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (14) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:29:05,861 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 14 +galaxy.jobs DEBUG 2023-10-24 06:29:05,956 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [14] prepared (79.333 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:29:05,974 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/14/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/14/registry.xml' '/galaxy/server/database/jobs_directory/000/14/upload_params.json' '14:/galaxy/server/database/objects/7/3/1/dataset_731f009c-9d5f-47be-87c7-f1653c70dd28_files:/galaxy/server/database/objects/7/3/1/dataset_731f009c-9d5f-47be-87c7-f1653c70dd28.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:29:05,987 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (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 $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 06:29:15,437 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 14: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:29:21,273 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 14 finished +galaxy.model.metadata DEBUG 2023-10-24 06:29:21,320 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 14 +galaxy.jobs INFO 2023-10-24 06:29:21,352 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 14 in /galaxy/server/database/jobs_directory/000/14 +galaxy.jobs DEBUG 2023-10-24 06:29:21,401 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 14 executed (112.424 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:29:22,236 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 15 +tpv.core.entities DEBUG 2023-10-24 06:29:22,271 [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={'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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, gpus=None, 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 2023-10-24 06:29:22,271 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (15) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:29:22,276 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (15) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:29:22,289 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (15) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:29:22,305 [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 2023-10-24 06:29:22,314 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [15] queued (38.037 ms) +galaxy.jobs.handler INFO 2023-10-24 06:29:22,317 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (15) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:29:22,321 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 15 +galaxy.jobs DEBUG 2023-10-24 06:29:22,391 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [15] prepared (52.341 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 06:29:22,391 [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 2023-10-24 06:29:22,392 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:29:22,417 [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--py_0,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 06:29:22,436 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/15/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/7/3/1/dataset_731f009c-9d5f-47be-87c7-f1653c70dd28.dat' sanger '/galaxy/server/database/objects/8/c/8/dataset_8c875dbd-9a4a-4696-ada1-babebafcd667.dat' sanger ascii summarize_input --no-fix-id] +galaxy.jobs.runners DEBUG 2023-10-24 06:29:22,449 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (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.tool_util.deps.containers INFO 2023-10-24 06:29:22,459 [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 2023-10-24 06:29:22,459 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:29:22,476 [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--py_0,type=docker]] +galaxy.jobs.runners.kubernetes ERROR 2023-10-24 06:29:27,544 [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://10.112.0.1:443/apis/batch/v1/namespaces/edge-23-10-24-06-08-1/jobs/gxy-sg9z7 + +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-sg9z7": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:29:27,585 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (15/gxy-sg9z7) Terminated at user's request +galaxy.jobs.handler DEBUG 2023-10-24 06:29:29,466 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 16 +tpv.core.entities DEBUG 2023-10-24 06:29:29,501 [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={'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=None, 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 2023-10-24 06:29:29,502 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (16) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:29:29,506 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (16) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:29:29,520 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (16) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:29:29,534 [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 2023-10-24 06:29:29,540 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [16] queued (34.268 ms) +galaxy.jobs.handler INFO 2023-10-24 06:29:29,544 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (16) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:29:29,548 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 16 +galaxy.jobs DEBUG 2023-10-24 06:29:29,640 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [16] prepared (75.735 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:29:29,658 [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 [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/16/registry.xml' '/galaxy/server/database/jobs_directory/000/16/upload_params.json' '16:/galaxy/server/database/objects/2/4/d/dataset_24d7c15b-3b8e-492c-b1c8-417762230968_files:/galaxy/server/database/objects/2/4/d/dataset_24d7c15b-3b8e-492c-b1c8-417762230968.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:29:29,670 [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 $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 06:29:39,870 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 16: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:29:45,796 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 16 finished +galaxy.model.metadata DEBUG 2023-10-24 06:29:45,850 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 16 +galaxy.jobs INFO 2023-10-24 06:29:45,883 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 16 in /galaxy/server/database/jobs_directory/000/16 +galaxy.jobs DEBUG 2023-10-24 06:29:45,931 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 16 executed (114.137 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:29:46,940 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 17 +tpv.core.entities DEBUG 2023-10-24 06:29:46,975 [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={'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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, gpus=None, 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 2023-10-24 06:29:46,976 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (17) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:29:46,981 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (17) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:29:46,995 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (17) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:29:47,011 [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 2023-10-24 06:29:47,019 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [17] queued (37.672 ms) +galaxy.jobs.handler INFO 2023-10-24 06:29:47,025 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (17) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:29:47,028 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 17 +galaxy.jobs DEBUG 2023-10-24 06:29:47,095 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [17] prepared (50.524 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 06:29:47,096 [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 2023-10-24 06:29:47,096 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:29:47,132 [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--py_0,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 06:29:47,151 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/17/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/2/4/d/dataset_24d7c15b-3b8e-492c-b1c8-417762230968.dat' sanger '/galaxy/server/database/objects/6/f/4/dataset_6f426233-f411-4c66-a6a8-268cf5f06d26.dat' sanger ascii summarize_input] +galaxy.jobs.runners DEBUG 2023-10-24 06:29:47,164 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (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 $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 06:29:47,175 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 06:29:47,176 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:29:47,198 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--py_0,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 06:29:52,004 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 17: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:29:57,968 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 17 finished +galaxy.model.metadata DEBUG 2023-10-24 06:29:58,015 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 17 +galaxy.jobs INFO 2023-10-24 06:29:58,047 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 17 in /galaxy/server/database/jobs_directory/000/17 +galaxy.jobs DEBUG 2023-10-24 06:29:58,082 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 17 executed (97.761 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:30:00,465 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 18 +tpv.core.entities DEBUG 2023-10-24 06:30:00,501 [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={'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=None, 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 2023-10-24 06:30:00,502 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (18) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:30:00,507 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (18) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:30:00,521 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (18) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:30:00,536 [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 2023-10-24 06:30:00,544 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [18] queued (36.853 ms) +galaxy.jobs.handler INFO 2023-10-24 06:30:00,549 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (18) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:30:00,551 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 18 +galaxy.jobs DEBUG 2023-10-24 06:30:00,653 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [18] prepared (86.174 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:30:00,673 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/18/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/18/registry.xml' '/galaxy/server/database/jobs_directory/000/18/upload_params.json' '18:/galaxy/server/database/objects/f/f/a/dataset_ffa08cf2-7ee4-418e-bfdb-62f03829572d_files:/galaxy/server/database/objects/f/f/a/dataset_ffa08cf2-7ee4-418e-bfdb-62f03829572d.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:30:00,686 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (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 $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 06:30:11,245 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 18: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:30:17,198 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 18 finished +galaxy.model.metadata DEBUG 2023-10-24 06:30:17,254 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 18 +galaxy.jobs INFO 2023-10-24 06:30:17,287 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 18 in /galaxy/server/database/jobs_directory/000/18 +galaxy.jobs DEBUG 2023-10-24 06:30:17,315 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 18 executed (90.626 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:30:17,953 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 19 +tpv.core.entities DEBUG 2023-10-24 06:30:17,992 [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={'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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, gpus=None, 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 2023-10-24 06:30:17,993 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (19) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:30:17,998 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (19) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:30:18,012 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (19) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:30:18,026 [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 2023-10-24 06:30:18,034 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [19] queued (35.745 ms) +galaxy.jobs.handler INFO 2023-10-24 06:30:18,037 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (19) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:30:18,041 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 19 +galaxy.jobs DEBUG 2023-10-24 06:30:18,109 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [19] prepared (51.210 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 06:30:18,110 [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 2023-10-24 06:30:18,110 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:30:18,142 [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--py_0,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 06:30:18,161 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/19/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/f/f/a/dataset_ffa08cf2-7ee4-418e-bfdb-62f03829572d.dat' cssanger '/galaxy/server/database/objects/2/b/1/dataset_2b16b589-e1fd-47a9-82a3-2189df275673.dat' cssanger ascii summarize_input] +galaxy.jobs.runners DEBUG 2023-10-24 06:30:18,175 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (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 $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 06:30:18,185 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 06:30:18,185 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:30:18,202 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--py_0,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 06:30:23,389 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 19: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:30:29,362 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 19 finished +galaxy.model.metadata DEBUG 2023-10-24 06:30:29,407 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 19 +galaxy.jobs INFO 2023-10-24 06:30:29,442 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 19 in /galaxy/server/database/jobs_directory/000/19 +galaxy.jobs DEBUG 2023-10-24 06:30:29,473 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 19 executed (95.379 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:30:31,353 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 20 +tpv.core.entities DEBUG 2023-10-24 06:30:31,389 [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={'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=None, 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 2023-10-24 06:30:31,390 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (20) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:30:31,395 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (20) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:30:31,409 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (20) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:30:31,424 [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 2023-10-24 06:30:31,431 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [20] queued (35.737 ms) +galaxy.jobs.handler INFO 2023-10-24 06:30:31,435 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (20) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:30:31,440 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 20 +galaxy.jobs DEBUG 2023-10-24 06:30:31,541 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [20] prepared (82.587 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:30:31,561 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/20/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/20/registry.xml' '/galaxy/server/database/jobs_directory/000/20/upload_params.json' '20:/galaxy/server/database/objects/e/4/8/dataset_e48ec717-63ce-4f27-8c05-6c32341d007c_files:/galaxy/server/database/objects/e/4/8/dataset_e48ec717-63ce-4f27-8c05-6c32341d007c.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:30:31,574 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (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; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 06:30:41,613 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 20: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:30:47,580 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 20 finished +galaxy.model.metadata DEBUG 2023-10-24 06:30:47,626 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 20 +galaxy.jobs INFO 2023-10-24 06:30:47,659 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 20 in /galaxy/server/database/jobs_directory/000/20 +galaxy.jobs DEBUG 2023-10-24 06:30:47,690 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 20 executed (94.371 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:30:48,838 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 21 +tpv.core.entities DEBUG 2023-10-24 06:30:48,874 [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={'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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, gpus=None, 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 2023-10-24 06:30:48,875 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (21) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:30:48,879 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (21) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:30:48,893 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (21) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:30:48,906 [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 2023-10-24 06:30:48,914 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [21] queued (34.319 ms) +galaxy.jobs.handler INFO 2023-10-24 06:30:48,917 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (21) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:30:48,921 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 21 +galaxy.jobs DEBUG 2023-10-24 06:30:48,988 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [21] prepared (51.068 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 06:30:48,989 [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 2023-10-24 06:30:48,990 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:30:49,186 [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--py_0,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 06:30:49,206 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/21/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/e/4/8/dataset_e48ec717-63ce-4f27-8c05-6c32341d007c.dat' illumina '/galaxy/server/database/objects/c/a/3/dataset_ca3af834-2bb2-4939-918c-f8e321d88ff4.dat' sanger ascii summarize_input] +galaxy.jobs.runners DEBUG 2023-10-24 06:30:49,219 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (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 $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 06:30:49,230 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 06:30:49,230 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:30:49,247 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--py_0,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 06:30:54,793 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 21: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:31:00,753 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 21 finished +galaxy.model.metadata DEBUG 2023-10-24 06:31:00,803 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 21 +galaxy.jobs INFO 2023-10-24 06:31:00,840 [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 2023-10-24 06:31:00,877 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 21 executed (106.745 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:31:03,369 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 22 +tpv.core.entities DEBUG 2023-10-24 06:31:03,404 [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={'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=None, 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 2023-10-24 06:31:03,405 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (22) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:31:03,410 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (22) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:31:03,426 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (22) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:31:03,442 [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 2023-10-24 06:31:03,449 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [22] queued (39.112 ms) +galaxy.jobs.handler INFO 2023-10-24 06:31:03,454 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (22) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:31:03,456 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 22 +galaxy.jobs DEBUG 2023-10-24 06:31:03,557 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [22] prepared (82.832 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:31:03,575 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] 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/f/4/2/dataset_f42b6dd4-4090-433e-abb5-1c210f4171fa_files:/galaxy/server/database/objects/f/4/2/dataset_f42b6dd4-4090-433e-abb5-1c210f4171fa.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:31:03,588 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (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 $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 06:31:13,003 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 22: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:31:18,978 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 22 finished +galaxy.model.metadata DEBUG 2023-10-24 06:31:19,026 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 22 +galaxy.jobs INFO 2023-10-24 06:31:19,066 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 22 in /galaxy/server/database/jobs_directory/000/22 +galaxy.jobs DEBUG 2023-10-24 06:31:19,100 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 22 executed (105.124 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:31:19,823 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 23 +tpv.core.entities DEBUG 2023-10-24 06:31:19,861 [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={'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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, gpus=None, 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 2023-10-24 06:31:19,862 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (23) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:31:19,867 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (23) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:31:19,888 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (23) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:31:19,903 [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 2023-10-24 06:31:19,911 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [23] queued (43.029 ms) +galaxy.jobs.handler INFO 2023-10-24 06:31:19,914 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (23) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:31:19,919 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 23 +galaxy.jobs DEBUG 2023-10-24 06:31:19,986 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [23] prepared (51.575 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 06:31:19,987 [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 2023-10-24 06:31:19,987 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:31:20,007 [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--py_0,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 06:31:20,027 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/23/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/f/4/2/dataset_f42b6dd4-4090-433e-abb5-1c210f4171fa.dat' solexa '/galaxy/server/database/objects/3/0/d/dataset_30d706a9-fed7-4e1e-af9d-a39780741c06.dat' sanger ascii summarize_input] +galaxy.jobs.runners DEBUG 2023-10-24 06:31:20,040 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (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 $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 06:31:20,050 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 06:31:20,051 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:31:20,067 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--py_0,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 06:31:25,159 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 23: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:31:30,980 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 23 finished +galaxy.model.metadata DEBUG 2023-10-24 06:31:31,028 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 23 +galaxy.jobs INFO 2023-10-24 06:31:31,062 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 23 in /galaxy/server/database/jobs_directory/000/23 +galaxy.jobs DEBUG 2023-10-24 06:31:31,090 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 23 executed (93.261 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:31:33,222 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 24 +tpv.core.entities DEBUG 2023-10-24 06:31:33,260 [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={'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=None, 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 2023-10-24 06:31:33,261 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (24) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:31:33,267 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (24) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:31:33,283 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (24) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:31:33,297 [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 2023-10-24 06:31:33,305 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [24] queued (37.934 ms) +galaxy.jobs.handler INFO 2023-10-24 06:31:33,310 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (24) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:31:33,314 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 24 +galaxy.jobs DEBUG 2023-10-24 06:31:33,411 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [24] prepared (80.043 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:31:33,430 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] 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/a/9/f/dataset_a9f318ad-988c-4626-beaf-7083a35c6122_files:/galaxy/server/database/objects/a/9/f/dataset_a9f318ad-988c-4626-beaf-7083a35c6122.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:31:33,444 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (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 $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 06:31:43,373 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 24: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:31:49,368 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 24 finished +galaxy.model.metadata DEBUG 2023-10-24 06:31:49,416 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 24 +galaxy.jobs INFO 2023-10-24 06:31:49,452 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 24 in /galaxy/server/database/jobs_directory/000/24 +galaxy.jobs DEBUG 2023-10-24 06:31:49,493 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 24 executed (109.122 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:31:49,810 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 25 +tpv.core.entities DEBUG 2023-10-24 06:31:49,847 [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={'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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, gpus=None, 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 2023-10-24 06:31:49,847 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (25) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:31:49,852 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (25) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:31:49,865 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (25) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:31:49,880 [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 2023-10-24 06:31:49,888 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [25] queued (35.307 ms) +galaxy.jobs.handler INFO 2023-10-24 06:31:49,891 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (25) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:31:49,895 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 25 +galaxy.jobs DEBUG 2023-10-24 06:31:49,961 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [25] prepared (49.239 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 06:31:49,962 [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 2023-10-24 06:31:49,962 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:31:49,981 [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--py_0,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 06:31:49,999 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/25/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/a/9/f/dataset_a9f318ad-988c-4626-beaf-7083a35c6122.dat' sanger '/galaxy/server/database/objects/b/5/8/dataset_b58a1a9d-d6ff-49c0-9df7-ead5a67d552b.dat' sanger ascii summarize_input] +galaxy.jobs.runners DEBUG 2023-10-24 06:31:50,013 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (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; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 06:31:50,030 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 06:31:50,030 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:31:50,047 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--py_0,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 06:31:55,557 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 25: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:32:01,371 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 25 finished +galaxy.model.metadata DEBUG 2023-10-24 06:32:01,416 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 25 +galaxy.jobs INFO 2023-10-24 06:32:01,449 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 25 in /galaxy/server/database/jobs_directory/000/25 +galaxy.jobs DEBUG 2023-10-24 06:32:01,478 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 25 executed (90.813 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:32:04,206 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 26 +tpv.core.entities DEBUG 2023-10-24 06:32:04,242 [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={'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=None, 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 2023-10-24 06:32:04,243 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (26) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:32:04,247 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (26) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:32:04,260 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (26) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:32:04,275 [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 2023-10-24 06:32:04,282 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [26] queued (34.372 ms) +galaxy.jobs.handler INFO 2023-10-24 06:32:04,285 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (26) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:32:04,289 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 26 +galaxy.jobs DEBUG 2023-10-24 06:32:04,382 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [26] prepared (78.244 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:32:04,402 [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/4/4/2/dataset_4426d7ac-37c1-46d2-b6bc-be44649b218b_files:/galaxy/server/database/objects/4/4/2/dataset_4426d7ac-37c1-46d2-b6bc-be44649b218b.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:32:04,415 [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 $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 06:32:14,752 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 26: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:32:20,629 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 26 finished +galaxy.model.metadata DEBUG 2023-10-24 06:32:20,685 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 26 +galaxy.jobs INFO 2023-10-24 06:32:20,715 [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 2023-10-24 06:32:20,753 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 26 executed (99.228 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:32:21,671 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 27 +tpv.core.entities DEBUG 2023-10-24 06:32:21,706 [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={'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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, gpus=None, 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 2023-10-24 06:32:21,706 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (27) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:32:21,711 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (27) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:32:21,724 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (27) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:32:21,738 [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 2023-10-24 06:32:21,745 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [27] queued (33.948 ms) +galaxy.jobs.handler INFO 2023-10-24 06:32:21,749 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (27) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:32:21,751 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 27 +galaxy.jobs DEBUG 2023-10-24 06:32:21,815 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [27] prepared (48.076 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 06:32:21,816 [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 2023-10-24 06:32:21,816 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:32:21,835 [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--py_0,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 06:32:21,856 [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 [gx-fastq-groomer '/galaxy/server/database/objects/4/4/2/dataset_4426d7ac-37c1-46d2-b6bc-be44649b218b.dat' illumina '/galaxy/server/database/objects/f/3/1/dataset_f310ade4-c065-42db-af0c-003891584872.dat' illumina None summarize_input --fix-id] +galaxy.jobs.runners DEBUG 2023-10-24 06:32:21,869 [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; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 06:32:21,879 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 06:32:21,879 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:32:21,896 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--py_0,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 06:32:27,921 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 27: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:32:33,678 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 27 finished +galaxy.model.metadata DEBUG 2023-10-24 06:32:33,721 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 27 +galaxy.jobs INFO 2023-10-24 06:32:33,753 [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 2023-10-24 06:32:33,777 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 27 executed (83.064 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:32:36,069 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 28 +tpv.core.entities DEBUG 2023-10-24 06:32:36,104 [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={'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=None, 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 2023-10-24 06:32:36,105 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (28) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:32:36,109 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (28) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:32:36,124 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (28) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:32:36,138 [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 2023-10-24 06:32:36,145 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [28] queued (35.552 ms) +galaxy.jobs.handler INFO 2023-10-24 06:32:36,150 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (28) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:32:36,153 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 28 +galaxy.jobs DEBUG 2023-10-24 06:32:36,262 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [28] prepared (91.135 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:32:36,280 [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/2/e/c/dataset_2ec3cb50-2bfe-4273-8b69-f289645d10bf_files:/galaxy/server/database/objects/2/e/c/dataset_2ec3cb50-2bfe-4273-8b69-f289645d10bf.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:32:36,291 [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 $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 06:32:47,124 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 28: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:32:52,872 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 28 finished +galaxy.model.metadata DEBUG 2023-10-24 06:32:52,921 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 28 +galaxy.jobs INFO 2023-10-24 06:32:52,954 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 28 in /galaxy/server/database/jobs_directory/000/28 +galaxy.jobs DEBUG 2023-10-24 06:32:52,991 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 28 executed (103.285 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:32:53,536 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 29 +tpv.core.entities DEBUG 2023-10-24 06:32:53,572 [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={'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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, gpus=None, 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 2023-10-24 06:32:53,573 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (29) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:32:53,577 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (29) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:32:53,590 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (29) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:32:53,604 [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 2023-10-24 06:32:53,611 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [29] queued (33.610 ms) +galaxy.jobs.handler INFO 2023-10-24 06:32:53,616 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (29) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:32:53,617 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 29 +galaxy.jobs DEBUG 2023-10-24 06:32:53,682 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [29] prepared (49.345 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 06:32:53,683 [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 2023-10-24 06:32:53,683 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:32:53,703 [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--py_0,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 06:32:53,721 [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 [gx-fastq-groomer '/galaxy/server/database/objects/2/e/c/dataset_2ec3cb50-2bfe-4273-8b69-f289645d10bf.dat' illumina '/galaxy/server/database/objects/f/d/1/dataset_fd12f761-f765-49f9-9a5a-6d6ae1a7ce4b.dat' sanger None summarize_input --fix-id] +galaxy.jobs.runners DEBUG 2023-10-24 06:32:53,733 [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; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 06:32:53,743 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 06:32:53,744 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:32:53,760 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--py_0,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 06:32:59,275 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 29: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:33:05,046 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 29 finished +galaxy.model.metadata DEBUG 2023-10-24 06:33:05,124 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 29 +galaxy.jobs INFO 2023-10-24 06:33:05,158 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 29 in /galaxy/server/database/jobs_directory/000/29 +galaxy.jobs DEBUG 2023-10-24 06:33:05,215 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 29 executed (152.625 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:33:07,935 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 30 +tpv.core.entities DEBUG 2023-10-24 06:33:07,968 [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={'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=None, 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 2023-10-24 06:33:07,969 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (30) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:33:07,973 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (30) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:33:07,986 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (30) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:33:08,000 [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 2023-10-24 06:33:08,007 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [30] queued (33.907 ms) +galaxy.jobs.handler INFO 2023-10-24 06:33:08,011 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (30) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:33:08,015 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 30 +galaxy.jobs DEBUG 2023-10-24 06:33:08,119 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [30] prepared (87.754 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:33:08,137 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] 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/a/1/dataset_6a14e7b1-cfaa-4a0a-916d-865647f4512f_files:/galaxy/server/database/objects/6/a/1/dataset_6a14e7b1-cfaa-4a0a-916d-865647f4512f.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:33:08,148 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (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 $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 06:33:18,516 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 30: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:33:24,299 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 30 finished +galaxy.model.metadata DEBUG 2023-10-24 06:33:24,345 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 30 +galaxy.jobs INFO 2023-10-24 06:33:24,396 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 30 in /galaxy/server/database/jobs_directory/000/30 +galaxy.jobs DEBUG 2023-10-24 06:33:24,427 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 30 executed (113.346 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:33:25,397 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 31 +tpv.core.entities DEBUG 2023-10-24 06:33:25,437 [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={'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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, gpus=None, 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 2023-10-24 06:33:25,438 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (31) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:33:25,443 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (31) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:33:25,457 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (31) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:33:25,470 [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 2023-10-24 06:33:25,478 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [31] queued (34.991 ms) +galaxy.jobs.handler INFO 2023-10-24 06:33:25,482 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (31) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:33:25,485 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 31 +galaxy.jobs DEBUG 2023-10-24 06:33:25,548 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [31] prepared (47.931 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 06:33:25,549 [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 2023-10-24 06:33:25,549 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:33:25,567 [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--py_0,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 06:33:25,585 [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 [gx-fastq-groomer '/galaxy/server/database/objects/6/a/1/dataset_6a14e7b1-cfaa-4a0a-916d-865647f4512f.dat' illumina '/galaxy/server/database/objects/4/9/0/dataset_490e6c0c-daff-458d-9afc-5e955b9a9ad3.dat' solexa None summarize_input --fix-id] +galaxy.jobs.runners DEBUG 2023-10-24 06:33:25,597 [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; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 06:33:25,607 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 06:33:25,607 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:33:25,623 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--py_0,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 06:33:30,658 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 31: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:33:36,790 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 31 finished +galaxy.model.metadata DEBUG 2023-10-24 06:33:36,836 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 31 +galaxy.jobs INFO 2023-10-24 06:33:36,870 [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 2023-10-24 06:33:36,905 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 31 executed (99.427 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:33:38,800 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 32 +tpv.core.entities DEBUG 2023-10-24 06:33:38,836 [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={'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=None, 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 2023-10-24 06:33:38,836 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (32) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:33:38,841 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (32) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:33:38,857 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (32) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:33:38,873 [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 2023-10-24 06:33:38,880 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [32] queued (37.941 ms) +galaxy.jobs.handler INFO 2023-10-24 06:33:38,884 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (32) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:33:38,887 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 32 +galaxy.jobs DEBUG 2023-10-24 06:33:39,009 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [32] prepared (104.583 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:33:39,029 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] 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/7/0/1/dataset_7018d51b-0dd9-4b39-a520-f5ab00241cdf_files:/galaxy/server/database/objects/7/0/1/dataset_7018d51b-0dd9-4b39-a520-f5ab00241cdf.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:33:39,042 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (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 $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 06:33:49,885 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 32: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:33:55,837 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 32 finished +galaxy.model.metadata DEBUG 2023-10-24 06:33:55,884 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 32 +galaxy.jobs INFO 2023-10-24 06:33:55,919 [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 2023-10-24 06:33:55,948 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 32 executed (95.130 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:33:57,352 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 33 +tpv.core.entities DEBUG 2023-10-24 06:33:57,387 [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={'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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, gpus=None, 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 2023-10-24 06:33:57,388 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (33) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:33:57,393 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (33) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:33:57,407 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (33) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:33:57,424 [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 2023-10-24 06:33:57,431 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [33] queued (38.656 ms) +galaxy.jobs.handler INFO 2023-10-24 06:33:57,436 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (33) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:33:57,438 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 33 +galaxy.jobs DEBUG 2023-10-24 06:33:57,500 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [33] prepared (46.905 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 06:33:57,501 [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 2023-10-24 06:33:57,501 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:33:57,520 [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--py_0,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 06:33:57,538 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/33/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/7/0/1/dataset_7018d51b-0dd9-4b39-a520-f5ab00241cdf.dat' illumina '/galaxy/server/database/objects/e/7/6/dataset_e76bef91-bcff-4128-a1eb-c73f0fffc85f.dat' cssanger None summarize_input --fix-id] +galaxy.jobs.runners DEBUG 2023-10-24 06:33:57,549 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (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; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 06:33:57,558 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 06:33:57,559 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:33:57,574 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--py_0,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 06:34:03,038 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 33: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:34:09,066 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 33 finished +galaxy.model.metadata DEBUG 2023-10-24 06:34:09,112 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 33 +galaxy.jobs INFO 2023-10-24 06:34:09,145 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 33 in /galaxy/server/database/jobs_directory/000/33 +galaxy.jobs DEBUG 2023-10-24 06:34:09,174 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 33 executed (92.070 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:34:11,762 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 34 +tpv.core.entities DEBUG 2023-10-24 06:34:11,797 [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={'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=None, 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 2023-10-24 06:34:11,798 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (34) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:34:11,803 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (34) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:34:11,816 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (34) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:34:11,832 [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 2023-10-24 06:34:11,839 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [34] queued (35.875 ms) +galaxy.jobs.handler INFO 2023-10-24 06:34:11,844 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (34) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:34:11,845 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 34 +galaxy.jobs DEBUG 2023-10-24 06:34:11,945 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [34] prepared (82.843 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:34:11,963 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] 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/4/d/0/dataset_4d0ad9d0-7b65-4a63-ad73-d5e7b7139ce7_files:/galaxy/server/database/objects/4/d/0/dataset_4d0ad9d0-7b65-4a63-ad73-d5e7b7139ce7.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:34:11,976 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (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 $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 06:34:22,335 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 34: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:34:28,306 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 34 finished +galaxy.model.metadata DEBUG 2023-10-24 06:34:28,351 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 34 +galaxy.jobs INFO 2023-10-24 06:34:28,382 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 34 in /galaxy/server/database/jobs_directory/000/34 +galaxy.jobs DEBUG 2023-10-24 06:34:28,411 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 34 executed (90.358 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:34:29,284 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 35 +tpv.core.entities DEBUG 2023-10-24 06:34:29,319 [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={'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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, gpus=None, 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 2023-10-24 06:34:29,320 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (35) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:34:29,325 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (35) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:34:29,338 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (35) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:34:29,352 [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 2023-10-24 06:34:29,360 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [35] queued (34.850 ms) +galaxy.jobs.handler INFO 2023-10-24 06:34:29,363 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (35) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:34:29,367 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 35 +galaxy.jobs DEBUG 2023-10-24 06:34:29,437 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [35] prepared (52.011 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 06:34:29,438 [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 2023-10-24 06:34:29,438 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:34:29,465 [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--py_0,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 06:34:29,484 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/35/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/4/d/0/dataset_4d0ad9d0-7b65-4a63-ad73-d5e7b7139ce7.dat' sanger '/galaxy/server/database/objects/8/7/5/dataset_875566a2-6a49-426f-aa20-f69ddcd7eaba.dat' sanger None summarize_input --fix-id] +galaxy.jobs.runners DEBUG 2023-10-24 06:34:29,496 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (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; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 06:34:29,506 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 06:34:29,506 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:34:29,523 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--py_0,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 06:34:35,475 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 35: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:34:41,232 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 35 finished +galaxy.model.metadata DEBUG 2023-10-24 06:34:41,277 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 35 +galaxy.jobs INFO 2023-10-24 06:34:41,323 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 35 in /galaxy/server/database/jobs_directory/000/35 +galaxy.jobs DEBUG 2023-10-24 06:34:41,354 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 35 executed (104.994 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:34:43,689 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 36 +tpv.core.entities DEBUG 2023-10-24 06:34:43,724 [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={'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=None, 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 2023-10-24 06:34:43,724 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (36) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:34:43,729 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (36) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:34:43,743 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (36) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:34:43,756 [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 2023-10-24 06:34:43,763 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [36] queued (33.675 ms) +galaxy.jobs.handler INFO 2023-10-24 06:34:43,766 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (36) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:34:43,770 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 36 +galaxy.jobs DEBUG 2023-10-24 06:34:43,864 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [36] prepared (79.100 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:34:43,886 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] 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/8/1/d/dataset_81d279e6-156b-4eda-93e1-668c92dca708_files:/galaxy/server/database/objects/8/1/d/dataset_81d279e6-156b-4eda-93e1-668c92dca708.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:34:43,899 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (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 $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 06:34:54,721 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 36: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:35:00,797 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 36 finished +galaxy.model.metadata DEBUG 2023-10-24 06:35:00,850 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 36 +galaxy.jobs INFO 2023-10-24 06:35:00,885 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 36 in /galaxy/server/database/jobs_directory/000/36 +galaxy.jobs DEBUG 2023-10-24 06:35:00,920 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 36 executed (105.638 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:35:01,318 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 37 +tpv.core.entities DEBUG 2023-10-24 06:35:01,359 [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={'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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, gpus=None, 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 2023-10-24 06:35:01,359 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (37) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:35:01,365 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (37) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:35:01,380 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (37) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:35:01,396 [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 2023-10-24 06:35:01,404 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [37] queued (39.043 ms) +galaxy.jobs.handler INFO 2023-10-24 06:35:01,409 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (37) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:35:01,411 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 37 +galaxy.jobs DEBUG 2023-10-24 06:35:01,491 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [37] prepared (61.065 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 06:35:01,491 [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 2023-10-24 06:35:01,492 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:35:01,526 [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--py_0,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 06:35:01,546 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/37/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/8/1/d/dataset_81d279e6-156b-4eda-93e1-668c92dca708.dat' sanger '/galaxy/server/database/objects/a/1/c/dataset_a1c05f07-bc20-42a5-a8e5-3083723487e0.dat' illumina None summarize_input --fix-id] +galaxy.jobs.runners DEBUG 2023-10-24 06:35:01,559 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (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; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 06:35:01,570 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 06:35:01,570 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:35:01,590 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--py_0,type=docker]] +sqlitedict.SqliteMultithread DEBUG 2023-10-24 06:35:03,047 [pN:job_handler_0,p:8,tN:Thread-3] received: --close--, send: --no more-- +galaxy.jobs.runners DEBUG 2023-10-24 06:35:07,270 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 37: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:35:13,215 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 37 finished +galaxy.model.metadata DEBUG 2023-10-24 06:35:13,267 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 37 +galaxy.jobs INFO 2023-10-24 06:35:13,307 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 37 in /galaxy/server/database/jobs_directory/000/37 +galaxy.jobs DEBUG 2023-10-24 06:35:13,345 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 37 executed (111.705 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:35:15,781 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 38 +tpv.core.entities DEBUG 2023-10-24 06:35:15,819 [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={'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=None, 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 2023-10-24 06:35:15,820 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (38) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:35:15,826 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (38) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:35:15,841 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (38) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:35:15,859 [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 2023-10-24 06:35:15,866 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [38] queued (40.080 ms) +galaxy.jobs.handler INFO 2023-10-24 06:35:15,870 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (38) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:35:15,875 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 38 +galaxy.jobs DEBUG 2023-10-24 06:35:15,984 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [38] prepared (92.005 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:35:16,004 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] 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/8/8/7/dataset_8871534f-7566-4023-9449-6364ba6c7805_files:/galaxy/server/database/objects/8/8/7/dataset_8871534f-7566-4023-9449-6364ba6c7805.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:35:16,019 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (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 $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 06:35:25,521 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 38: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:35:31,384 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 38 finished +galaxy.model.metadata DEBUG 2023-10-24 06:35:31,434 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 38 +galaxy.jobs INFO 2023-10-24 06:35:31,469 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 38 in /galaxy/server/database/jobs_directory/000/38 +galaxy.jobs DEBUG 2023-10-24 06:35:31,507 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 38 executed (107.687 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:35:32,266 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 39 +tpv.core.entities DEBUG 2023-10-24 06:35:32,307 [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={'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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, gpus=None, 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 2023-10-24 06:35:32,308 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (39) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:35:32,313 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (39) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:35:32,327 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (39) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:35:32,342 [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 2023-10-24 06:35:32,351 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [39] queued (37.700 ms) +galaxy.jobs.handler INFO 2023-10-24 06:35:32,356 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (39) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:35:32,357 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 39 +galaxy.jobs DEBUG 2023-10-24 06:35:32,435 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [39] prepared (60.645 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 06:35:32,436 [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 2023-10-24 06:35:32,436 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:35:32,464 [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--py_0,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 06:35:32,484 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/39/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/8/8/7/dataset_8871534f-7566-4023-9449-6364ba6c7805.dat' sanger '/galaxy/server/database/objects/9/4/6/dataset_94629f16-7997-4413-a695-264f9aa097e3.dat' solexa None summarize_input --fix-id] +galaxy.jobs.runners DEBUG 2023-10-24 06:35:32,497 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (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; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 06:35:32,507 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 06:35:32,507 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:35:32,523 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--py_0,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 06:35:38,656 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 39: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:35:44,664 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 39 finished +galaxy.model.metadata DEBUG 2023-10-24 06:35:44,720 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 39 +galaxy.jobs INFO 2023-10-24 06:35:44,759 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 39 in /galaxy/server/database/jobs_directory/000/39 +galaxy.jobs DEBUG 2023-10-24 06:35:44,796 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 39 executed (108.177 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:35:46,706 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 40 +tpv.core.entities DEBUG 2023-10-24 06:35:46,741 [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={'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=None, 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 2023-10-24 06:35:46,742 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (40) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:35:46,747 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (40) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:35:46,762 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (40) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:35:46,777 [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 2023-10-24 06:35:46,785 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [40] queued (37.246 ms) +galaxy.jobs.handler INFO 2023-10-24 06:35:46,789 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (40) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:35:46,793 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 40 +galaxy.jobs DEBUG 2023-10-24 06:35:46,902 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [40] prepared (91.655 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:35:46,925 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] 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/e/b/1/dataset_eb1df349-5bf4-4311-ba16-4822ccbbf3dd_files:/galaxy/server/database/objects/e/b/1/dataset_eb1df349-5bf4-4311-ba16-4822ccbbf3dd.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:35:46,938 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (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 $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 06:35:57,910 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 40: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:36:03,833 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 40 finished +galaxy.model.metadata DEBUG 2023-10-24 06:36:03,887 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 40 +galaxy.jobs INFO 2023-10-24 06:36:03,928 [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 2023-10-24 06:36:03,967 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 40 executed (115.663 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:36:05,349 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 41 +tpv.core.entities DEBUG 2023-10-24 06:36:05,389 [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={'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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, gpus=None, 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 2023-10-24 06:36:05,390 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (41) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:36:05,395 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (41) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:36:05,410 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (41) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:36:05,426 [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 2023-10-24 06:36:05,435 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [41] queued (39.284 ms) +galaxy.jobs.handler INFO 2023-10-24 06:36:05,439 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (41) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:36:05,441 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 41 +galaxy.jobs DEBUG 2023-10-24 06:36:05,516 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [41] prepared (56.240 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 06:36:05,516 [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 2023-10-24 06:36:05,517 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:36:05,736 [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--py_0,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 06:36:05,759 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/41/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/e/b/1/dataset_eb1df349-5bf4-4311-ba16-4822ccbbf3dd.dat' sanger '/galaxy/server/database/objects/e/4/5/dataset_e45c9788-b2de-4733-a695-bac9b2cef89f.dat' cssanger None summarize_input --fix-id] +galaxy.jobs.runners DEBUG 2023-10-24 06:36:05,773 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (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; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 06:36:05,784 [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 2023-10-24 06:36:05,784 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:36:05,803 [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--py_0,type=docker]] +galaxy.jobs.runners.kubernetes ERROR 2023-10-24 06:36:10,978 [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://10.112.0.1:443/apis/batch/v1/namespaces/edge-23-10-24-06-08-1/jobs/gxy-s6hm5 + +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-s6hm5": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:36:11,027 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (41/gxy-s6hm5) Terminated at user's request +galaxy.jobs.handler DEBUG 2023-10-24 06:36:13,618 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 42 +tpv.core.entities DEBUG 2023-10-24 06:36:13,653 [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={'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=None, 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 2023-10-24 06:36:13,654 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (42) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:36:13,658 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (42) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:36:13,673 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (42) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:36:13,689 [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 2023-10-24 06:36:13,696 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [42] queued (37.858 ms) +galaxy.jobs.handler INFO 2023-10-24 06:36:13,701 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (42) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:36:13,703 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 42 +galaxy.jobs DEBUG 2023-10-24 06:36:13,807 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [42] prepared (85.273 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:36:13,827 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] 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/a/1/2/dataset_a129b20e-36bb-4353-be83-a9c2c39ec8c1_files:/galaxy/server/database/objects/a/1/2/dataset_a129b20e-36bb-4353-be83-a9c2c39ec8c1.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:36:13,840 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (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 $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 06:36:24,363 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 42: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:36:30,449 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 42 finished +galaxy.model.metadata DEBUG 2023-10-24 06:36:30,499 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 42 +galaxy.jobs INFO 2023-10-24 06:36:30,534 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 42 in /galaxy/server/database/jobs_directory/000/42 +galaxy.jobs DEBUG 2023-10-24 06:36:30,567 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 42 executed (102.694 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:36:31,139 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 43 +tpv.core.entities DEBUG 2023-10-24 06:36:31,179 [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={'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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, gpus=None, 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 2023-10-24 06:36:31,180 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (43) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:36:31,186 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (43) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:36:31,199 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (43) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:36:31,216 [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 2023-10-24 06:36:31,224 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [43] queued (38.429 ms) +galaxy.jobs.handler INFO 2023-10-24 06:36:31,228 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (43) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:36:31,232 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 43 +galaxy.jobs DEBUG 2023-10-24 06:36:31,305 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [43] prepared (54.440 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 06:36:31,306 [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 2023-10-24 06:36:31,306 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:36:31,327 [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--py_0,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 06:36:31,348 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/43/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/a/1/2/dataset_a129b20e-36bb-4353-be83-a9c2c39ec8c1.dat' solexa '/galaxy/server/database/objects/e/c/2/dataset_ec2f2645-fe53-4e05-a52b-3cc66d3797ce.dat' solexa None summarize_input --fix-id] +galaxy.jobs.runners DEBUG 2023-10-24 06:36:31,362 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (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 $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 06:36:31,373 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 06:36:31,373 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:36:31,391 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--py_0,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 06:36:36,516 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 43: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:36:42,400 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 43 finished +galaxy.model.metadata DEBUG 2023-10-24 06:36:42,457 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 43 +galaxy.jobs INFO 2023-10-24 06:36:42,506 [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 2023-10-24 06:36:42,541 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 43 executed (115.653 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:36:44,537 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 44 +tpv.core.entities DEBUG 2023-10-24 06:36:44,573 [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={'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=None, 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 2023-10-24 06:36:44,574 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (44) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:36:44,579 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (44) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:36:44,596 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (44) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:36:44,612 [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 2023-10-24 06:36:44,618 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [44] queued (39.219 ms) +galaxy.jobs.handler INFO 2023-10-24 06:36:44,622 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (44) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:36:44,626 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 44 +galaxy.jobs DEBUG 2023-10-24 06:36:44,727 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [44] prepared (84.062 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:36:44,745 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/44/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/44/registry.xml' '/galaxy/server/database/jobs_directory/000/44/upload_params.json' '44:/galaxy/server/database/objects/8/d/4/dataset_8d48e671-176f-4028-9d2d-85ee2eead8b0_files:/galaxy/server/database/objects/8/d/4/dataset_8d48e671-176f-4028-9d2d-85ee2eead8b0.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:36:44,757 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (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; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 06:36:54,722 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 44: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:37:00,787 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 44 finished +galaxy.model.metadata DEBUG 2023-10-24 06:37:00,840 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 44 +galaxy.jobs INFO 2023-10-24 06:37:00,876 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 44 in /galaxy/server/database/jobs_directory/000/44 +galaxy.jobs DEBUG 2023-10-24 06:37:00,906 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 44 executed (100.768 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:37:02,019 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 45 +tpv.core.entities DEBUG 2023-10-24 06:37:02,057 [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={'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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, gpus=None, 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 2023-10-24 06:37:02,058 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (45) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:37:02,063 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (45) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:37:02,077 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (45) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:37:02,091 [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 2023-10-24 06:37:02,099 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [45] queued (35.600 ms) +galaxy.jobs.handler INFO 2023-10-24 06:37:02,103 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (45) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:37:02,105 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 45 +galaxy.jobs DEBUG 2023-10-24 06:37:02,176 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [45] prepared (53.739 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 06:37:02,176 [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 2023-10-24 06:37:02,177 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:37:02,197 [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--py_0,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 06:37:02,217 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/45/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/8/d/4/dataset_8d48e671-176f-4028-9d2d-85ee2eead8b0.dat' solexa '/galaxy/server/database/objects/9/a/0/dataset_9a016b34-e40b-4c84-bfc6-6aa4da7701a4.dat' illumina None summarize_input --fix-id] +galaxy.jobs.runners DEBUG 2023-10-24 06:37:02,232 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (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 $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 06:37:02,242 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 06:37:02,242 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:37:02,259 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--py_0,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 06:37:07,891 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 45: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:37:13,788 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 45 finished +galaxy.model.metadata DEBUG 2023-10-24 06:37:13,841 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 45 +galaxy.jobs INFO 2023-10-24 06:37:13,884 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 45 in /galaxy/server/database/jobs_directory/000/45 +galaxy.jobs DEBUG 2023-10-24 06:37:13,920 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 45 executed (113.487 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:37:16,441 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 46 +tpv.core.entities DEBUG 2023-10-24 06:37:16,477 [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={'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=None, 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 2023-10-24 06:37:16,477 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (46) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:37:16,482 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (46) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:37:16,494 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (46) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:37:16,509 [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 2023-10-24 06:37:16,517 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [46] queued (34.923 ms) +galaxy.jobs.handler INFO 2023-10-24 06:37:16,521 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (46) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:37:16,525 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 46 +galaxy.jobs DEBUG 2023-10-24 06:37:16,628 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [46] prepared (85.824 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:37:16,646 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] 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/6/9/7/dataset_697b2ed7-8013-442d-bd2d-43e59b4122be_files:/galaxy/server/database/objects/6/9/7/dataset_697b2ed7-8013-442d-bd2d-43e59b4122be.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:37:16,659 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (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 $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 06:37:27,139 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 46: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:37:32,958 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 46 finished +galaxy.model.metadata DEBUG 2023-10-24 06:37:33,013 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 46 +galaxy.jobs INFO 2023-10-24 06:37:33,051 [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 2023-10-24 06:37:33,089 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 46 executed (114.009 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:37:33,913 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 47 +tpv.core.entities DEBUG 2023-10-24 06:37:33,953 [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={'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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, gpus=None, 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 2023-10-24 06:37:33,954 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (47) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:37:33,960 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (47) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:37:33,975 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (47) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:37:33,992 [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 2023-10-24 06:37:34,003 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [47] queued (43.115 ms) +galaxy.jobs.handler INFO 2023-10-24 06:37:34,009 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (47) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:37:34,011 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 47 +galaxy.jobs DEBUG 2023-10-24 06:37:34,093 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [47] prepared (62.155 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 06:37:34,094 [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 2023-10-24 06:37:34,094 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:37:34,132 [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--py_0,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 06:37:34,153 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/47/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/6/9/7/dataset_697b2ed7-8013-442d-bd2d-43e59b4122be.dat' solexa '/galaxy/server/database/objects/6/a/f/dataset_6af1da0b-d22b-4110-b0c5-7bf7f536583f.dat' sanger None summarize_input --fix-id] +galaxy.jobs.runners DEBUG 2023-10-24 06:37:34,168 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (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; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 06:37:34,179 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 06:37:34,179 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:37:34,203 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--py_0,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 06:37:40,317 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 47: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:37:46,260 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 47 finished +galaxy.model.metadata DEBUG 2023-10-24 06:37:46,306 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 47 +galaxy.jobs INFO 2023-10-24 06:37:46,348 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 47 in /galaxy/server/database/jobs_directory/000/47 +galaxy.jobs DEBUG 2023-10-24 06:37:46,384 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 47 executed (106.809 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:37:48,368 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 48 +tpv.core.entities DEBUG 2023-10-24 06:37:48,404 [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={'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=None, 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 2023-10-24 06:37:48,405 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (48) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:37:48,410 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (48) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:37:48,424 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (48) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:37:48,438 [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 2023-10-24 06:37:48,445 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [48] queued (34.664 ms) +galaxy.jobs.handler INFO 2023-10-24 06:37:48,450 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (48) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:37:48,451 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 48 +galaxy.jobs DEBUG 2023-10-24 06:37:48,548 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [48] prepared (79.491 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:37:48,566 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] 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/7/9/1/dataset_791fcede-e78a-48eb-9af5-10c8a8c3f59b_files:/galaxy/server/database/objects/7/9/1/dataset_791fcede-e78a-48eb-9af5-10c8a8c3f59b.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:37:48,578 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (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 $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 06:37:58,528 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 48: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:38:04,292 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 48 finished +galaxy.model.metadata DEBUG 2023-10-24 06:38:04,346 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 48 +galaxy.jobs INFO 2023-10-24 06:38:04,384 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 48 in /galaxy/server/database/jobs_directory/000/48 +galaxy.jobs DEBUG 2023-10-24 06:38:04,423 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 48 executed (114.550 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:38:04,920 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 49 +tpv.core.entities DEBUG 2023-10-24 06:38:04,959 [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={'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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, gpus=None, 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 2023-10-24 06:38:04,959 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (49) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:38:04,965 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (49) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:38:04,980 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (49) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:38:05,006 [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 2023-10-24 06:38:05,015 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [49] queued (49.681 ms) +galaxy.jobs.handler INFO 2023-10-24 06:38:05,018 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (49) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:38:05,023 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 49 +galaxy.jobs DEBUG 2023-10-24 06:38:05,119 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [49] prepared (78.250 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 06:38:05,120 [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 2023-10-24 06:38:05,120 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:38:05,141 [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--py_0,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 06:38:05,160 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/49/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/7/9/1/dataset_791fcede-e78a-48eb-9af5-10c8a8c3f59b.dat' solexa '/galaxy/server/database/objects/5/3/4/dataset_5346666b-a0db-43a9-a06e-8e03852a8b42.dat' cssanger None summarize_input --fix-id] +galaxy.jobs.runners DEBUG 2023-10-24 06:38:05,174 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (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 $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 06:38:05,202 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 06:38:05,202 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:38:05,220 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--py_0,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 06:38:10,733 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 49: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:38:16,684 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 49 finished +galaxy.model.metadata DEBUG 2023-10-24 06:38:16,734 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 49 +galaxy.jobs INFO 2023-10-24 06:38:16,768 [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 2023-10-24 06:38:16,797 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 49 executed (93.691 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:38:19,383 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 50 +tpv.core.entities DEBUG 2023-10-24 06:38:19,417 [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={'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=None, 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 2023-10-24 06:38:19,418 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (50) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:38:19,422 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (50) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:38:19,437 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (50) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:38:19,452 [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 2023-10-24 06:38:19,459 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [50] queued (35.955 ms) +galaxy.jobs.handler INFO 2023-10-24 06:38:19,462 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (50) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:38:19,466 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 50 +galaxy.jobs DEBUG 2023-10-24 06:38:19,579 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [50] prepared (95.853 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:38:19,600 [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 [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/50/registry.xml' '/galaxy/server/database/jobs_directory/000/50/upload_params.json' '50:/galaxy/server/database/objects/6/a/f/dataset_6af18c03-bef4-4fe2-83ca-aa31eda56680_files:/galaxy/server/database/objects/6/a/f/dataset_6af18c03-bef4-4fe2-83ca-aa31eda56680.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:38:19,614 [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; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 06:38:29,945 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 50: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:38:35,978 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 50 finished +galaxy.model.metadata DEBUG 2023-10-24 06:38:36,028 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 50 +galaxy.jobs INFO 2023-10-24 06:38:36,061 [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 2023-10-24 06:38:36,097 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 50 executed (104.417 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:38:36,868 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 51 +tpv.core.entities DEBUG 2023-10-24 06:38:36,906 [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={'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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, gpus=None, 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 2023-10-24 06:38:36,907 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (51) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:38:36,912 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (51) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:38:36,926 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (51) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:38:36,941 [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 2023-10-24 06:38:36,949 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [51] queued (36.811 ms) +galaxy.jobs.handler INFO 2023-10-24 06:38:36,952 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (51) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:38:36,956 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 51 +galaxy.jobs DEBUG 2023-10-24 06:38:37,025 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [51] prepared (52.100 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 06:38:37,026 [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 2023-10-24 06:38:37,026 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:38:37,047 [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--py_0,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 06:38:37,064 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/51/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/6/a/f/dataset_6af18c03-bef4-4fe2-83ca-aa31eda56680.dat' cssanger '/galaxy/server/database/objects/c/9/6/dataset_c965df51-d317-4f27-b962-2bee2d0a5ddc.dat' cssanger None summarize_input --fix-id] +galaxy.jobs.runners DEBUG 2023-10-24 06:38:37,077 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (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 $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 06:38:37,087 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 06:38:37,088 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:38:37,105 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--py_0,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 06:38:42,087 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 51: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:38:48,064 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 51 finished +galaxy.model.metadata DEBUG 2023-10-24 06:38:48,110 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 51 +galaxy.jobs INFO 2023-10-24 06:38:48,152 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 51 in /galaxy/server/database/jobs_directory/000/51 +galaxy.jobs DEBUG 2023-10-24 06:38:48,184 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 51 executed (103.304 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:38:50,256 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 52 +tpv.core.entities DEBUG 2023-10-24 06:38:50,289 [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={'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=None, 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 2023-10-24 06:38:50,290 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (52) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:38:50,297 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (52) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:38:50,311 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (52) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:38:50,326 [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 2023-10-24 06:38:50,333 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [52] queued (35.958 ms) +galaxy.jobs.handler INFO 2023-10-24 06:38:50,338 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (52) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:38:50,340 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 52 +galaxy.jobs DEBUG 2023-10-24 06:38:50,448 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [52] prepared (91.313 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:38:50,469 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] 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/6/8/4/dataset_68410e5e-51d4-4de1-8e40-67ec016871c9_files:/galaxy/server/database/objects/6/8/4/dataset_68410e5e-51d4-4de1-8e40-67ec016871c9.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:38:50,483 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (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 $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 06:39:00,332 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 52: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:39:06,282 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 52 finished +galaxy.model.metadata DEBUG 2023-10-24 06:39:06,333 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 52 +galaxy.jobs INFO 2023-10-24 06:39:06,369 [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 2023-10-24 06:39:06,408 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 52 executed (108.659 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:39:06,725 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 53 +tpv.core.entities DEBUG 2023-10-24 06:39:06,762 [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={'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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, gpus=None, 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 2023-10-24 06:39:06,763 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (53) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:39:06,768 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (53) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:39:06,782 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (53) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:39:06,799 [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 2023-10-24 06:39:06,808 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [53] queued (40.004 ms) +galaxy.jobs.handler INFO 2023-10-24 06:39:06,812 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (53) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:39:06,817 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 53 +galaxy.jobs DEBUG 2023-10-24 06:39:06,886 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [53] prepared (51.495 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 06:39:06,887 [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 2023-10-24 06:39:06,887 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:39:06,907 [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--py_0,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 06:39:06,932 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/53/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/6/8/4/dataset_68410e5e-51d4-4de1-8e40-67ec016871c9.dat' cssanger '/galaxy/server/database/objects/d/f/7/dataset_df7c9849-cb1c-4f43-8b33-dc4433ab4f69.dat' sanger None summarize_input --fix-id] +galaxy.jobs.runners DEBUG 2023-10-24 06:39:06,945 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (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; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 06:39:06,956 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 06:39:06,956 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:39:06,976 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--py_0,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 06:39:12,524 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 53: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:39:18,566 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 53 finished +galaxy.model.metadata DEBUG 2023-10-24 06:39:18,613 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 53 +galaxy.jobs INFO 2023-10-24 06:39:18,648 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 53 in /galaxy/server/database/jobs_directory/000/53 +galaxy.jobs DEBUG 2023-10-24 06:39:18,680 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 53 executed (99.068 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:39:21,158 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 54 +tpv.core.entities DEBUG 2023-10-24 06:39:21,195 [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={'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=None, 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 2023-10-24 06:39:21,195 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (54) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:39:21,200 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (54) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:39:21,215 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (54) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:39:21,232 [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 2023-10-24 06:39:21,239 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [54] queued (38.735 ms) +galaxy.jobs.handler INFO 2023-10-24 06:39:21,243 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (54) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:39:21,247 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 54 +galaxy.jobs DEBUG 2023-10-24 06:39:21,355 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [54] prepared (90.116 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:39:21,375 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] 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/c/4/a/dataset_c4a2498a-928f-4245-a05b-7d01405e627f_files:/galaxy/server/database/objects/c/4/a/dataset_c4a2498a-928f-4245-a05b-7d01405e627f.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:39:21,389 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (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 $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 06:39:31,744 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 54: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:39:37,810 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 54 finished +galaxy.model.metadata DEBUG 2023-10-24 06:39:37,856 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 54 +galaxy.jobs INFO 2023-10-24 06:39:37,889 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 54 in /galaxy/server/database/jobs_directory/000/54 +galaxy.jobs DEBUG 2023-10-24 06:39:37,925 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 54 executed (99.683 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:39:38,649 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 55 +tpv.core.entities DEBUG 2023-10-24 06:39:38,685 [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={'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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, gpus=None, 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 2023-10-24 06:39:38,686 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (55) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:39:38,690 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (55) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:39:38,704 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (55) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:39:38,720 [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 2023-10-24 06:39:38,727 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [55] queued (36.893 ms) +galaxy.jobs.handler INFO 2023-10-24 06:39:38,732 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (55) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:39:38,734 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 55 +galaxy.jobs DEBUG 2023-10-24 06:39:38,801 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [55] prepared (51.318 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 06:39:38,802 [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 2023-10-24 06:39:38,802 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:39:38,822 [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--py_0,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 06:39:38,841 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/55/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/c/4/a/dataset_c4a2498a-928f-4245-a05b-7d01405e627f.dat' cssanger '/galaxy/server/database/objects/e/5/4/dataset_e54f6384-5bdd-4d7c-9ad1-6d946e3b4591.dat' illumina None summarize_input --fix-id] +galaxy.jobs.runners DEBUG 2023-10-24 06:39:38,854 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (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 $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 06:39:38,864 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 06:39:38,864 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:39:38,882 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--py_0,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 06:39:43,888 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 55: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:39:49,958 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 55 finished +galaxy.model.metadata DEBUG 2023-10-24 06:39:50,019 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 55 +galaxy.jobs INFO 2023-10-24 06:39:50,060 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 55 in /galaxy/server/database/jobs_directory/000/55 +galaxy.jobs DEBUG 2023-10-24 06:39:50,090 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 55 executed (115.696 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:39:52,037 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 56 +tpv.core.entities DEBUG 2023-10-24 06:39:52,075 [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={'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=None, 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 2023-10-24 06:39:52,075 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (56) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:39:52,080 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (56) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:39:52,096 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (56) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:39:52,111 [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 2023-10-24 06:39:52,118 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [56] queued (37.465 ms) +galaxy.jobs.handler INFO 2023-10-24 06:39:52,123 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (56) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:39:52,125 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 56 +galaxy.jobs DEBUG 2023-10-24 06:39:52,242 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [56] prepared (99.135 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:39:52,260 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/56/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/56/registry.xml' '/galaxy/server/database/jobs_directory/000/56/upload_params.json' '56:/galaxy/server/database/objects/8/c/9/dataset_8c9d95a3-c000-4eae-8db7-aa17ff1d4aa3_files:/galaxy/server/database/objects/8/c/9/dataset_8c9d95a3-c000-4eae-8db7-aa17ff1d4aa3.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:39:52,274 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (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; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 06:40:02,120 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 56: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:40:08,404 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 56 finished +galaxy.model.metadata DEBUG 2023-10-24 06:40:08,455 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 56 +galaxy.jobs INFO 2023-10-24 06:40:08,489 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 56 in /galaxy/server/database/jobs_directory/000/56 +galaxy.jobs DEBUG 2023-10-24 06:40:08,522 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 56 executed (102.512 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:40:09,655 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 57 +tpv.core.entities DEBUG 2023-10-24 06:40:09,694 [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={'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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, gpus=None, 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 2023-10-24 06:40:09,695 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (57) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:40:09,701 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (57) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:40:09,716 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (57) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:40:09,732 [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 2023-10-24 06:40:09,740 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [57] queued (38.604 ms) +galaxy.jobs.handler INFO 2023-10-24 06:40:09,743 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (57) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:40:09,748 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 57 +galaxy.jobs DEBUG 2023-10-24 06:40:09,818 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [57] prepared (51.564 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 06:40:09,818 [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 2023-10-24 06:40:09,818 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:40:09,839 [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--py_0,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 06:40:09,861 [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 [gx-fastq-groomer '/galaxy/server/database/objects/8/c/9/dataset_8c9d95a3-c000-4eae-8db7-aa17ff1d4aa3.dat' cssanger '/galaxy/server/database/objects/9/1/4/dataset_914e8f4c-27d6-4054-9adf-6ca4dde67cef.dat' solexa None summarize_input --fix-id] +galaxy.jobs.runners DEBUG 2023-10-24 06:40:09,875 [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 $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 06:40:09,886 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 06:40:09,886 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:40:09,906 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--py_0,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 06:40:15,297 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 57: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:40:21,134 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 57 finished +galaxy.model.metadata DEBUG 2023-10-24 06:40:21,191 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 57 +galaxy.jobs INFO 2023-10-24 06:40:21,225 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 57 in /galaxy/server/database/jobs_directory/000/57 +galaxy.jobs DEBUG 2023-10-24 06:40:21,258 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 57 executed (97.780 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:40:24,086 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 58 +tpv.core.entities DEBUG 2023-10-24 06:40:24,126 [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={'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=None, 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 2023-10-24 06:40:24,127 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (58) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:40:24,133 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (58) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:40:24,149 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (58) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:40:24,166 [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 2023-10-24 06:40:24,172 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [58] queued (39.480 ms) +galaxy.jobs.handler INFO 2023-10-24 06:40:24,178 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (58) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:40:24,179 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 58 +galaxy.jobs DEBUG 2023-10-24 06:40:24,282 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [58] prepared (83.574 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:40:24,300 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] 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/1/4/4/dataset_1441990d-e1b4-4c9e-976b-14ab75683299_files:/galaxy/server/database/objects/1/4/4/dataset_1441990d-e1b4-4c9e-976b-14ab75683299.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:40:24,313 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (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 $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 06:40:34,528 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 58: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:40:40,615 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 58 finished +galaxy.model.metadata DEBUG 2023-10-24 06:40:40,665 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 58 +galaxy.jobs INFO 2023-10-24 06:40:40,700 [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 2023-10-24 06:40:40,736 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 58 executed (106.079 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:40:41,613 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 59 +tpv.core.entities DEBUG 2023-10-24 06:40:41,652 [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={'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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, gpus=None, 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 2023-10-24 06:40:41,652 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (59) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:40:41,658 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (59) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:40:41,672 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (59) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:40:41,687 [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 2023-10-24 06:40:41,695 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [59] queued (37.441 ms) +galaxy.jobs.handler INFO 2023-10-24 06:40:41,699 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (59) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:40:41,703 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 59 +galaxy.jobs DEBUG 2023-10-24 06:40:41,775 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [59] prepared (52.363 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 06:40:41,776 [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 2023-10-24 06:40:41,776 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:40:41,797 [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/galaxy_sequence_utils:1.1.5--py_0,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 06:40:41,817 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/59/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/1/4/4/dataset_1441990d-e1b4-4c9e-976b-14ab75683299.dat' cssanger '/galaxy/server/database/objects/1/2/6/dataset_126e020d-c002-4709-a115-ee92710b3f5c.dat' cssanger None summarize_input --fix-id] +galaxy.jobs.runners DEBUG 2023-10-24 06:40:41,831 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (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 $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 06:40:41,841 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 06:40:41,841 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:40:41,859 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--py_0,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 06:40:47,688 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 59: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:40:53,590 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 59 finished +galaxy.model.metadata DEBUG 2023-10-24 06:40:53,639 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 59 +galaxy.jobs INFO 2023-10-24 06:40:53,676 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 59 in /galaxy/server/database/jobs_directory/000/59 +galaxy.jobs DEBUG 2023-10-24 06:40:53,709 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 59 executed (102.662 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:40:56,183 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 60 +tpv.core.entities DEBUG 2023-10-24 06:40:56,217 [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={'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=None, 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 2023-10-24 06:40:56,218 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (60) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:40:56,222 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (60) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:40:56,236 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (60) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:40:56,254 [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 2023-10-24 06:40:56,261 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [60] queued (38.361 ms) +galaxy.jobs.handler INFO 2023-10-24 06:40:56,265 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (60) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:40:56,269 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 60 +galaxy.jobs DEBUG 2023-10-24 06:40:56,379 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [60] prepared (90.674 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:40:56,400 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/60/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/60/registry.xml' '/galaxy/server/database/jobs_directory/000/60/upload_params.json' '60:/galaxy/server/database/objects/c/2/4/dataset_c248a62b-d008-47cc-b18c-28a3fb3d41b1_files:/galaxy/server/database/objects/c/2/4/dataset_c248a62b-d008-47cc-b18c-28a3fb3d41b1.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:40:56,414 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (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; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 06:41:06,941 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 60: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:41:12,741 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 60 finished +galaxy.model.metadata DEBUG 2023-10-24 06:41:12,799 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 60 +galaxy.jobs INFO 2023-10-24 06:41:12,834 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 60 in /galaxy/server/database/jobs_directory/000/60 +galaxy.jobs DEBUG 2023-10-24 06:41:12,869 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 60 executed (105.706 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:41:13,673 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 61 +tpv.core.entities DEBUG 2023-10-24 06:41:13,712 [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={'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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, gpus=None, 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 2023-10-24 06:41:13,713 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (61) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:41:13,718 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (61) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:41:13,732 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (61) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:41:13,747 [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 2023-10-24 06:41:13,755 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [61] queued (37.040 ms) +galaxy.jobs.handler INFO 2023-10-24 06:41:13,761 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (61) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:41:13,763 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 61 +galaxy.jobs DEBUG 2023-10-24 06:41:13,832 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [61] prepared (52.338 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 06:41:13,833 [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 2023-10-24 06:41:13,833 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:41:14,047 [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--py_0,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 06:41:14,067 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/61/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/c/2/4/dataset_c248a62b-d008-47cc-b18c-28a3fb3d41b1.dat' sanger '/galaxy/server/database/objects/f/6/8/dataset_f68bc387-d79a-41c3-96b1-b1f0d38b6ae1.dat' sanger None summarize_input --fix-id] +galaxy.jobs.runners DEBUG 2023-10-24 06:41:14,080 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (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 $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 06:41:14,090 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 06:41:14,090 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:41:14,110 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--py_0,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 06:41:20,105 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 61: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:41:26,244 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 61 finished +galaxy.model.metadata DEBUG 2023-10-24 06:41:26,295 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 61 +galaxy.jobs INFO 2023-10-24 06:41:26,331 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 61 in /galaxy/server/database/jobs_directory/000/61 +galaxy.jobs DEBUG 2023-10-24 06:41:26,373 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 61 executed (111.798 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:41:29,142 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 62 +tpv.core.entities DEBUG 2023-10-24 06:41:29,177 [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={'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=None, 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 2023-10-24 06:41:29,178 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (62) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:41:29,183 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (62) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:41:29,197 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (62) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:41:29,213 [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 2023-10-24 06:41:29,220 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [62] queued (37.053 ms) +galaxy.jobs.handler INFO 2023-10-24 06:41:29,225 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (62) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:41:29,228 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 62 +galaxy.jobs DEBUG 2023-10-24 06:41:29,331 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [62] prepared (85.456 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:41:29,351 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/62/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/62/registry.xml' '/galaxy/server/database/jobs_directory/000/62/upload_params.json' '62:/galaxy/server/database/objects/5/d/9/dataset_5d989378-4020-4184-a09d-5cb092a89ccf_files:/galaxy/server/database/objects/5/d/9/dataset_5d989378-4020-4184-a09d-5cb092a89ccf.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:41:29,365 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (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; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes ERROR 2023-10-24 06:41:39,386 [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://10.112.0.1:443/apis/batch/v1/namespaces/edge-23-10-24-06-08-1/jobs/gxy-vbnlp + +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-vbnlp": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:41:39,478 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (62/gxy-vbnlp) Terminated at user's request +galaxy.jobs.handler DEBUG 2023-10-24 06:41:41,497 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 63 +tpv.core.entities DEBUG 2023-10-24 06:41:41,531 [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={'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=None, 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 2023-10-24 06:41:41,532 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (63) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:41:41,537 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (63) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:41:41,557 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (63) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:41:41,572 [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 2023-10-24 06:41:41,579 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [63] queued (41.773 ms) +galaxy.jobs.handler INFO 2023-10-24 06:41:41,584 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (63) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:41:41,586 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 63 +galaxy.jobs DEBUG 2023-10-24 06:41:41,700 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [63] prepared (96.730 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:41:41,720 [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/0/4/a/dataset_04a6cd85-ad27-4b4a-aeb7-7714f070342c_files:/galaxy/server/database/objects/0/4/a/dataset_04a6cd85-ad27-4b4a-aeb7-7714f070342c.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:41:41,734 [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 $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 06:41:51,726 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 63: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:41:58,009 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 63 finished +galaxy.model.metadata DEBUG 2023-10-24 06:41:58,060 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 63 +galaxy.jobs INFO 2023-10-24 06:41:58,096 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 63 in /galaxy/server/database/jobs_directory/000/63 +galaxy.jobs DEBUG 2023-10-24 06:41:58,131 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 63 executed (105.082 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:41:59,002 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 64 +tpv.core.entities DEBUG 2023-10-24 06:41:59,041 [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={'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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, gpus=None, 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 2023-10-24 06:41:59,042 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (64) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:41:59,047 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (64) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:41:59,061 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (64) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:41:59,076 [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 2023-10-24 06:41:59,083 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [64] queued (36.420 ms) +galaxy.jobs.handler INFO 2023-10-24 06:41:59,089 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (64) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:41:59,090 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 64 +galaxy.jobs DEBUG 2023-10-24 06:41:59,161 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [64] prepared (53.608 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 06:41:59,161 [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 2023-10-24 06:41:59,162 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:41:59,183 [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--py_0,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 06:41:59,202 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/64/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/0/4/a/dataset_04a6cd85-ad27-4b4a-aeb7-7714f070342c.dat' sanger '/galaxy/server/database/objects/e/2/9/dataset_e29a7380-4bc2-41d8-a92d-482577b81122.dat' solexa None summarize_input --fix-id] +galaxy.jobs.runners DEBUG 2023-10-24 06:41:59,215 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (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; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 06:41:59,226 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 06:41:59,226 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:41:59,244 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--py_0,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 06:42:04,856 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 64: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:42:10,845 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 64 finished +galaxy.model.metadata DEBUG 2023-10-24 06:42:10,892 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 64 +galaxy.jobs INFO 2023-10-24 06:42:10,926 [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 2023-10-24 06:42:10,965 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 64 executed (103.163 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:42:13,475 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 65 +tpv.core.entities DEBUG 2023-10-24 06:42:13,509 [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={'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=None, 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 2023-10-24 06:42:13,509 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (65) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:42:13,514 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (65) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:42:13,527 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (65) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:42:13,542 [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 2023-10-24 06:42:13,549 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [65] queued (35.050 ms) +galaxy.jobs.handler INFO 2023-10-24 06:42:13,554 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (65) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:42:13,556 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 65 +galaxy.jobs DEBUG 2023-10-24 06:42:13,660 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [65] prepared (86.869 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:42:13,679 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] 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/a/c/5/dataset_ac53ad0c-4184-4e42-bc75-5820dac71ad9_files:/galaxy/server/database/objects/a/c/5/dataset_ac53ad0c-4184-4e42-bc75-5820dac71ad9.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:42:13,692 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (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 $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 06:42:24,108 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 65: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:42:30,265 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 65 finished +galaxy.model.metadata DEBUG 2023-10-24 06:42:30,316 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 65 +galaxy.jobs INFO 2023-10-24 06:42:30,354 [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 2023-10-24 06:42:30,387 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 65 executed (105.152 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:42:31,988 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 66 +tpv.core.entities DEBUG 2023-10-24 06:42:32,026 [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={'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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, gpus=None, 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 2023-10-24 06:42:32,027 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (66) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:42:32,032 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (66) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:42:32,046 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (66) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:42:32,060 [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 2023-10-24 06:42:32,068 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [66] queued (36.064 ms) +galaxy.jobs.handler INFO 2023-10-24 06:42:32,073 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (66) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:42:32,075 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 66 +galaxy.jobs DEBUG 2023-10-24 06:42:32,143 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [66] prepared (52.180 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 06:42:32,144 [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 2023-10-24 06:42:32,144 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:42:32,164 [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--py_0,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 06:42:32,183 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/66/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/a/c/5/dataset_ac53ad0c-4184-4e42-bc75-5820dac71ad9.dat' sanger '/galaxy/server/database/objects/6/1/a/dataset_61a55ba7-9fcf-4a46-afd7-b4dbb11e7c70.dat' sanger ascii summarize_input --fix-id] +galaxy.jobs.runners DEBUG 2023-10-24 06:42:32,198 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (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; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 06:42:32,208 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 06:42:32,209 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:42:32,228 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--py_0,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 06:42:38,272 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 66: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:42:44,155 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 66 finished +galaxy.model.metadata DEBUG 2023-10-24 06:42:44,204 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 66 +galaxy.jobs INFO 2023-10-24 06:42:44,243 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 66 in /galaxy/server/database/jobs_directory/000/66 +galaxy.jobs DEBUG 2023-10-24 06:42:44,276 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 66 executed (103.349 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:42:46,411 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 67 +tpv.core.entities DEBUG 2023-10-24 06:42:46,448 [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={'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=None, 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 2023-10-24 06:42:46,449 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (67) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:42:46,454 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (67) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:42:46,470 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (67) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:42:46,486 [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 2023-10-24 06:42:46,493 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [67] queued (38.912 ms) +galaxy.jobs.handler INFO 2023-10-24 06:42:46,496 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (67) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:42:46,500 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 67 +galaxy.jobs DEBUG 2023-10-24 06:42:46,623 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [67] prepared (105.686 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:42:46,644 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] 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/b/1/b/dataset_b1b16d87-f629-4c00-a346-abbce9e808bf_files:/galaxy/server/database/objects/b/1/b/dataset_b1b16d87-f629-4c00-a346-abbce9e808bf.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:42:46,658 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (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 $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 06:42:56,499 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 67: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:43:02,434 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 67 finished +galaxy.model.metadata DEBUG 2023-10-24 06:43:02,482 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 67 +galaxy.jobs INFO 2023-10-24 06:43:02,516 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 67 in /galaxy/server/database/jobs_directory/000/67 +galaxy.jobs DEBUG 2023-10-24 06:43:02,549 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 67 executed (98.459 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:43:03,957 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 68 +tpv.core.entities DEBUG 2023-10-24 06:43:03,995 [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={'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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, gpus=None, 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 2023-10-24 06:43:03,995 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (68) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:43:04,002 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (68) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:43:04,018 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (68) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:43:04,034 [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 2023-10-24 06:43:04,043 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [68] queued (40.496 ms) +galaxy.jobs.handler INFO 2023-10-24 06:43:04,048 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (68) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:43:04,050 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 68 +galaxy.jobs DEBUG 2023-10-24 06:43:04,125 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [68] prepared (57.404 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 06:43:04,125 [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 2023-10-24 06:43:04,125 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:43:04,147 [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/galaxy_sequence_utils:1.1.5--py_0,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 06:43:04,169 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/68/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/b/1/b/dataset_b1b16d87-f629-4c00-a346-abbce9e808bf.dat' sanger '/galaxy/server/database/objects/e/a/f/dataset_eaf97a9b-26a5-4579-bb7f-ee0b5d9d02fa.dat' sanger decimal summarize_input --fix-id] +galaxy.jobs.runners DEBUG 2023-10-24 06:43:04,183 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (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; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 06:43:04,195 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 06:43:04,195 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:43:04,218 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--py_0,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 06:43:09,699 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 68: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:43:15,757 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 68 finished +galaxy.model.metadata DEBUG 2023-10-24 06:43:15,813 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 68 +galaxy.jobs INFO 2023-10-24 06:43:15,851 [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 2023-10-24 06:43:15,881 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 68 executed (100.507 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:43:18,385 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 69 +tpv.core.entities DEBUG 2023-10-24 06:43:18,421 [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={'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=None, 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 2023-10-24 06:43:18,422 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (69) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:43:18,426 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (69) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:43:18,441 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (69) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:43:18,455 [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 2023-10-24 06:43:18,462 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [69] queued (35.488 ms) +galaxy.jobs.handler INFO 2023-10-24 06:43:18,467 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (69) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:43:18,469 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 69 +galaxy.jobs DEBUG 2023-10-24 06:43:18,574 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [69] prepared (87.481 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:43:18,594 [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/7/d/9/dataset_7d9e1700-53e7-4ed0-bcf7-3167d26e99cd_files:/galaxy/server/database/objects/7/d/9/dataset_7d9e1700-53e7-4ed0-bcf7-3167d26e99cd.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:43:18,607 [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 $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 06:43:28,913 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 69: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:43:34,847 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 69 finished +galaxy.model.metadata DEBUG 2023-10-24 06:43:34,906 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 69 +galaxy.jobs INFO 2023-10-24 06:43:34,942 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 69 in /galaxy/server/database/jobs_directory/000/69 +galaxy.jobs DEBUG 2023-10-24 06:43:34,982 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 69 executed (110.763 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:43:35,882 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 70 +tpv.core.entities DEBUG 2023-10-24 06:43:35,919 [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={'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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, gpus=None, 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 2023-10-24 06:43:35,920 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (70) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:43:35,924 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (70) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:43:35,938 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (70) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:43:35,952 [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 2023-10-24 06:43:35,959 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [70] queued (34.796 ms) +galaxy.jobs.handler INFO 2023-10-24 06:43:35,963 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (70) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:43:35,967 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 70 +galaxy.jobs DEBUG 2023-10-24 06:43:36,037 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [70] prepared (52.808 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 06:43:36,037 [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 2023-10-24 06:43:36,038 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:43:36,057 [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--py_0,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 06:43:36,078 [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 [gx-fastq-groomer '/galaxy/server/database/objects/7/d/9/dataset_7d9e1700-53e7-4ed0-bcf7-3167d26e99cd.dat' sanger '/galaxy/server/database/objects/d/4/6/dataset_d461c721-73f1-47a4-a610-7f073fe62dc0.dat' sanger ascii summarize_input --fix-id] +galaxy.jobs.runners DEBUG 2023-10-24 06:43:36,094 [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; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 06:43:36,114 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 06:43:36,114 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:43:36,132 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--py_0,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 06:43:41,060 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 70: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:43:47,193 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 70 finished +galaxy.model.metadata DEBUG 2023-10-24 06:43:47,249 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 70 +galaxy.jobs INFO 2023-10-24 06:43:47,291 [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 2023-10-24 06:43:47,323 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 70 executed (107.252 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:43:49,307 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 71 +tpv.core.entities DEBUG 2023-10-24 06:43:49,343 [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={'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=None, 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 2023-10-24 06:43:49,343 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (71) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:43:49,348 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (71) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:43:49,363 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (71) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:43:49,379 [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 2023-10-24 06:43:49,386 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [71] queued (37.424 ms) +galaxy.jobs.handler INFO 2023-10-24 06:43:49,391 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (71) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:43:49,393 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 71 +galaxy.jobs DEBUG 2023-10-24 06:43:49,493 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [71] prepared (82.939 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:43:49,514 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] 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/9/e/b/dataset_9ebf0243-f17d-4c3b-bb10-4d3495dd9719_files:/galaxy/server/database/objects/9/e/b/dataset_9ebf0243-f17d-4c3b-bb10-4d3495dd9719.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:43:49,527 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (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 $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 06:43:59,291 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 71: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:44:05,309 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 71 finished +galaxy.model.metadata DEBUG 2023-10-24 06:44:05,356 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 71 +galaxy.jobs INFO 2023-10-24 06:44:05,390 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 71 in /galaxy/server/database/jobs_directory/000/71 +galaxy.jobs DEBUG 2023-10-24 06:44:05,429 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 71 executed (104.505 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:44:05,765 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 72 +tpv.core.entities DEBUG 2023-10-24 06:44:05,803 [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={'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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, gpus=None, 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 2023-10-24 06:44:05,804 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (72) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:44:05,808 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (72) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:44:05,822 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (72) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:44:05,836 [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 2023-10-24 06:44:05,844 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [72] queued (34.975 ms) +galaxy.jobs.handler INFO 2023-10-24 06:44:05,847 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (72) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:44:05,852 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 72 +galaxy.jobs DEBUG 2023-10-24 06:44:05,917 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [72] prepared (48.647 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 06:44:05,918 [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 2023-10-24 06:44:05,918 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:44:05,945 [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--py_0,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 06:44:05,964 [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 [gx-fastq-groomer '/galaxy/server/database/objects/9/e/b/dataset_9ebf0243-f17d-4c3b-bb10-4d3495dd9719.dat' solexa '/galaxy/server/database/objects/6/b/7/dataset_6b75ce1f-c66b-4656-9567-e3c41ba969b9.dat' solexa ascii summarize_input --fix-id] +galaxy.jobs.runners DEBUG 2023-10-24 06:44:05,976 [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; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 06:44:05,985 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 06:44:05,986 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:44:06,003 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--py_0,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 06:44:11,462 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 72: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:44:17,490 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 72 finished +galaxy.model.metadata DEBUG 2023-10-24 06:44:17,539 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 72 +galaxy.jobs INFO 2023-10-24 06:44:17,571 [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 2023-10-24 06:44:17,615 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 72 executed (106.959 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:44:19,185 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 73 +tpv.core.entities DEBUG 2023-10-24 06:44:19,219 [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={'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=None, 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 2023-10-24 06:44:19,220 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (73) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:44:19,224 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (73) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:44:19,239 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (73) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:44:19,253 [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 2023-10-24 06:44:19,259 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [73] queued (34.446 ms) +galaxy.jobs.handler INFO 2023-10-24 06:44:19,264 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (73) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:44:19,266 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 73 +galaxy.jobs DEBUG 2023-10-24 06:44:19,364 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [73] prepared (81.971 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:44:19,383 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] 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/b/1/e/dataset_b1e624eb-301a-4a80-8c3a-2e20f7c2306c_files:/galaxy/server/database/objects/b/1/e/dataset_b1e624eb-301a-4a80-8c3a-2e20f7c2306c.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:44:19,396 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (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 $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 06:44:29,702 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 73: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:44:35,659 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 73 finished +galaxy.model.metadata DEBUG 2023-10-24 06:44:35,705 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 73 +galaxy.jobs INFO 2023-10-24 06:44:35,739 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 73 in /galaxy/server/database/jobs_directory/000/73 +galaxy.jobs DEBUG 2023-10-24 06:44:35,776 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 73 executed (102.348 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:44:36,664 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 74 +tpv.core.entities DEBUG 2023-10-24 06:44:36,700 [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={'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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, gpus=None, 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 2023-10-24 06:44:36,701 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (74) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:44:36,706 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (74) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:44:36,719 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (74) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:44:36,734 [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 2023-10-24 06:44:36,742 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [74] queued (36.420 ms) +galaxy.jobs.handler INFO 2023-10-24 06:44:36,747 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (74) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:44:36,750 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 74 +galaxy.jobs DEBUG 2023-10-24 06:44:36,819 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [74] prepared (52.269 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 06:44:36,820 [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 2023-10-24 06:44:36,820 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:44:36,841 [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--py_0,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 06:44:36,860 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/74/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/b/1/e/dataset_b1e624eb-301a-4a80-8c3a-2e20f7c2306c.dat' solexa '/galaxy/server/database/objects/5/3/f/dataset_53f3bf70-0101-4542-a3bd-7233e004098a.dat' solexa decimal summarize_input --fix-id] +galaxy.jobs.runners DEBUG 2023-10-24 06:44:36,873 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (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; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 06:44:36,883 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 06:44:36,883 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:44:36,900 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--py_0,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 06:44:42,834 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 74: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:44:48,742 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 74 finished +galaxy.model.metadata DEBUG 2023-10-24 06:44:48,793 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 74 +galaxy.jobs INFO 2023-10-24 06:44:48,826 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 74 in /galaxy/server/database/jobs_directory/000/74 +galaxy.jobs DEBUG 2023-10-24 06:44:48,854 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 74 executed (90.850 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:44:51,070 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 75 +tpv.core.entities DEBUG 2023-10-24 06:44:51,104 [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={'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=None, 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 2023-10-24 06:44:51,105 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (75) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:44:51,110 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (75) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:44:51,123 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (75) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:44:51,138 [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 2023-10-24 06:44:51,145 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [75] queued (34.780 ms) +galaxy.jobs.handler INFO 2023-10-24 06:44:51,150 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (75) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:44:51,151 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 75 +galaxy.jobs DEBUG 2023-10-24 06:44:51,248 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [75] prepared (80.155 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:44:51,266 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] 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/5/0/7/dataset_507aeea3-1a79-4c7f-85b3-60d7c32e2270_files:/galaxy/server/database/objects/5/0/7/dataset_507aeea3-1a79-4c7f-85b3-60d7c32e2270.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:44:51,279 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (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 $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 06:45:01,056 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 75: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:45:07,090 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 75 finished +galaxy.model.metadata DEBUG 2023-10-24 06:45:07,141 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 75 +galaxy.jobs INFO 2023-10-24 06:45:07,175 [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 2023-10-24 06:45:07,204 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 75 executed (96.060 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:45:08,550 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 76 +tpv.core.entities DEBUG 2023-10-24 06:45:08,589 [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={'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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, gpus=None, 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 2023-10-24 06:45:08,590 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (76) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:45:08,595 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (76) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:45:08,609 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (76) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:45:08,627 [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 2023-10-24 06:45:08,635 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [76] queued (40.493 ms) +galaxy.jobs.handler INFO 2023-10-24 06:45:08,641 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (76) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:45:08,643 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 76 +galaxy.jobs DEBUG 2023-10-24 06:45:08,712 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [76] prepared (51.727 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 06:45:08,713 [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 2023-10-24 06:45:08,713 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:45:08,745 [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--py_0,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 06:45:08,765 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/76/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/5/0/7/dataset_507aeea3-1a79-4c7f-85b3-60d7c32e2270.dat' sanger.gz '/galaxy/server/database/objects/4/5/9/dataset_45939652-a97e-457d-bcb6-c5e2262df31b.dat' sanger ascii summarize_input] +galaxy.jobs.runners DEBUG 2023-10-24 06:45:08,778 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (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; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 06:45:08,790 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 06:45:08,790 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:45:08,814 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--py_0,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 06:45:14,232 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 76: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:45:20,337 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 76 finished +galaxy.model.metadata DEBUG 2023-10-24 06:45:20,386 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 76 +galaxy.jobs INFO 2023-10-24 06:45:20,424 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 76 in /galaxy/server/database/jobs_directory/000/76 +galaxy.jobs DEBUG 2023-10-24 06:45:20,468 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 76 executed (114.276 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:45:22,980 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 77 +tpv.core.entities DEBUG 2023-10-24 06:45:23,017 [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={'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=None, 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 2023-10-24 06:45:23,018 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (77) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:45:23,023 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (77) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:45:23,038 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (77) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:45:23,054 [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 2023-10-24 06:45:23,062 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [77] queued (39.109 ms) +galaxy.jobs.handler INFO 2023-10-24 06:45:23,067 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (77) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:45:23,071 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 77 +galaxy.jobs DEBUG 2023-10-24 06:45:23,197 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [77] prepared (105.949 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:45:23,217 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] 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/f/d/e/dataset_fde9b032-0028-421a-85b9-922e8ad5986b_files:/galaxy/server/database/objects/f/d/e/dataset_fde9b032-0028-421a-85b9-922e8ad5986b.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:45:23,230 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (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 $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 06:45:33,477 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 77: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:45:39,532 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 77 finished +galaxy.model.metadata DEBUG 2023-10-24 06:45:39,588 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 77 +galaxy.jobs INFO 2023-10-24 06:45:39,625 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 77 in /galaxy/server/database/jobs_directory/000/77 +galaxy.jobs DEBUG 2023-10-24 06:45:39,664 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 77 executed (113.384 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:45:40,474 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 78 +tpv.core.entities DEBUG 2023-10-24 06:45:40,513 [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={'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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, gpus=None, 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 2023-10-24 06:45:40,514 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (78) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:45:40,519 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (78) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:45:40,533 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (78) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:45:40,547 [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 2023-10-24 06:45:40,555 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [78] queued (35.636 ms) +galaxy.jobs.handler INFO 2023-10-24 06:45:40,558 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (78) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:45:40,562 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 78 +galaxy.jobs DEBUG 2023-10-24 06:45:40,632 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [78] prepared (53.768 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 06:45:40,633 [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 2023-10-24 06:45:40,633 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:45:40,653 [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--py_0,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 06:45:40,673 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/78/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/f/d/e/dataset_fde9b032-0028-421a-85b9-922e8ad5986b.dat' cssanger.bz2 '/galaxy/server/database/objects/2/b/a/dataset_2baef198-7c70-4196-b100-76ac2912afdd.dat' cssanger ascii summarize_input] +galaxy.jobs.runners DEBUG 2023-10-24 06:45:40,686 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (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; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 06:45:40,696 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 06:45:40,696 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:45:40,714 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--py_0,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 06:45:46,625 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 78: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:45:52,445 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 78 finished +galaxy.model.metadata DEBUG 2023-10-24 06:45:52,492 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 78 +galaxy.jobs INFO 2023-10-24 06:45:52,542 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 78 in /galaxy/server/database/jobs_directory/000/78 +galaxy.jobs DEBUG 2023-10-24 06:45:52,577 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 78 executed (116.464 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:45:56,931 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 79 +tpv.core.entities DEBUG 2023-10-24 06:45:56,965 [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={'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=None, 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 2023-10-24 06:45:56,965 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (79) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:45:56,970 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (79) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:45:56,983 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (79) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:45:56,998 [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 2023-10-24 06:45:57,005 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [79] queued (35.218 ms) +galaxy.jobs.handler INFO 2023-10-24 06:45:57,011 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (79) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:45:57,012 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 79 +galaxy.jobs DEBUG 2023-10-24 06:45:57,108 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [79] prepared (79.639 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:45:57,127 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] 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/e/f/7/dataset_ef7eaa53-713b-44ea-835b-99f63d32f046_files:/galaxy/server/database/objects/e/f/7/dataset_ef7eaa53-713b-44ea-835b-99f63d32f046.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:45:57,140 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (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.handler DEBUG 2023-10-24 06:45:58,013 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 81, 80 +tpv.core.entities DEBUG 2023-10-24 06:45:58,048 [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={'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=None, 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 2023-10-24 06:45:58,049 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (80) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:45:58,053 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (80) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:45:58,068 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (80) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:45:58,083 [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 2023-10-24 06:45:58,090 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [80] queued (36.822 ms) +galaxy.jobs.handler INFO 2023-10-24 06:45:58,094 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (80) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:45:58,099 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 80 +tpv.core.entities DEBUG 2023-10-24 06:45:58,110 [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={'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=None, 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 2023-10-24 06:45:58,111 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (81) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:45:58,117 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (81) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:45:58,132 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (81) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:45:58,158 [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 2023-10-24 06:45:58,166 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [81] queued (48.944 ms) +galaxy.jobs.handler INFO 2023-10-24 06:45:58,171 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (81) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:45:58,175 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 81 +galaxy.jobs DEBUG 2023-10-24 06:45:58,219 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [80] prepared (98.066 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:45:58,245 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/80/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/80/registry.xml' '/galaxy/server/database/jobs_directory/000/80/upload_params.json' '80:/galaxy/server/database/objects/3/c/3/dataset_3c33843b-1aa1-487d-a705-7371a5b5282b_files:/galaxy/server/database/objects/3/c/3/dataset_3c33843b-1aa1-487d-a705-7371a5b5282b.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:45:58,260 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (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 $return_code" +galaxy.jobs DEBUG 2023-10-24 06:45:58,293 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [81] prepared (96.150 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:45:58,317 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/81/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/81/registry.xml' '/galaxy/server/database/jobs_directory/000/81/upload_params.json' '81:/galaxy/server/database/objects/9/d/4/dataset_9d47488c-ba8c-47e1-aa2f-89e29be7a192_files:/galaxy/server/database/objects/9/d/4/dataset_9d47488c-ba8c-47e1-aa2f-89e29be7a192.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:45:58,330 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (81) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 06:46:08,223 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 79: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:46:10,339 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] 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 . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2023-10-24 06:46:11,377 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 80: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:46:16,532 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 79 finished +galaxy.model.metadata DEBUG 2023-10-24 06:46:16,615 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 79 +galaxy.jobs INFO 2023-10-24 06:46:16,650 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 79 in /galaxy/server/database/jobs_directory/000/79 +galaxy.jobs DEBUG 2023-10-24 06:46:16,713 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 79 executed (162.822 ms) +galaxy.jobs.runners DEBUG 2023-10-24 06:46:18,460 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 81 finished +galaxy.model.metadata DEBUG 2023-10-24 06:46:18,506 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 81 +galaxy.jobs INFO 2023-10-24 06:46:18,538 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 81 in /galaxy/server/database/jobs_directory/000/81 +galaxy.jobs DEBUG 2023-10-24 06:46:18,574 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 81 executed (100.937 ms) +galaxy.jobs.runners DEBUG 2023-10-24 06:46:19,516 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 80 finished +galaxy.model.metadata DEBUG 2023-10-24 06:46:19,559 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 80 +galaxy.jobs INFO 2023-10-24 06:46:19,590 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 80 in /galaxy/server/database/jobs_directory/000/80 +galaxy.jobs DEBUG 2023-10-24 06:46:19,621 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 80 executed (91.635 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:46:20,928 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 82 +tpv.core.entities DEBUG 2023-10-24 06:46:20,972 [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={'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=None, 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 2023-10-24 06:46:20,973 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (82) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:46:20,978 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (82) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:46:20,993 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (82) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:46:21,015 [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 2023-10-24 06:46:21,025 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [82] queued (46.729 ms) +galaxy.jobs.handler INFO 2023-10-24 06:46:21,029 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (82) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:46:21,034 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 82 +galaxy.jobs DEBUG 2023-10-24 06:46:21,148 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [82] prepared (96.148 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 06:46:21,149 [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 2023-10-24 06:46:21,149 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0beta2+galaxy1: mulled-v2-c5f548bbd369f6c53d1c17c3956a106c0348c719:a35fc6d6deba8537e98b27e27bb305fb3def739c +galaxy.tool_util.deps.containers INFO 2023-10-24 06:46:21,380 [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-c5f548bbd369f6c53d1c17c3956a106c0348c719:a35fc6d6deba8537e98b27e27bb305fb3def739c-0,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 06:46:21,401 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/82/tool_script.sh] for tool command [ln -s /galaxy/server/database/objects/3/c/3/dataset_3c33843b-1aa1-487d-a705-7371a5b5282b.dat reference.fa && ln -s /galaxy/server/database/objects/9/d/4/dataset_9d47488c-ba8c-47e1-aa2f-89e29be7a192.dat query.fa && mummerplot -b '20' -s 'small' -terminal png -title 'Title' '/galaxy/server/database/objects/e/f/7/dataset_ef7eaa53-713b-44ea-835b-99f63d32f046.dat' && gnuplot < out.gp] +galaxy.jobs.runners DEBUG 2023-10-24 06:46:21,448 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (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; +if [ -f "/galaxy/server/database/jobs_directory/000/82/working/out.gp" ] ; then cp "/galaxy/server/database/jobs_directory/000/82/working/out.gp" "/galaxy/server/database/objects/2/7/8/dataset_278d583c-60b4-43a8-aa41-6b0a8a3d3bd2.dat" ; fi; +if [ -f "/galaxy/server/database/jobs_directory/000/82/working/out.fplot" ] ; then cp "/galaxy/server/database/jobs_directory/000/82/working/out.fplot" "/galaxy/server/database/objects/f/6/c/dataset_f6c2124c-7b9a-4330-9fa4-75f8126a2cdf.dat" ; fi; +if [ -f "/galaxy/server/database/jobs_directory/000/82/working/out.rplot" ] ; then cp "/galaxy/server/database/jobs_directory/000/82/working/out.rplot" "/galaxy/server/database/objects/3/d/9/dataset_3d92f148-2d50-4bd0-bd0c-8235f8f68b87.dat" ; fi; +if [ -f "/galaxy/server/database/jobs_directory/000/82/working/out.hplot" ] ; then cp "/galaxy/server/database/jobs_directory/000/82/working/out.hplot" "/galaxy/server/database/objects/5/a/c/dataset_5ac96cc3-1ebe-4c02-9ba2-8065ec2af4bf.dat" ; fi; +if [ -f "/galaxy/server/database/jobs_directory/000/82/working/out.png" ] ; then cp "/galaxy/server/database/jobs_directory/000/82/working/out.png" "/galaxy/server/database/objects/a/c/2/dataset_ac29144d-c809-4919-914c-2f0c7134b3e5.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 06:46:21,457 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 06:46:21,458 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0beta2+galaxy1: mulled-v2-c5f548bbd369f6c53d1c17c3956a106c0348c719:a35fc6d6deba8537e98b27e27bb305fb3def739c +galaxy.tool_util.deps.containers INFO 2023-10-24 06:46:21,483 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-c5f548bbd369f6c53d1c17c3956a106c0348c719:a35fc6d6deba8537e98b27e27bb305fb3def739c-0,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 06:46:57,194 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 82: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:47:03,009 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 82 finished +galaxy.model.metadata DEBUG 2023-10-24 06:47:03,075 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 82 +galaxy.model.metadata DEBUG 2023-10-24 06:47:03,086 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 83 +galaxy.model.metadata DEBUG 2023-10-24 06:47:03,096 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 84 +galaxy.model.metadata DEBUG 2023-10-24 06:47:03,105 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 85 +galaxy.model.metadata DEBUG 2023-10-24 06:47:03,115 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 86 +galaxy.jobs INFO 2023-10-24 06:47:03,157 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 82 in /galaxy/server/database/jobs_directory/000/82 +galaxy.jobs DEBUG 2023-10-24 06:47:03,204 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 82 executed (176.565 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:47:12,278 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 83 +tpv.core.entities DEBUG 2023-10-24 06:47:12,317 [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={'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=None, 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 2023-10-24 06:47:12,317 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (83) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:47:12,322 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (83) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:47:12,336 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (83) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:47:12,351 [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 2023-10-24 06:47:12,359 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [83] queued (36.540 ms) +galaxy.jobs.handler INFO 2023-10-24 06:47:12,362 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (83) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:47:12,367 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 83 +galaxy.jobs DEBUG 2023-10-24 06:47:12,480 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [83] prepared (96.104 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:47:12,498 [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 [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/83/registry.xml' '/galaxy/server/database/jobs_directory/000/83/upload_params.json' '87:/galaxy/server/database/objects/7/9/0/dataset_79087b2d-7192-4f7a-8acd-939f28a6999a_files:/galaxy/server/database/objects/7/9/0/dataset_79087b2d-7192-4f7a-8acd-939f28a6999a.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:47:12,511 [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 $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 06:47:23,364 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 83: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:47:29,435 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 83 finished +galaxy.model.metadata DEBUG 2023-10-24 06:47:29,481 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 87 +galaxy.jobs INFO 2023-10-24 06:47:29,513 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 83 in /galaxy/server/database/jobs_directory/000/83 +galaxy.jobs DEBUG 2023-10-24 06:47:29,547 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 83 executed (95.152 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:47:30,847 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 84 +tpv.core.entities DEBUG 2023-10-24 06:47:30,886 [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={'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/poretools_qualpos/poretools_qualpos/.*, abstract=False, cores=1, mem=11.4, gpus=None, 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 2023-10-24 06:47:30,887 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (84) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:47:30,892 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (84) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:47:30,907 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (84) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:47:30,921 [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 2023-10-24 06:47:30,929 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [84] queued (36.874 ms) +galaxy.jobs.handler INFO 2023-10-24 06:47:30,934 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (84) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:47:30,936 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 84 +galaxy.jobs DEBUG 2023-10-24 06:47:31,009 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [84] prepared (55.797 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 06:47:31,010 [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 2023-10-24 06:47:31,010 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualpos/poretools_qualpos/0.6.1a1.1: poretools:0.6.1a1 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:47:31,259 [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/poretools:0.6.1a1--py_8,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 06:47:31,279 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/84/tool_script.sh] for tool command [export MPLBACKEND="agg" && poretools qualpos '/galaxy/server/database/objects/7/9/0/dataset_79087b2d-7192-4f7a-8acd-939f28a6999a.dat' --saveas qualpos.png --min-length 0 --max-length 1000000000 --bin-width 1000 && mv qualpos.png '/galaxy/server/database/objects/6/4/b/dataset_64b1076b-c6ce-4a77-b0ab-fd148486cb42.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:47:31,292 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (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 $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 06:47:31,303 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 06:47:31,303 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualpos/poretools_qualpos/0.6.1a1.1: poretools:0.6.1a1 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:47:31,321 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/poretools:0.6.1a1--py_8,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 06:48:09,055 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 84: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:48:14,687 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 84 finished +galaxy.model.metadata DEBUG 2023-10-24 06:48:14,737 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 88 +galaxy.util WARNING 2023-10-24 06:48:14,741 [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/6/4/b/dataset_64b1076b-c6ce-4a77-b0ab-fd148486cb42.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/b/dataset_64b1076b-c6ce-4a77-b0ab-fd148486cb42.dat' +galaxy.jobs INFO 2023-10-24 06:48:14,768 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 84 in /galaxy/server/database/jobs_directory/000/84 +galaxy.jobs DEBUG 2023-10-24 06:48:14,798 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 84 executed (91.804 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:48:18,066 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 85 +tpv.core.entities DEBUG 2023-10-24 06:48:18,099 [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={'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=None, 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 2023-10-24 06:48:18,099 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (85) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:48:18,104 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (85) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:48:18,118 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (85) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:48:18,132 [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 2023-10-24 06:48:18,139 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [85] queued (34.714 ms) +galaxy.jobs.handler INFO 2023-10-24 06:48:18,143 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (85) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:48:18,147 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 85 +galaxy.jobs DEBUG 2023-10-24 06:48:18,243 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [85] prepared (78.666 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:48:18,260 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] 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' '89:/galaxy/server/database/objects/1/8/8/dataset_18874cc2-5ca5-4f68-9786-c48b4cfe72f7_files:/galaxy/server/database/objects/1/8/8/dataset_18874cc2-5ca5-4f68-9786-c48b4cfe72f7.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:48:18,273 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (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 $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 06:48:28,284 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 85: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:48:34,163 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 85 finished +galaxy.model.metadata DEBUG 2023-10-24 06:48:34,213 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 89 +galaxy.jobs INFO 2023-10-24 06:48:34,246 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 85 in /galaxy/server/database/jobs_directory/000/85 +galaxy.jobs DEBUG 2023-10-24 06:48:34,275 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 85 executed (95.868 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:48:35,644 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 86 +tpv.core.entities DEBUG 2023-10-24 06:48:35,680 [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={'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/poretools_qualpos/poretools_qualpos/.*, abstract=False, cores=1, mem=11.4, gpus=None, 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 2023-10-24 06:48:35,681 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (86) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:48:35,685 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (86) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:48:35,699 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (86) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:48:35,714 [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 2023-10-24 06:48:35,722 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [86] queued (36.667 ms) +galaxy.jobs.handler INFO 2023-10-24 06:48:35,727 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (86) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:48:35,729 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 86 +galaxy.jobs DEBUG 2023-10-24 06:48:35,797 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [86] prepared (51.310 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 06:48:35,798 [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 2023-10-24 06:48:35,798 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualpos/poretools_qualpos/0.6.1a1.1: poretools:0.6.1a1 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:48:35,819 [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/poretools:0.6.1a1--py_8,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 06:48:35,838 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/86/tool_script.sh] for tool command [export MPLBACKEND="agg" && poretools qualpos '/galaxy/server/database/objects/1/8/8/dataset_18874cc2-5ca5-4f68-9786-c48b4cfe72f7.dat' --saveas qualpos.pdf --min-length 0 --max-length 1000000000 --bin-width 1000 && mv qualpos.pdf '/galaxy/server/database/objects/0/1/7/dataset_0179b3aa-fd69-417e-ba94-207181e88dd5.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:48:35,854 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (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 $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 06:48:35,864 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 06:48:35,864 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualpos/poretools_qualpos/0.6.1a1.1: poretools:0.6.1a1 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:48:35,882 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/poretools:0.6.1a1--py_8,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 06:48:43,487 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 86: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:48:49,264 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 86 finished +galaxy.model.metadata DEBUG 2023-10-24 06:48:49,316 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 90 +galaxy.util WARNING 2023-10-24 06:48:49,320 [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/0/1/7/dataset_0179b3aa-fd69-417e-ba94-207181e88dd5.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/0/1/7/dataset_0179b3aa-fd69-417e-ba94-207181e88dd5.dat' +galaxy.jobs INFO 2023-10-24 06:48:49,348 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 86 in /galaxy/server/database/jobs_directory/000/86 +galaxy.jobs DEBUG 2023-10-24 06:48:49,378 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 86 executed (91.889 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:48:54,145 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 88, 87 +tpv.core.entities DEBUG 2023-10-24 06:48:54,186 [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={'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=None, 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 2023-10-24 06:48:54,187 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (87) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:48:54,193 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (87) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:48:54,208 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (87) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:48:54,226 [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 2023-10-24 06:48:54,234 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [87] queued (41.216 ms) +galaxy.jobs.handler INFO 2023-10-24 06:48:54,240 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (87) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:48:54,242 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 87 +tpv.core.entities DEBUG 2023-10-24 06:48:54,257 [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={'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=None, 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 2023-10-24 06:48:54,258 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (88) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:48:54,265 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (88) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:48:54,283 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (88) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:48:54,314 [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 2023-10-24 06:48:54,323 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [88] queued (57.618 ms) +galaxy.jobs.handler INFO 2023-10-24 06:48:54,328 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (88) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:48:54,333 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 88 +galaxy.jobs DEBUG 2023-10-24 06:48:54,377 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [87] prepared (111.707 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:48:54,406 [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' '91:/galaxy/server/database/objects/a/5/9/dataset_a59b2029-0a5f-4401-8235-04d685c5f4b8_files:/galaxy/server/database/objects/a/5/9/dataset_a59b2029-0a5f-4401-8235-04d685c5f4b8.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:48:54,421 [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 $return_code" +galaxy.jobs DEBUG 2023-10-24 06:48:54,456 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [88] prepared (103.144 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:48:54,475 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/88/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/88/registry.xml' '/galaxy/server/database/jobs_directory/000/88/upload_params.json' '92:/galaxy/server/database/objects/0/d/e/dataset_0de2cba0-ec4b-42cc-bf7f-6ffd984f4a82_files:/galaxy/server/database/objects/0/d/e/dataset_0de2cba0-ec4b-42cc-bf7f-6ffd984f4a82.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:48:54,492 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (88) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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.handler DEBUG 2023-10-24 06:48:55,331 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 89 +tpv.core.entities DEBUG 2023-10-24 06:48:55,364 [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={'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=None, 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 2023-10-24 06:48:55,365 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (89) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:48:55,369 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (89) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:48:55,384 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (89) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:48:55,402 [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 2023-10-24 06:48:55,411 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [89] queued (41.993 ms) +galaxy.jobs.handler INFO 2023-10-24 06:48:55,415 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (89) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:48:55,421 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 89 +galaxy.jobs DEBUG 2023-10-24 06:48:55,530 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [89] prepared (88.858 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:48:55,550 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/89/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/89/registry.xml' '/galaxy/server/database/jobs_directory/000/89/upload_params.json' '93:/galaxy/server/database/objects/a/8/c/dataset_a8ce847e-295c-47a5-b440-a91f5ea028e0_files:/galaxy/server/database/objects/a/8/c/dataset_a8ce847e-295c-47a5-b440-a91f5ea028e0.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:48:55,562 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (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 $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 06:49:05,067 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 87: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:49:05,120 [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 . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2023-10-24 06:49:08,148 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 89: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:49:13,139 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 87 finished +galaxy.jobs.runners DEBUG 2023-10-24 06:49:13,216 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 88 finished +galaxy.model.metadata DEBUG 2023-10-24 06:49:13,230 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 91 +galaxy.jobs INFO 2023-10-24 06:49:13,270 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 87 in /galaxy/server/database/jobs_directory/000/87 +galaxy.model.metadata DEBUG 2023-10-24 06:49:13,277 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 92 +galaxy.jobs INFO 2023-10-24 06:49:13,314 [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 2023-10-24 06:49:13,330 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 87 executed (173.691 ms) +galaxy.jobs DEBUG 2023-10-24 06:49:13,357 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 88 executed (115.045 ms) +galaxy.jobs.runners DEBUG 2023-10-24 06:49:15,757 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 89 finished +galaxy.model.metadata DEBUG 2023-10-24 06:49:15,803 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 93 +galaxy.jobs INFO 2023-10-24 06:49:15,836 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 89 in /galaxy/server/database/jobs_directory/000/89 +galaxy.jobs DEBUG 2023-10-24 06:49:15,873 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 89 executed (101.414 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:49:16,232 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 90 +tpv.core.entities DEBUG 2023-10-24 06:49:16,277 [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={'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=None, 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 2023-10-24 06:49:16,277 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (90) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:49:16,282 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (90) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:49:16,295 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (90) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:49:16,312 [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 2023-10-24 06:49:16,322 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [90] queued (39.322 ms) +galaxy.jobs.handler INFO 2023-10-24 06:49:16,325 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (90) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:49:16,330 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 90 +galaxy.jobs DEBUG 2023-10-24 06:49:16,441 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [90] prepared (92.072 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 06:49:16,441 [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 2023-10-24 06:49:16,442 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1: mulled-v2-143e618e2d6eef454186ce14739a2cabc5ecf645:98aaf7a4902bd7819cc39c943cb2ccd018ec6f95 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:49:16,690 [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-v2-143e618e2d6eef454186ce14739a2cabc5ecf645:98aaf7a4902bd7819cc39c943cb2ccd018ec6f95-0,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 06:49:16,710 [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 [ln -s '/galaxy/server/database/objects/a/5/9/dataset_a59b2029-0a5f-4401-8235-04d685c5f4b8.dat' reference.fa && kallisto index reference.fa -i reference.kallisto && kallisto pseudo -i 'reference.kallisto' --threads ${GALAXY_SLOTS:-1} -o . --batch '/galaxy/server/database/jobs_directory/000/90/configs/tmpd61o5l4x' --umi && if [ -f run_info.json ] ; then cat run_info.json ; fi && mkdir outputs && if [ -f matrix.ec ] ; then mv matrix.ec outputs/Matrix.ec ; fi && if [ -f matrix.tcc.mtx ] ; then mv matrix.tcc.mtx outputs/Matrix.tabular ; fi && if [ -f matrix.cells ] ; then mv matrix.cells outputs/Matrix.cells ; fi && if [ -f pseudoalignments.tsv ] ; then mv pseudoalignments.tsv outputs/Pseudoalignments.tabular ; fi && if [ -f pseudoalignments.ec ] ; then mv pseudoalignments.ec outputs/Pseudoalignments.ec ; fi] +galaxy.jobs.runners DEBUG 2023-10-24 06:49:16,723 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (90) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 06:49:16,733 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 06:49:16,734 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1: mulled-v2-143e618e2d6eef454186ce14739a2cabc5ecf645:98aaf7a4902bd7819cc39c943cb2ccd018ec6f95 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:49:16,750 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-143e618e2d6eef454186ce14739a2cabc5ecf645:98aaf7a4902bd7819cc39c943cb2ccd018ec6f95-0,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 06:49:25,357 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 90: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:49:30,964 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 90 finished +galaxy.model.metadata DEBUG 2023-10-24 06:49:31,230 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 94 +galaxy.jobs INFO 2023-10-24 06:49:31,312 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 90 in /galaxy/server/database/jobs_directory/000/90 +galaxy.objectstore CRITICAL 2023-10-24 06:49:31,344 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] None delete error [Errno 13] Permission denied: 'Matrix.cells' +galaxy.jobs DEBUG 2023-10-24 06:49:31,344 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 90 executed (364.477 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:49:34,799 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 91 +tpv.core.entities DEBUG 2023-10-24 06:49:34,834 [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={'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=None, 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 2023-10-24 06:49:34,835 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (91) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:49:34,839 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (91) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:49:34,854 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (91) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:49:34,870 [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 2023-10-24 06:49:34,878 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [91] queued (37.912 ms) +galaxy.jobs.handler INFO 2023-10-24 06:49:34,883 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (91) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:49:34,885 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 91 +galaxy.jobs DEBUG 2023-10-24 06:49:35,006 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [91] prepared (101.042 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:49:35,028 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] 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' '98:/galaxy/server/database/objects/9/8/c/dataset_98cdf8c1-5f2c-4fbe-9699-86c7f45c44cb_files:/galaxy/server/database/objects/9/8/c/dataset_98cdf8c1-5f2c-4fbe-9699-86c7f45c44cb.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:49:35,044 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (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.handler DEBUG 2023-10-24 06:49:35,885 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 92, 93 +tpv.core.entities DEBUG 2023-10-24 06:49:35,924 [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={'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=None, 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 2023-10-24 06:49:35,925 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (92) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:49:35,929 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (92) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:49:35,944 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (92) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:49:35,960 [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 2023-10-24 06:49:35,967 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [92] queued (37.461 ms) +galaxy.jobs.handler INFO 2023-10-24 06:49:35,972 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (92) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:49:35,974 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 92 +tpv.core.entities DEBUG 2023-10-24 06:49:35,988 [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={'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=None, 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 2023-10-24 06:49:35,988 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (93) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:49:35,994 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (93) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:49:36,009 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (93) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:49:36,038 [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 2023-10-24 06:49:36,045 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [93] queued (51.342 ms) +galaxy.jobs.handler INFO 2023-10-24 06:49:36,049 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (93) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:49:36,054 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 93 +galaxy.jobs DEBUG 2023-10-24 06:49:36,098 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [92] prepared (100.359 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:49:36,127 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] 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' '99:/galaxy/server/database/objects/b/d/3/dataset_bd3e4057-f67d-4507-a4e4-272e21e063e0_files:/galaxy/server/database/objects/b/d/3/dataset_bd3e4057-f67d-4507-a4e4-272e21e063e0.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:49:36,143 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (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 $return_code" +galaxy.jobs DEBUG 2023-10-24 06:49:36,183 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [93] prepared (108.151 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:49:36,205 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/93/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/93/registry.xml' '/galaxy/server/database/jobs_directory/000/93/upload_params.json' '100:/galaxy/server/database/objects/3/8/7/dataset_387d13f6-4b53-460a-ac1a-cd5598ca80a4_files:/galaxy/server/database/objects/3/8/7/dataset_387d13f6-4b53-460a-ac1a-cd5598ca80a4.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:49:36,218 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (93) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 06:49:46,020 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 91: GALAXY_LIB="/galaxy/server/lib"; if [ "$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.runners DEBUG 2023-10-24 06:49:47,075 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] 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 . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2023-10-24 06:49:49,136 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 93: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:49:53,637 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 91 finished +galaxy.model.metadata DEBUG 2023-10-24 06:49:53,717 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 98 +galaxy.jobs INFO 2023-10-24 06:49:53,750 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 91 in /galaxy/server/database/jobs_directory/000/91 +galaxy.jobs DEBUG 2023-10-24 06:49:53,810 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 91 executed (156.960 ms) +galaxy.jobs.runners DEBUG 2023-10-24 06:49:54,794 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 92 finished +galaxy.model.metadata DEBUG 2023-10-24 06:49:54,839 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 99 +galaxy.jobs INFO 2023-10-24 06:49:54,872 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 92 in /galaxy/server/database/jobs_directory/000/92 +galaxy.jobs DEBUG 2023-10-24 06:49:54,911 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 92 executed (99.838 ms) +galaxy.jobs.runners DEBUG 2023-10-24 06:49:56,601 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 93 finished +galaxy.model.metadata DEBUG 2023-10-24 06:49:56,644 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 100 +galaxy.jobs INFO 2023-10-24 06:49:56,683 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 93 in /galaxy/server/database/jobs_directory/000/93 +galaxy.jobs DEBUG 2023-10-24 06:49:56,716 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 93 executed (99.939 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:49:57,683 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 94 +tpv.core.entities DEBUG 2023-10-24 06:49:57,723 [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={'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=None, 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 2023-10-24 06:49:57,723 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (94) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:49:57,728 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (94) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:49:57,742 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (94) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:49:57,757 [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 2023-10-24 06:49:57,764 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [94] queued (35.862 ms) +galaxy.jobs.handler INFO 2023-10-24 06:49:57,769 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (94) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:49:57,771 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 94 +galaxy.jobs DEBUG 2023-10-24 06:49:57,884 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [94] prepared (97.171 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 06:49:57,885 [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 2023-10-24 06:49:57,885 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1: mulled-v2-143e618e2d6eef454186ce14739a2cabc5ecf645:98aaf7a4902bd7819cc39c943cb2ccd018ec6f95 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:49:57,904 [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-v2-143e618e2d6eef454186ce14739a2cabc5ecf645:98aaf7a4902bd7819cc39c943cb2ccd018ec6f95-0,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 06:49:57,924 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/94/tool_script.sh] for tool command [ln -s '/galaxy/server/database/objects/9/8/c/dataset_98cdf8c1-5f2c-4fbe-9699-86c7f45c44cb.dat' reference.fa && kallisto index reference.fa -i reference.kallisto && kallisto pseudo -i 'reference.kallisto' --threads ${GALAXY_SLOTS:-1} -o . '/galaxy/server/database/objects/b/d/3/dataset_bd3e4057-f67d-4507-a4e4-272e21e063e0.dat' '/galaxy/server/database/objects/3/8/7/dataset_387d13f6-4b53-460a-ac1a-cd5598ca80a4.dat' && if [ -f run_info.json ] ; then cat run_info.json ; fi && mkdir outputs && if [ -f matrix.ec ] ; then mv matrix.ec outputs/Matrix.ec ; fi && if [ -f matrix.tcc.mtx ] ; then mv matrix.tcc.mtx outputs/Matrix.tabular ; fi && if [ -f matrix.cells ] ; then mv matrix.cells outputs/Matrix.cells ; fi && if [ -f pseudoalignments.tsv ] ; then mv pseudoalignments.tsv outputs/Pseudoalignments.tabular ; fi && if [ -f pseudoalignments.ec ] ; then mv pseudoalignments.ec outputs/Pseudoalignments.ec ; fi] +galaxy.jobs.runners DEBUG 2023-10-24 06:49:57,937 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (94) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 06:49:57,947 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 06:49:57,948 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1: mulled-v2-143e618e2d6eef454186ce14739a2cabc5ecf645:98aaf7a4902bd7819cc39c943cb2ccd018ec6f95 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:49:57,964 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-143e618e2d6eef454186ce14739a2cabc5ecf645:98aaf7a4902bd7819cc39c943cb2ccd018ec6f95-0,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 06:50:03,302 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 94: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:50:09,390 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 94 finished +galaxy.model.metadata DEBUG 2023-10-24 06:50:09,849 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 101 +galaxy.jobs INFO 2023-10-24 06:50:09,935 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 94 in /galaxy/server/database/jobs_directory/000/94 +galaxy.objectstore CRITICAL 2023-10-24 06:50:09,965 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] None delete error [Errno 13] Permission denied: 'Pseudoalignments.tabular' +galaxy.jobs DEBUG 2023-10-24 06:50:09,965 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 94 executed (558.265 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:50:13,140 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 95 +tpv.core.entities DEBUG 2023-10-24 06:50:13,178 [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={'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=None, 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 2023-10-24 06:50:13,179 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (95) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:50:13,184 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (95) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:50:13,198 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (95) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:50:13,213 [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 2023-10-24 06:50:13,220 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [95] queued (35.723 ms) +galaxy.jobs.handler INFO 2023-10-24 06:50:13,225 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (95) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:50:13,227 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 95 +galaxy.jobs DEBUG 2023-10-24 06:50:13,320 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [95] prepared (77.187 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:50:13,338 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] 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' '107:/galaxy/server/database/objects/5/3/b/dataset_53bd9e37-5be2-4968-8e86-9954f5afd12d_files:/galaxy/server/database/objects/5/3/b/dataset_53bd9e37-5be2-4968-8e86-9954f5afd12d.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:50:13,351 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (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.handler DEBUG 2023-10-24 06:50:14,227 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 96 +tpv.core.entities DEBUG 2023-10-24 06:50:14,263 [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={'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=None, 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 2023-10-24 06:50:14,264 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (96) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:50:14,268 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (96) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:50:14,283 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (96) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:50:14,299 [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 2023-10-24 06:50:14,308 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [96] queued (39.111 ms) +galaxy.jobs.handler INFO 2023-10-24 06:50:14,314 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (96) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:50:14,316 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 96 +galaxy.jobs DEBUG 2023-10-24 06:50:14,417 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [96] prepared (82.283 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:50:14,435 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] 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' '108:/galaxy/server/database/objects/6/1/2/dataset_612a1a9e-c5b4-46a4-a199-27deb0969203_files:/galaxy/server/database/objects/6/1/2/dataset_612a1a9e-c5b4-46a4-a199-27deb0969203.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:50:14,448 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (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 $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 06:50:23,659 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 95: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:50:24,696 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 96: 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 2023-10-24 06:50:30,248 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 95 finished +galaxy.model.metadata DEBUG 2023-10-24 06:50:30,308 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 107 +galaxy.jobs INFO 2023-10-24 06:50:30,345 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 95 in /galaxy/server/database/jobs_directory/000/95 +galaxy.jobs DEBUG 2023-10-24 06:50:30,383 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 95 executed (117.564 ms) +galaxy.jobs.runners DEBUG 2023-10-24 06:50:31,162 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 96 finished +galaxy.model.metadata DEBUG 2023-10-24 06:50:31,207 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 108 +galaxy.jobs INFO 2023-10-24 06:50:31,239 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 96 in /galaxy/server/database/jobs_directory/000/96 +galaxy.jobs DEBUG 2023-10-24 06:50:31,274 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 96 executed (97.155 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:50:31,771 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 97 +tpv.core.entities DEBUG 2023-10-24 06:50:31,811 [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={'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=None, 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 2023-10-24 06:50:31,811 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (97) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:50:31,816 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (97) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:50:31,829 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (97) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:50:31,844 [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 2023-10-24 06:50:31,854 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [97] queued (38.137 ms) +galaxy.jobs.handler INFO 2023-10-24 06:50:31,858 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (97) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:50:31,862 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 97 +galaxy.jobs DEBUG 2023-10-24 06:50:31,948 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [97] prepared (67.807 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 06:50:31,948 [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 2023-10-24 06:50:31,948 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1: mulled-v2-143e618e2d6eef454186ce14739a2cabc5ecf645:98aaf7a4902bd7819cc39c943cb2ccd018ec6f95 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:50:31,974 [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-v2-143e618e2d6eef454186ce14739a2cabc5ecf645:98aaf7a4902bd7819cc39c943cb2ccd018ec6f95-0,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 06:50:31,993 [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 [ln -s '/galaxy/server/database/objects/5/3/b/dataset_53bd9e37-5be2-4968-8e86-9954f5afd12d.dat' reference.fa && kallisto index reference.fa -i reference.kallisto && kallisto pseudo -i 'reference.kallisto' --threads ${GALAXY_SLOTS:-1} -o . --single --fragment-length 200 --sd 20 '/galaxy/server/database/objects/6/1/2/dataset_612a1a9e-c5b4-46a4-a199-27deb0969203.dat' && if [ -f run_info.json ] ; then cat run_info.json ; fi && mkdir outputs && if [ -f matrix.ec ] ; then mv matrix.ec outputs/Matrix.ec ; fi && if [ -f matrix.tcc.mtx ] ; then mv matrix.tcc.mtx outputs/Matrix.tabular ; fi && if [ -f matrix.cells ] ; then mv matrix.cells outputs/Matrix.cells ; fi && if [ -f pseudoalignments.tsv ] ; then mv pseudoalignments.tsv outputs/Pseudoalignments.tabular ; fi && if [ -f pseudoalignments.ec ] ; then mv pseudoalignments.ec outputs/Pseudoalignments.ec ; fi] +galaxy.jobs.runners DEBUG 2023-10-24 06:50:32,007 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (97) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 06:50:32,017 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 06:50:32,017 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1: mulled-v2-143e618e2d6eef454186ce14739a2cabc5ecf645:98aaf7a4902bd7819cc39c943cb2ccd018ec6f95 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:50:32,046 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-143e618e2d6eef454186ce14739a2cabc5ecf645:98aaf7a4902bd7819cc39c943cb2ccd018ec6f95-0,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 06:50:37,858 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 97: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:50:43,692 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 97 finished +galaxy.model.metadata DEBUG 2023-10-24 06:50:44,129 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 109 +galaxy.jobs INFO 2023-10-24 06:50:44,214 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 97 in /galaxy/server/database/jobs_directory/000/97 +galaxy.objectstore CRITICAL 2023-10-24 06:50:44,248 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] None delete error [Errno 13] Permission denied: 'Pseudoalignments.tabular' +galaxy.jobs DEBUG 2023-10-24 06:50:44,248 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 97 executed (539.789 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:50:47,401 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 98 +tpv.core.entities DEBUG 2023-10-24 06:50:47,438 [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={'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=None, 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 2023-10-24 06:50:47,438 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (98) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:50:47,443 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (98) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:50:47,457 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (98) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:50:47,470 [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 2023-10-24 06:50:47,477 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [98] queued (34.111 ms) +galaxy.jobs.handler INFO 2023-10-24 06:50:47,482 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (98) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:50:47,484 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 98 +galaxy.jobs DEBUG 2023-10-24 06:50:47,580 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [98] prepared (80.046 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:50:47,599 [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' '115:/galaxy/server/database/objects/b/e/4/dataset_be469919-acd0-4060-b657-5998fb931cfb_files:/galaxy/server/database/objects/b/e/4/dataset_be469919-acd0-4060-b657-5998fb931cfb.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:50:47,611 [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.handler DEBUG 2023-10-24 06:50:48,485 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 100, 99 +tpv.core.entities DEBUG 2023-10-24 06:50:48,521 [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={'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=None, 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 2023-10-24 06:50:48,522 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (99) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:50:48,526 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (99) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:50:48,541 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (99) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:50:48,557 [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 2023-10-24 06:50:48,564 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [99] queued (37.571 ms) +galaxy.jobs.handler INFO 2023-10-24 06:50:48,569 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (99) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:50:48,570 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 99 +tpv.core.entities DEBUG 2023-10-24 06:50:48,584 [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={'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=None, 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 2023-10-24 06:50:48,585 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (100) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:50:48,590 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (100) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:50:48,608 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (100) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:50:48,636 [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 2023-10-24 06:50:48,645 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [100] queued (54.754 ms) +galaxy.jobs.handler INFO 2023-10-24 06:50:48,649 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (100) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:50:48,654 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 100 +galaxy.jobs DEBUG 2023-10-24 06:50:48,683 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [99] prepared (92.138 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:50:48,704 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] 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' '116:/galaxy/server/database/objects/6/5/4/dataset_65473a5f-5ba4-43e3-a8e9-5a70b600b221_files:/galaxy/server/database/objects/6/5/4/dataset_65473a5f-5ba4-43e3-a8e9-5a70b600b221.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:50:48,718 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (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 $return_code" +galaxy.jobs DEBUG 2023-10-24 06:50:48,761 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [100] prepared (89.016 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:50:48,780 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/100/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/100/registry.xml' '/galaxy/server/database/jobs_directory/000/100/upload_params.json' '117:/galaxy/server/database/objects/1/2/9/dataset_1296f066-0260-492c-8a72-ff004ef505f2_files:/galaxy/server/database/objects/1/2/9/dataset_1296f066-0260-492c-8a72-ff004ef505f2.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:50:48,793 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (100) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 06:50:57,378 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 98: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:50:59,466 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] 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 . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2023-10-24 06:51:02,556 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 100: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:51:03,749 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 98 finished +galaxy.model.metadata DEBUG 2023-10-24 06:51:03,838 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 115 +galaxy.jobs INFO 2023-10-24 06:51:03,877 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 98 in /galaxy/server/database/jobs_directory/000/98 +galaxy.jobs DEBUG 2023-10-24 06:51:03,944 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 98 executed (178.778 ms) +galaxy.jobs.runners DEBUG 2023-10-24 06:51:06,513 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 99 finished +galaxy.model.metadata DEBUG 2023-10-24 06:51:06,560 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 116 +galaxy.jobs INFO 2023-10-24 06:51:06,595 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 99 in /galaxy/server/database/jobs_directory/000/99 +galaxy.jobs DEBUG 2023-10-24 06:51:06,628 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 99 executed (100.612 ms) +galaxy.jobs.runners DEBUG 2023-10-24 06:51:09,378 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 100 finished +galaxy.model.metadata DEBUG 2023-10-24 06:51:09,428 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 117 +galaxy.jobs INFO 2023-10-24 06:51:09,462 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 100 in /galaxy/server/database/jobs_directory/000/100 +galaxy.jobs DEBUG 2023-10-24 06:51:09,492 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 100 executed (98.759 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:51:10,230 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 101 +tpv.core.entities DEBUG 2023-10-24 06:51:10,273 [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={'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=None, 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 2023-10-24 06:51:10,274 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (101) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:51:10,279 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (101) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:51:10,293 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (101) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:51:10,308 [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 2023-10-24 06:51:10,318 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [101] queued (38.316 ms) +galaxy.jobs.handler INFO 2023-10-24 06:51:10,322 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (101) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:51:10,326 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 101 +galaxy.jobs DEBUG 2023-10-24 06:51:10,424 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [101] prepared (80.456 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 06:51:10,425 [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 2023-10-24 06:51:10,426 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1: mulled-v2-143e618e2d6eef454186ce14739a2cabc5ecf645:98aaf7a4902bd7819cc39c943cb2ccd018ec6f95 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:51:10,451 [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-v2-143e618e2d6eef454186ce14739a2cabc5ecf645:98aaf7a4902bd7819cc39c943cb2ccd018ec6f95-0,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 06:51:10,472 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/101/tool_script.sh] for tool command [ln -s '/galaxy/server/database/objects/b/e/4/dataset_be469919-acd0-4060-b657-5998fb931cfb.dat' reference.fa && kallisto index reference.fa -i reference.kallisto && kallisto pseudo -i 'reference.kallisto' --threads ${GALAXY_SLOTS:-1} -o . '/galaxy/server/database/objects/6/5/4/dataset_65473a5f-5ba4-43e3-a8e9-5a70b600b221.dat' '/galaxy/server/database/objects/1/2/9/dataset_1296f066-0260-492c-8a72-ff004ef505f2.dat' && if [ -f run_info.json ] ; then cat run_info.json ; fi && mkdir outputs && if [ -f matrix.ec ] ; then mv matrix.ec outputs/Matrix.ec ; fi && if [ -f matrix.tcc.mtx ] ; then mv matrix.tcc.mtx outputs/Matrix.tabular ; fi && if [ -f matrix.cells ] ; then mv matrix.cells outputs/Matrix.cells ; fi && if [ -f pseudoalignments.tsv ] ; then mv pseudoalignments.tsv outputs/Pseudoalignments.tabular ; fi && if [ -f pseudoalignments.ec ] ; then mv pseudoalignments.ec outputs/Pseudoalignments.ec ; fi] +galaxy.jobs.runners DEBUG 2023-10-24 06:51:10,486 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (101) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 06:51:10,497 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 06:51:10,497 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1: mulled-v2-143e618e2d6eef454186ce14739a2cabc5ecf645:98aaf7a4902bd7819cc39c943cb2ccd018ec6f95 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:51:10,513 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-143e618e2d6eef454186ce14739a2cabc5ecf645:98aaf7a4902bd7819cc39c943cb2ccd018ec6f95-0,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 06:51:15,719 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 101: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:51:21,751 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 101 finished +galaxy.model.metadata DEBUG 2023-10-24 06:51:22,202 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 118 +galaxy.jobs INFO 2023-10-24 06:51:22,290 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 101 in /galaxy/server/database/jobs_directory/000/101 +galaxy.objectstore CRITICAL 2023-10-24 06:51:22,324 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] None delete error [Errno 13] Permission denied: 'Pseudoalignments.tabular' +galaxy.jobs DEBUG 2023-10-24 06:51:22,324 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 101 executed (556.506 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:51:25,702 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 102, 103 +tpv.core.entities DEBUG 2023-10-24 06:51:25,738 [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={'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=None, 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 2023-10-24 06:51:25,739 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (102) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:51:25,743 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (102) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:51:25,757 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (102) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:51:25,772 [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 2023-10-24 06:51:25,779 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [102] queued (35.748 ms) +galaxy.jobs.handler INFO 2023-10-24 06:51:25,783 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (102) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:51:25,788 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 102 +tpv.core.entities DEBUG 2023-10-24 06:51:25,799 [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={'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=None, 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 2023-10-24 06:51:25,800 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (103) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:51:25,806 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (103) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:51:25,824 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (103) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:51:25,855 [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 2023-10-24 06:51:25,864 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [103] queued (57.956 ms) +galaxy.jobs.handler INFO 2023-10-24 06:51:25,867 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (103) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:51:25,873 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 103 +galaxy.jobs DEBUG 2023-10-24 06:51:25,902 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [102] prepared (94.649 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:51:25,928 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] 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' '124:/galaxy/server/database/objects/2/8/7/dataset_287b932b-ad9a-4985-8ee5-05a3df8de718_files:/galaxy/server/database/objects/2/8/7/dataset_287b932b-ad9a-4985-8ee5-05a3df8de718.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:51:25,943 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (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 $return_code" +galaxy.jobs DEBUG 2023-10-24 06:51:25,990 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [103] prepared (98.311 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:51:26,012 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/103/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/103/registry.xml' '/galaxy/server/database/jobs_directory/000/103/upload_params.json' '125:/galaxy/server/database/objects/0/3/3/dataset_0338df1a-fbe4-4cf4-9147-7c9b4669a80d_files:/galaxy/server/database/objects/0/3/3/dataset_0338df1a-fbe4-4cf4-9147-7c9b4669a80d.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:51:26,026 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (103) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 06:51:35,108 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 102: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:51:38,166 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] 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 2023-10-24 06:51:41,151 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 102 finished +galaxy.model.metadata DEBUG 2023-10-24 06:51:41,200 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 124 +galaxy.jobs INFO 2023-10-24 06:51:41,238 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 102 in /galaxy/server/database/jobs_directory/000/102 +galaxy.jobs DEBUG 2023-10-24 06:51:41,288 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 102 executed (121.132 ms) +galaxy.jobs.runners DEBUG 2023-10-24 06:51:44,062 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 103 finished +galaxy.model.metadata DEBUG 2023-10-24 06:51:44,110 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 125 +galaxy.jobs INFO 2023-10-24 06:51:44,144 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 103 in /galaxy/server/database/jobs_directory/000/103 +galaxy.jobs DEBUG 2023-10-24 06:51:44,175 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 103 executed (98.264 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:51:47,418 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 104, 105 +tpv.core.entities DEBUG 2023-10-24 06:51:47,455 [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={'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=None, 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 2023-10-24 06:51:47,456 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (104) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:51:47,461 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (104) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:51:47,474 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (104) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:51:47,488 [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 2023-10-24 06:51:47,495 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [104] queued (34.223 ms) +galaxy.jobs.handler INFO 2023-10-24 06:51:47,499 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (104) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:51:47,503 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 104 +tpv.core.entities DEBUG 2023-10-24 06:51:47,513 [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={'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=None, 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 2023-10-24 06:51:47,514 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (105) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:51:47,519 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (105) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:51:47,534 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (105) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:51:47,559 [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 2023-10-24 06:51:47,566 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [105] queued (47.406 ms) +galaxy.jobs.handler INFO 2023-10-24 06:51:47,571 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (105) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:51:47,575 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 105 +galaxy.jobs DEBUG 2023-10-24 06:51:47,614 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [104] prepared (87.855 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:51:47,640 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/104/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/104/registry.xml' '/galaxy/server/database/jobs_directory/000/104/upload_params.json' '126:/galaxy/server/database/objects/1/5/b/dataset_15b2290e-dd2b-41d0-b5e4-3af2f3bae9b2_files:/galaxy/server/database/objects/1/5/b/dataset_15b2290e-dd2b-41d0-b5e4-3af2f3bae9b2.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:51:47,653 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (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 $return_code" +galaxy.jobs DEBUG 2023-10-24 06:51:47,685 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [105] prepared (90.199 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:51:47,703 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/105/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/105/registry.xml' '/galaxy/server/database/jobs_directory/000/105/upload_params.json' '127:/galaxy/server/database/objects/1/8/5/dataset_18585bf8-66ce-43d3-a8e5-643d1a838a77_files:/galaxy/server/database/objects/1/8/5/dataset_18585bf8-66ce-43d3-a8e5-643d1a838a77.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:51:47,716 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (105) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 06:51:58,596 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 104: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:51:58,613 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] 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 2023-10-24 06:52:04,808 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 104 finished +galaxy.model.metadata DEBUG 2023-10-24 06:52:04,869 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 126 +galaxy.jobs.runners DEBUG 2023-10-24 06:52:04,935 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 105 finished +galaxy.jobs INFO 2023-10-24 06:52:04,962 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 104 in /galaxy/server/database/jobs_directory/000/104 +galaxy.model.metadata DEBUG 2023-10-24 06:52:05,015 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 127 +galaxy.jobs DEBUG 2023-10-24 06:52:05,046 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 104 executed (215.502 ms) +galaxy.jobs INFO 2023-10-24 06:52:05,054 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 105 in /galaxy/server/database/jobs_directory/000/105 +galaxy.jobs DEBUG 2023-10-24 06:52:05,135 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 105 executed (180.068 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:52:06,241 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 106 +tpv.core.entities DEBUG 2023-10-24 06:52:06,285 [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={'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=None, 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 2023-10-24 06:52:06,286 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (106) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:52:06,292 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (106) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:52:06,308 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (106) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:52:06,326 [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 2023-10-24 06:52:06,335 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [106] queued (42.934 ms) +galaxy.jobs.handler INFO 2023-10-24 06:52:06,339 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (106) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:52:06,344 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 106 +galaxy.jobs DEBUG 2023-10-24 06:52:06,441 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [106] prepared (77.756 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 06:52:06,442 [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 2023-10-24 06:52:06,442 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.3: samtools:0.1.16 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:52:06,728 [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:0.1.16,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 06:52:06,747 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/106/tool_script.sh] for tool command [ln -s '/galaxy/server/database/objects/1/5/b/dataset_15b2290e-dd2b-41d0-b5e4-3af2f3bae9b2.dat' input1.bam && ln -s '/galaxy/server/database/objects/_metadata_files/2/f/f/metadata_2ffd98a9-7424-4f3c-bcd0-a652ef3aa4f1.dat' 'input1.bam.bai' && ln -s '/galaxy/server/database/objects/1/8/5/dataset_18585bf8-66ce-43d3-a8e5-643d1a838a77.dat' reference.fasta && samtools faidx reference.fasta && samtools pileup -M 60 -f reference.fasta input1.bam > '/galaxy/server/database/objects/8/1/1/dataset_811d3f5c-0004-45af-a361-17b8d7e6c31e.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:52:06,760 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (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 $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 06:52:06,771 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 06:52:06,771 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.3: samtools:0.1.16 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:52:06,791 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:0.1.16,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 06:52:13,784 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 106: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:52:19,750 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 106 finished +galaxy.tool_util.output_checker INFO 2023-10-24 06:52:19,758 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job error detected, failing job. Reasons are [{'type': 'exit_code', 'desc': 'Fatal error: Exit code 127 ()', 'exit_code': 127, 'code_desc': '', 'error_level': 3}] +galaxy.jobs DEBUG 2023-10-24 06:52:19,814 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (106) setting dataset 128 state to ERROR +galaxy.jobs INFO 2023-10-24 06:52:19,843 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 106 in /galaxy/server/database/jobs_directory/000/106 +galaxy.jobs DEBUG 2023-10-24 06:52:19,882 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 106 executed (115.233 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:52:23,743 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 107 +tpv.core.entities DEBUG 2023-10-24 06:52:23,778 [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={'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=None, 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 2023-10-24 06:52:23,779 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (107) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:52:23,783 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (107) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:52:23,797 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (107) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:52:23,810 [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 2023-10-24 06:52:23,817 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [107] queued (32.868 ms) +galaxy.jobs.handler INFO 2023-10-24 06:52:23,821 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (107) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:52:23,823 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 107 +galaxy.jobs DEBUG 2023-10-24 06:52:23,927 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [107] prepared (85.708 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:52:23,948 [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 [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/107/registry.xml' '/galaxy/server/database/jobs_directory/000/107/upload_params.json' '129:/galaxy/server/database/objects/7/0/7/dataset_70747206-b018-47c5-9d35-7fac0f117944_files:/galaxy/server/database/objects/7/0/7/dataset_70747206-b018-47c5-9d35-7fac0f117944.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:52:23,961 [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.jobs.handler DEBUG 2023-10-24 06:52:24,824 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 108 +tpv.core.entities DEBUG 2023-10-24 06:52:24,859 [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={'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=None, 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 2023-10-24 06:52:24,860 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (108) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:52:24,864 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (108) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:52:24,879 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (108) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:52:24,894 [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 2023-10-24 06:52:24,902 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [108] queued (37.623 ms) +galaxy.jobs.handler INFO 2023-10-24 06:52:24,908 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (108) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:52:24,910 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 108 +galaxy.jobs DEBUG 2023-10-24 06:52:25,020 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [108] prepared (90.509 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:52:25,039 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] 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' '130:/galaxy/server/database/objects/7/2/f/dataset_72f6c4f1-7bec-4058-bee1-4eb5d892f439_files:/galaxy/server/database/objects/7/2/f/dataset_72f6c4f1-7bec-4058-bee1-4eb5d892f439.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:52:25,052 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (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 $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 06:52:35,187 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 107: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:52:37,244 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] 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 2023-10-24 06:52:41,108 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 107 finished +galaxy.model.metadata DEBUG 2023-10-24 06:52:41,153 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 129 +galaxy.jobs INFO 2023-10-24 06:52:41,215 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 107 in /galaxy/server/database/jobs_directory/000/107 +galaxy.jobs DEBUG 2023-10-24 06:52:41,249 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 107 executed (124.406 ms) +galaxy.jobs.runners DEBUG 2023-10-24 06:52:42,958 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 108 finished +galaxy.model.metadata DEBUG 2023-10-24 06:52:42,999 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 130 +galaxy.jobs INFO 2023-10-24 06:52:43,030 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 108 in /galaxy/server/database/jobs_directory/000/108 +galaxy.jobs DEBUG 2023-10-24 06:52:43,061 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 108 executed (89.118 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:52:44,358 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 109 +tpv.core.entities DEBUG 2023-10-24 06:52:44,401 [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={'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=None, 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 2023-10-24 06:52:44,401 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (109) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:52:44,406 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (109) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:52:44,420 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (109) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:52:44,435 [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 2023-10-24 06:52:44,443 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [109] queued (36.438 ms) +galaxy.jobs.handler INFO 2023-10-24 06:52:44,449 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (109) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:52:44,452 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 109 +galaxy.jobs DEBUG 2023-10-24 06:52:44,532 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [109] prepared (63.038 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 06:52:44,533 [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 2023-10-24 06:52:44,533 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2: samtools:1.9 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:52:44,556 [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/samtools:1.9--h10a08f8_12,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 06:52:44,576 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/109/tool_script.sh] for tool command [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/109/outputs/COMMAND_VERSION 2>&1; +addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && ln -s '/galaxy/server/database/objects/7/2/f/dataset_72f6c4f1-7bec-4058-bee1-4eb5d892f439.dat' ref.fa && samtools faidx ref.fa && samtools calmd -b -@ $addthreads '/galaxy/server/database/objects/7/0/7/dataset_70747206-b018-47c5-9d35-7fac0f117944.dat' 'ref.fa' > '/galaxy/server/database/objects/3/e/e/dataset_3ee6d011-23c7-4981-a7d4-799b97817b80.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:52:44,588 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (109) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 06:52:44,599 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 06:52:44,599 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2: samtools:1.9 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:52:44,618 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.9--h10a08f8_12,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 06:52:52,427 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 109: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:52:58,283 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 109 finished +galaxy.model.metadata DEBUG 2023-10-24 06:52:58,333 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 131 +galaxy.jobs INFO 2023-10-24 06:52:58,400 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 109 in /galaxy/server/database/jobs_directory/000/109 +galaxy.jobs DEBUG 2023-10-24 06:52:58,434 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 109 executed (134.674 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:53:01,914 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 110 +tpv.core.entities DEBUG 2023-10-24 06:53:01,948 [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={'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=None, 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 2023-10-24 06:53:01,948 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (110) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:53:01,953 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (110) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:53:01,965 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (110) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:53:01,978 [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 2023-10-24 06:53:01,984 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [110] queued (31.223 ms) +galaxy.jobs.handler INFO 2023-10-24 06:53:01,989 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (110) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:53:01,993 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 110 +galaxy.jobs DEBUG 2023-10-24 06:53:02,096 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [110] prepared (85.945 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:53:02,114 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/110/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/110/registry.xml' '/galaxy/server/database/jobs_directory/000/110/upload_params.json' '132:/galaxy/server/database/objects/1/2/c/dataset_12c767ce-c382-4d23-b516-039e46709a3f_files:/galaxy/server/database/objects/1/2/c/dataset_12c767ce-c382-4d23-b516-039e46709a3f.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:53:02,126 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (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.jobs.handler DEBUG 2023-10-24 06:53:02,991 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 111 +tpv.core.entities DEBUG 2023-10-24 06:53:03,026 [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={'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=None, 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 2023-10-24 06:53:03,027 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (111) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:53:03,031 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (111) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:53:03,045 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (111) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:53:03,060 [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 2023-10-24 06:53:03,066 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [111] queued (34.510 ms) +galaxy.jobs.handler INFO 2023-10-24 06:53:03,071 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (111) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:53:03,074 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 111 +galaxy.jobs DEBUG 2023-10-24 06:53:03,168 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [111] prepared (76.437 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:53:03,185 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] 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' '133:/galaxy/server/database/objects/d/e/e/dataset_dee8f6b5-4907-4c3f-a2c6-c38532914f56_files:/galaxy/server/database/objects/d/e/e/dataset_dee8f6b5-4907-4c3f-a2c6-c38532914f56.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:53:03,197 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (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 $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 06:53:11,798 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 110: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:53:12,845 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] 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 2023-10-24 06:53:18,110 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 110 finished +galaxy.model.metadata DEBUG 2023-10-24 06:53:18,156 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 132 +galaxy.jobs INFO 2023-10-24 06:53:18,225 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 110 in /galaxy/server/database/jobs_directory/000/110 +galaxy.jobs DEBUG 2023-10-24 06:53:18,255 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 110 executed (129.169 ms) +galaxy.jobs.runners DEBUG 2023-10-24 06:53:19,131 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 111 finished +galaxy.model.metadata DEBUG 2023-10-24 06:53:19,171 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 133 +galaxy.jobs INFO 2023-10-24 06:53:19,200 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 111 in /galaxy/server/database/jobs_directory/000/111 +galaxy.jobs DEBUG 2023-10-24 06:53:19,229 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 111 executed (85.435 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:53:20,534 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 112 +tpv.core.entities DEBUG 2023-10-24 06:53:20,574 [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={'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=None, 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 2023-10-24 06:53:20,575 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (112) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:53:20,580 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (112) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:53:20,596 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (112) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:53:20,612 [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 2023-10-24 06:53:20,620 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [112] queued (39.654 ms) +galaxy.jobs.handler INFO 2023-10-24 06:53:20,624 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (112) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:53:20,626 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 112 +galaxy.jobs DEBUG 2023-10-24 06:53:20,698 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [112] prepared (56.007 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 06:53:20,699 [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 2023-10-24 06:53:20,699 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2: samtools:1.9 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:53:20,722 [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/samtools:1.9--h10a08f8_12,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 06:53:20,742 [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 [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/112/outputs/COMMAND_VERSION 2>&1; +addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && ln -s '/galaxy/server/database/objects/d/e/e/dataset_dee8f6b5-4907-4c3f-a2c6-c38532914f56.dat' ref.fa && samtools faidx ref.fa && samtools calmd -r -E -e -C 50 -b -@ $addthreads '/galaxy/server/database/objects/1/2/c/dataset_12c767ce-c382-4d23-b516-039e46709a3f.dat' 'ref.fa' > '/galaxy/server/database/objects/0/7/a/dataset_07a59ebc-31f3-4652-8912-0cdb036fad9b.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:53:20,755 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (112) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 06:53:20,765 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 06:53:20,765 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2: samtools:1.9 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:53:20,784 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.9--h10a08f8_12,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 06:53:26,982 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 112: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:53:32,655 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 112 finished +galaxy.model.metadata DEBUG 2023-10-24 06:53:32,704 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 134 +galaxy.jobs INFO 2023-10-24 06:53:32,769 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 112 in /galaxy/server/database/jobs_directory/000/112 +galaxy.jobs DEBUG 2023-10-24 06:53:32,798 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 112 executed (126.163 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:53:40,075 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 113 +tpv.core.entities DEBUG 2023-10-24 06:53:40,110 [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={'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=None, 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 2023-10-24 06:53:40,111 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (113) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:53:40,115 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (113) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:53:40,129 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (113) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:53:40,144 [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 2023-10-24 06:53:40,151 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [113] queued (35.557 ms) +galaxy.jobs.handler INFO 2023-10-24 06:53:40,155 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (113) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:53:40,158 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 113 +galaxy.jobs DEBUG 2023-10-24 06:53:40,256 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [113] prepared (80.739 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:53:40,274 [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 [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/113/registry.xml' '/galaxy/server/database/jobs_directory/000/113/upload_params.json' '135:/galaxy/server/database/objects/8/9/8/dataset_8982029b-6ea0-4ec3-83b7-136b88db722a_files:/galaxy/server/database/objects/8/9/8/dataset_8982029b-6ea0-4ec3-83b7-136b88db722a.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:53:40,287 [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 $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 06:53:50,190 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 113: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:53:56,071 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 113 finished +galaxy.model.metadata DEBUG 2023-10-24 06:53:56,121 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 135 +galaxy.jobs INFO 2023-10-24 06:53:56,153 [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.jobs DEBUG 2023-10-24 06:53:56,189 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 113 executed (101.758 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:53:57,647 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 114 +tpv.core.entities DEBUG 2023-10-24 06:53:57,685 [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={'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=None, 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 2023-10-24 06:53:57,686 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (114) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:53:57,692 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (114) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:53:57,704 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (114) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:53:57,717 [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 2023-10-24 06:53:57,724 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [114] queued (32.332 ms) +galaxy.jobs.handler INFO 2023-10-24 06:53:57,727 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (114) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:53:57,732 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 114 +galaxy.jobs DEBUG 2023-10-24 06:53:57,801 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [114] prepared (54.167 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 06:53:57,802 [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 2023-10-24 06:53:57,802 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_exprs_freq/scater_plot_exprs_freq/1.12.2: mulled-v2-73a2658554da0b18a11a585a481ae725b820e94a:bc2e569e2a76e9ab09523a345979924ab514ebe9 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:53:58,055 [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-v2-73a2658554da0b18a11a585a481ae725b820e94a:bc2e569e2a76e9ab09523a345979924ab514ebe9-0,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 06:53:58,074 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/114/tool_script.sh] for tool command [Rscript '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_exprs_freq/058b40656107/scater_plot_exprs_freq/scater-plot-exprs-freq.R' -i '/galaxy/server/database/objects/8/9/8/dataset_8982029b-6ea0-4ec3-83b7-136b88db722a.dat' -o '/galaxy/server/database/objects/c/6/c/dataset_c6cb4916-bb05-44f2-9348-644ac95c379b.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:53:58,086 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (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.tool_util.deps.containers INFO 2023-10-24 06:53:58,096 [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 2023-10-24 06:53:58,096 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_exprs_freq/scater_plot_exprs_freq/1.12.2: mulled-v2-73a2658554da0b18a11a585a481ae725b820e94a:bc2e569e2a76e9ab09523a345979924ab514ebe9 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:53:58,111 [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-v2-73a2658554da0b18a11a585a481ae725b820e94a:bc2e569e2a76e9ab09523a345979924ab514ebe9-0,type=docker]] +galaxy.jobs.runners.kubernetes ERROR 2023-10-24 06:54:44,011 [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://10.112.0.1:443/apis/batch/v1/namespaces/edge-23-10-24-06-08-1/jobs/gxy-v7k2l + +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-v7k2l": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:54:44,044 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (114/gxy-v7k2l) Terminated at user's request +galaxy.jobs.handler DEBUG 2023-10-24 06:54:46,935 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 115 +tpv.core.entities DEBUG 2023-10-24 06:54:46,969 [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={'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=None, 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 2023-10-24 06:54:46,969 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (115) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:54:46,974 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (115) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:54:46,986 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (115) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:54:46,996 [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 2023-10-24 06:54:47,003 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [115] queued (28.811 ms) +galaxy.jobs.handler INFO 2023-10-24 06:54:47,007 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (115) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:54:47,010 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 115 +galaxy.jobs DEBUG 2023-10-24 06:54:47,071 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [115] prepared (45.542 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 06:54:47,072 [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 2023-10-24 06:54:47,072 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_parameter_iterator/scanpy_parameter_iterator/0.0.1+galaxy0: bioconductor-rtracklayer:1.42.1 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:54:47,333 [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/bioconductor-rtracklayer:1.42.1--r351h9d9f1b6_1,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 06:54:47,352 [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 [mkdir outputs; for param in $(echo '1, 5, 10' | sed 's/,/ /g'); do echo $param > outputs/'perplexity'_$param\.txt; done] +galaxy.jobs.runners DEBUG 2023-10-24 06:54:47,359 [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 $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 06:54:47,376 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 06:54:47,376 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_parameter_iterator/scanpy_parameter_iterator/0.0.1+galaxy0: bioconductor-rtracklayer:1.42.1 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:54:47,393 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/bioconductor-rtracklayer:1.42.1--r351h9d9f1b6_1,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 06:55:19,760 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 115: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:55:25,555 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 115 finished +galaxy.model.store.discover DEBUG 2023-10-24 06:55:25,606 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (115) Created dynamic collection dataset for path [/galaxy/server/database/jobs_directory/000/115/working/outputs/perplexity_1.txt] with element identifier [perplexity_1] for output [parameter_iteration] (9.545 ms) +galaxy.model.store.discover DEBUG 2023-10-24 06:55:25,607 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (115) Created dynamic collection dataset for path [/galaxy/server/database/jobs_directory/000/115/working/outputs/perplexity_10.txt] with element identifier [perplexity_10] for output [parameter_iteration] (0.790 ms) +galaxy.model.store.discover DEBUG 2023-10-24 06:55:25,607 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (115) Created dynamic collection dataset for path [/galaxy/server/database/jobs_directory/000/115/working/outputs/perplexity_5.txt] with element identifier [perplexity_5] for output [parameter_iteration] (0.591 ms) +galaxy.model.store.discover DEBUG 2023-10-24 06:55:25,632 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (115) Add dynamic collection datasets to history for output [parameter_iteration] (23.859 ms) +galaxy.jobs INFO 2023-10-24 06:55:25,717 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 115 in /galaxy/server/database/jobs_directory/000/115 +galaxy.objectstore CRITICAL 2023-10-24 06:55:25,744 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] None delete error [Errno 13] Permission denied: 'perplexity_10.txt' +galaxy.jobs DEBUG 2023-10-24 06:55:25,745 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 115 executed (172.629 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:55:30,071 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 117, 116 +tpv.core.entities DEBUG 2023-10-24 06:55:30,105 [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={'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=None, 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 2023-10-24 06:55:30,106 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (116) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:55:30,111 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (116) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:55:30,126 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (116) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:55:30,140 [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 2023-10-24 06:55:30,147 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [116] queued (35.820 ms) +galaxy.jobs.handler INFO 2023-10-24 06:55:30,151 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (116) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:55:30,154 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 116 +tpv.core.entities DEBUG 2023-10-24 06:55:30,166 [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={'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=None, 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 2023-10-24 06:55:30,166 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (117) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:55:30,172 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (117) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:55:30,185 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (117) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:55:30,214 [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 2023-10-24 06:55:30,221 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [117] queued (49.255 ms) +galaxy.jobs.handler INFO 2023-10-24 06:55:30,226 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (117) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:55:30,232 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 117 +galaxy.jobs DEBUG 2023-10-24 06:55:30,269 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [116] prepared (93.752 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:55:30,295 [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 [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/116/registry.xml' '/galaxy/server/database/jobs_directory/000/116/upload_params.json' '140:/galaxy/server/database/objects/5/0/b/dataset_50b2313b-26ae-48e9-8c30-6ab5bb930854_files:/galaxy/server/database/objects/5/0/b/dataset_50b2313b-26ae-48e9-8c30-6ab5bb930854.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:55:30,309 [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 $return_code" +galaxy.jobs DEBUG 2023-10-24 06:55:30,340 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [117] prepared (89.710 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:55:30,361 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/117/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/117/registry.xml' '/galaxy/server/database/jobs_directory/000/117/upload_params.json' '141:/galaxy/server/database/objects/f/d/6/dataset_fd676cb1-e39f-4f01-b34c-6c8881ee0e1e_files:/galaxy/server/database/objects/f/d/6/dataset_fd676cb1-e39f-4f01-b34c-6c8881ee0e1e.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:55:30,373 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (117) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 06:55:41,167 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 116: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:55:42,204 [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 2023-10-24 06:55:47,443 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 116 finished +galaxy.model.metadata DEBUG 2023-10-24 06:55:47,492 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 140 +galaxy.jobs INFO 2023-10-24 06:55:47,529 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 116 in /galaxy/server/database/jobs_directory/000/116 +galaxy.jobs DEBUG 2023-10-24 06:55:47,564 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 116 executed (104.561 ms) +galaxy.jobs.runners DEBUG 2023-10-24 06:55:48,491 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 117 finished +galaxy.model.metadata DEBUG 2023-10-24 06:55:48,535 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 141 +galaxy.jobs INFO 2023-10-24 06:55:48,566 [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 2023-10-24 06:55:48,596 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 117 executed (90.632 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:55:49,839 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 118 +tpv.core.entities DEBUG 2023-10-24 06:55:49,880 [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={'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=None, 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 2023-10-24 06:55:49,880 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (118) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:55:49,886 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (118) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:55:49,900 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (118) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:55:49,914 [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 2023-10-24 06:55:49,922 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [118] queued (36.059 ms) +galaxy.jobs.handler INFO 2023-10-24 06:55:49,925 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (118) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:55:49,930 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 118 +galaxy.security.object_wrapper WARNING 2023-10-24 06:55:49,985 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] 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 2023-10-24 06:55:50,073 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [118] prepared (126.173 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 06:55:50,074 [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 2023-10-24 06:55:50,074 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0: python:3.7 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:55:50,294 [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/python:3.7--1,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 06:55:50,313 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/118/tool_script.sh] for tool command [cat '/galaxy/server/database/jobs_directory/000/118/configs/tmpi_296pfs' && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/cf34c344508d/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/118/configs/tmp23_aahur' -Q '/galaxy/server/database/jobs_directory/000/118/configs/tmpi_296pfs' --comment_char='#' -o '/galaxy/server/database/objects/7/d/3/dataset_7d3c0066-63b5-4d1d-9334-f80cb6051ca6.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:55:50,326 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (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 $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 06:55:50,337 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 06:55:50,338 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0: python:3.7 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:55:50,363 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/python:3.7--1,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 06:56:01,474 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 118: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:56:07,217 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 118 finished +galaxy.model.metadata DEBUG 2023-10-24 06:56:07,265 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 142 +galaxy.jobs INFO 2023-10-24 06:56:07,299 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 118 in /galaxy/server/database/jobs_directory/000/118 +galaxy.objectstore CRITICAL 2023-10-24 06:56:07,329 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] None delete error [Errno 13] Permission denied: 'tmpi_296pfs' +galaxy.jobs DEBUG 2023-10-24 06:56:07,329 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 118 executed (95.546 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:56:09,414 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 120, 119 +tpv.core.entities DEBUG 2023-10-24 06:56:09,451 [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={'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=None, 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 2023-10-24 06:56:09,452 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (119) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:56:09,457 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (119) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:56:09,470 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (119) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:56:09,482 [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 2023-10-24 06:56:09,488 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [119] queued (31.682 ms) +galaxy.jobs.handler INFO 2023-10-24 06:56:09,493 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (119) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:56:09,496 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 119 +tpv.core.entities DEBUG 2023-10-24 06:56:09,508 [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={'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=None, 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 2023-10-24 06:56:09,509 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (120) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:56:09,515 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (120) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:56:09,531 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (120) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:56:09,560 [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 2023-10-24 06:56:09,567 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [120] queued (51.516 ms) +galaxy.jobs.handler INFO 2023-10-24 06:56:09,572 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (120) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:56:09,579 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 120 +galaxy.jobs DEBUG 2023-10-24 06:56:09,621 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [119] prepared (101.017 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:56:09,650 [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' '143:/galaxy/server/database/objects/a/c/6/dataset_ac65080c-e627-4585-bd34-3b4bfbd1514c_files:/galaxy/server/database/objects/a/c/6/dataset_ac65080c-e627-4585-bd34-3b4bfbd1514c.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:56:09,665 [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 $return_code" +galaxy.jobs DEBUG 2023-10-24 06:56:09,702 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [120] prepared (96.468 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:56:09,721 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/120/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/120/registry.xml' '/galaxy/server/database/jobs_directory/000/120/upload_params.json' '144:/galaxy/server/database/objects/0/7/0/dataset_0704719f-85f2-4978-84bd-ab22d4cfc233_files:/galaxy/server/database/objects/0/7/0/dataset_0704719f-85f2-4978-84bd-ab22d4cfc233.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:56:09,732 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (120) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 06:56:19,848 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 119: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:56:20,892 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] 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 2023-10-24 06:56:26,232 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 119 finished +galaxy.model.metadata DEBUG 2023-10-24 06:56:26,278 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 143 +galaxy.jobs INFO 2023-10-24 06:56:26,316 [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 2023-10-24 06:56:26,349 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 119 executed (101.524 ms) +galaxy.jobs.runners DEBUG 2023-10-24 06:56:27,302 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 120 finished +galaxy.model.metadata DEBUG 2023-10-24 06:56:27,353 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 144 +galaxy.jobs INFO 2023-10-24 06:56:27,385 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 120 in /galaxy/server/database/jobs_directory/000/120 +galaxy.jobs DEBUG 2023-10-24 06:56:27,430 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 120 executed (107.661 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:56:28,009 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 121 +tpv.core.entities DEBUG 2023-10-24 06:56:28,049 [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={'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=None, 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 2023-10-24 06:56:28,050 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (121) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:56:28,054 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (121) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:56:28,067 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (121) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:56:28,080 [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 2023-10-24 06:56:28,088 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [121] queued (33.844 ms) +galaxy.jobs.handler INFO 2023-10-24 06:56:28,092 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (121) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:56:28,096 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 121 +galaxy.jobs DEBUG 2023-10-24 06:56:28,184 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [121] prepared (71.946 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 06:56:28,185 [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 2023-10-24 06:56:28,185 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0: python:3.7 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:56:28,205 [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/python:3.7--1,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 06:56:28,225 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/121/tool_script.sh] for tool command [cat '/galaxy/server/database/jobs_directory/000/121/configs/tmpm44nhpdj' && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/cf34c344508d/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/121/configs/tmpfxjqlhvh' -Q '/galaxy/server/database/jobs_directory/000/121/configs/tmpm44nhpdj' --comment_char='#' -o '/galaxy/server/database/objects/f/0/6/dataset_f06c33b5-5254-4c9a-ac23-3f4cdb3325cb.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:56:28,238 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (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 $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 06:56:28,249 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 06:56:28,249 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0: python:3.7 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:56:28,266 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/python:3.7--1,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 06:56:34,047 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 121: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:56:39,895 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 121 finished +galaxy.model.metadata DEBUG 2023-10-24 06:56:39,941 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 145 +galaxy.jobs INFO 2023-10-24 06:56:39,975 [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.objectstore CRITICAL 2023-10-24 06:56:40,007 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] None delete error [Errno 13] Permission denied: 'tmpm44nhpdj' +galaxy.jobs DEBUG 2023-10-24 06:56:40,008 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 121 executed (96.722 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:56:42,559 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 122 +tpv.core.entities DEBUG 2023-10-24 06:56:42,594 [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={'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=None, 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 2023-10-24 06:56:42,594 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (122) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:56:42,599 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (122) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:56:42,613 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (122) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:56:42,627 [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 2023-10-24 06:56:42,633 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [122] queued (34.518 ms) +galaxy.jobs.handler INFO 2023-10-24 06:56:42,638 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (122) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:56:42,640 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 122 +galaxy.jobs DEBUG 2023-10-24 06:56:42,735 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [122] prepared (79.252 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:56:42,756 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/122/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/122/registry.xml' '/galaxy/server/database/jobs_directory/000/122/upload_params.json' '146:/galaxy/server/database/objects/f/6/4/dataset_f64d601c-6819-4f97-a6e6-31460789f26a_files:/galaxy/server/database/objects/f/6/4/dataset_f64d601c-6819-4f97-a6e6-31460789f26a.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:56:42,768 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (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 $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 06:56:53,300 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 122: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:56:59,125 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 122 finished +galaxy.model.metadata DEBUG 2023-10-24 06:56:59,171 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 146 +galaxy.jobs INFO 2023-10-24 06:56:59,204 [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.jobs DEBUG 2023-10-24 06:56:59,238 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 122 executed (96.802 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:57:00,036 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 123 +tpv.core.entities DEBUG 2023-10-24 06:57:00,074 [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={'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=None, 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 2023-10-24 06:57:00,075 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (123) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:57:00,080 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (123) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:57:00,092 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (123) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:57:00,106 [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 2023-10-24 06:57:00,114 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [123] queued (34.316 ms) +galaxy.jobs.handler INFO 2023-10-24 06:57:00,117 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (123) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:57:00,122 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 123 +galaxy.jobs DEBUG 2023-10-24 06:57:00,206 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [123] prepared (67.582 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 06:57:00,207 [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 2023-10-24 06:57:00,207 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0: python:3.7 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:57:00,234 [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/python:3.7--1,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 06:57:00,254 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/123/tool_script.sh] for tool command [cat '/galaxy/server/database/jobs_directory/000/123/configs/tmp4it7886o' && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/cf34c344508d/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/123/configs/tmpnzi0reyf' -Q '/galaxy/server/database/jobs_directory/000/123/configs/tmp4it7886o' --comment_char='#' -o '/galaxy/server/database/objects/2/4/3/dataset_243ecf36-dd3a-4d88-83bd-2ae44308991b.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:57:00,267 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (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 $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 06:57:00,277 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 06:57:00,277 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0: python:3.7 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:57:00,294 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/python:3.7--1,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 06:57:05,442 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 123: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:57:11,335 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 123 finished +galaxy.model.metadata DEBUG 2023-10-24 06:57:11,392 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 147 +galaxy.jobs INFO 2023-10-24 06:57:11,431 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 123 in /galaxy/server/database/jobs_directory/000/123 +galaxy.objectstore CRITICAL 2023-10-24 06:57:11,462 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] None delete error [Errno 13] Permission denied: 'tmp4it7886o' +galaxy.jobs DEBUG 2023-10-24 06:57:11,462 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 123 executed (109.287 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:57:13,430 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 124 +tpv.core.entities DEBUG 2023-10-24 06:57:13,469 [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={'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=None, 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 2023-10-24 06:57:13,470 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (124) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:57:13,474 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (124) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:57:13,495 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (124) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:57:13,511 [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 2023-10-24 06:57:13,518 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [124] queued (43.339 ms) +galaxy.jobs.handler INFO 2023-10-24 06:57:13,521 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (124) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:57:13,526 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 124 +galaxy.jobs DEBUG 2023-10-24 06:57:13,623 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [124] prepared (79.168 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:57:13,641 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] 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' '148:/galaxy/server/database/objects/1/7/5/dataset_1757fefb-3436-4e88-af51-9b7c72829efe_files:/galaxy/server/database/objects/1/7/5/dataset_1757fefb-3436-4e88-af51-9b7c72829efe.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:57:13,653 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (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.handler DEBUG 2023-10-24 06:57:14,524 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 125 +tpv.core.entities DEBUG 2023-10-24 06:57:14,559 [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={'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=None, 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 2023-10-24 06:57:14,560 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (125) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:57:14,566 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (125) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:57:14,582 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (125) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:57:14,598 [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 2023-10-24 06:57:14,605 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [125] queued (38.844 ms) +galaxy.jobs.handler INFO 2023-10-24 06:57:14,611 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (125) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:57:14,613 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 125 +galaxy.jobs DEBUG 2023-10-24 06:57:14,713 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [125] prepared (81.448 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:57:14,731 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/125/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/125/registry.xml' '/galaxy/server/database/jobs_directory/000/125/upload_params.json' '149:/galaxy/server/database/objects/8/0/9/dataset_809854ab-c155-4ad7-a2eb-b800365d78fc_files:/galaxy/server/database/objects/8/0/9/dataset_809854ab-c155-4ad7-a2eb-b800365d78fc.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:57:14,744 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (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 $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 06:57:23,793 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 124: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:57:24,832 [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 2023-10-24 06:57:30,090 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 124 finished +galaxy.model.metadata DEBUG 2023-10-24 06:57:30,145 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 148 +galaxy.jobs INFO 2023-10-24 06:57:30,181 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 124 in /galaxy/server/database/jobs_directory/000/124 +galaxy.jobs DEBUG 2023-10-24 06:57:30,215 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 124 executed (102.784 ms) +galaxy.jobs.runners DEBUG 2023-10-24 06:57:31,252 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 125 finished +galaxy.model.metadata DEBUG 2023-10-24 06:57:31,299 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 149 +galaxy.jobs INFO 2023-10-24 06:57:31,333 [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 2023-10-24 06:57:31,366 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 125 executed (100.076 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:57:32,044 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 126 +tpv.core.entities DEBUG 2023-10-24 06:57:32,084 [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={'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=None, 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 2023-10-24 06:57:32,085 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (126) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:57:32,090 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (126) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:57:32,103 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (126) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:57:32,118 [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 2023-10-24 06:57:32,126 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [126] queued (36.077 ms) +galaxy.jobs.handler INFO 2023-10-24 06:57:32,131 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (126) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:57:32,133 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 126 +galaxy.jobs DEBUG 2023-10-24 06:57:32,227 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [126] prepared (77.499 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 06:57:32,228 [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 2023-10-24 06:57:32,228 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0: python:3.7 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:57:32,465 [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/python:3.7--1,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 06:57:32,484 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/126/tool_script.sh] for tool command [cat '/galaxy/server/database/jobs_directory/000/126/configs/tmpzt7nusp0' && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/cf34c344508d/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/126/configs/tmpj2td2193' -Q '/galaxy/server/database/jobs_directory/000/126/configs/tmpzt7nusp0' --comment_char='#' -o '/galaxy/server/database/objects/9/5/0/dataset_950f612a-2fba-4fe0-8620-483ff86dcaf0.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:57:32,496 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (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 $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 06:57:32,506 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 06:57:32,507 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0: python:3.7 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:57:32,538 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/python:3.7--1,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 06:57:37,983 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 126: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:57:43,855 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 126 finished +galaxy.model.metadata DEBUG 2023-10-24 06:57:43,905 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 150 +galaxy.jobs INFO 2023-10-24 06:57:43,941 [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.objectstore CRITICAL 2023-10-24 06:57:43,972 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] None delete error [Errno 13] Permission denied: 'tmpzt7nusp0' +galaxy.jobs DEBUG 2023-10-24 06:57:43,972 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 126 executed (99.667 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:57:46,483 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 127, 128 +tpv.core.entities DEBUG 2023-10-24 06:57:46,518 [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={'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=None, 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 2023-10-24 06:57:46,519 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (127) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:57:46,523 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (127) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:57:46,537 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (127) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:57:46,549 [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 2023-10-24 06:57:46,555 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [127] queued (32.058 ms) +galaxy.jobs.handler INFO 2023-10-24 06:57:46,561 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (127) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:57:46,565 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 127 +tpv.core.entities DEBUG 2023-10-24 06:57:46,575 [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={'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=None, 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 2023-10-24 06:57:46,576 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (128) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:57:46,581 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (128) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:57:46,596 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (128) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:57:46,623 [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 2023-10-24 06:57:46,630 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [128] queued (48.330 ms) +galaxy.jobs.handler INFO 2023-10-24 06:57:46,635 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (128) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:57:46,639 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 128 +galaxy.jobs DEBUG 2023-10-24 06:57:46,675 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [127] prepared (89.931 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:57:46,706 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/127/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/127/registry.xml' '/galaxy/server/database/jobs_directory/000/127/upload_params.json' '151:/galaxy/server/database/objects/c/4/4/dataset_c44b2bea-960c-498d-8197-035dc99cfd00_files:/galaxy/server/database/objects/c/4/4/dataset_c44b2bea-960c-498d-8197-035dc99cfd00.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:57:46,719 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (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 $return_code" +galaxy.jobs DEBUG 2023-10-24 06:57:46,754 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [128] prepared (93.637 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:57:46,772 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/128/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/128/registry.xml' '/galaxy/server/database/jobs_directory/000/128/upload_params.json' '152:/galaxy/server/database/objects/a/d/f/dataset_adf80f14-c180-4217-b554-155534825961_files:/galaxy/server/database/objects/a/d/f/dataset_adf80f14-c180-4217-b554-155534825961.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:57:46,786 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (128) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 06:57:57,468 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 127: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:57:58,514 [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 2023-10-24 06:58:03,525 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 127 finished +galaxy.model.metadata DEBUG 2023-10-24 06:58:03,578 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 151 +galaxy.jobs INFO 2023-10-24 06:58:03,612 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 127 in /galaxy/server/database/jobs_directory/000/127 +galaxy.jobs DEBUG 2023-10-24 06:58:03,651 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 127 executed (106.466 ms) +galaxy.jobs.runners DEBUG 2023-10-24 06:58:04,561 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 128 finished +galaxy.model.metadata DEBUG 2023-10-24 06:58:04,607 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 152 +galaxy.jobs INFO 2023-10-24 06:58:04,640 [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 2023-10-24 06:58:04,673 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 128 executed (96.890 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:58:06,163 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 129 +tpv.core.entities DEBUG 2023-10-24 06:58:06,205 [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={'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=None, 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 2023-10-24 06:58:06,205 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (129) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:58:06,211 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (129) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:58:06,225 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (129) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:58:06,240 [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 2023-10-24 06:58:06,248 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [129] queued (37.492 ms) +galaxy.jobs.handler INFO 2023-10-24 06:58:06,252 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (129) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:58:06,256 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 129 +galaxy.jobs DEBUG 2023-10-24 06:58:06,353 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [129] prepared (80.246 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 06:58:06,353 [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 2023-10-24 06:58:06,353 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0: python:3.7 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:58:06,388 [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/python:3.7--1,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 06:58:06,408 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/129/tool_script.sh] for tool command [cat '/galaxy/server/database/jobs_directory/000/129/configs/tmpwnxe09ke' && cp '/galaxy/server/database/objects/c/4/4/dataset_c44b2bea-960c-498d-8197-035dc99cfd00.dat' 'workdb.sqlite' && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/cf34c344508d/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/129/configs/tmp9m01rjnp' -Q '/galaxy/server/database/jobs_directory/000/129/configs/tmpwnxe09ke' --comment_char='#' -o '/galaxy/server/database/objects/e/e/1/dataset_ee13ebf3-8a7a-4ac9-a645-c3565f72e525.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:58:06,420 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (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; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 06:58:06,431 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 06:58:06,431 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0: python:3.7 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:58:06,463 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/python:3.7--1,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 06:58:12,659 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 129: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:58:18,453 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 129 finished +galaxy.model.metadata DEBUG 2023-10-24 06:58:18,499 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 153 +galaxy.jobs INFO 2023-10-24 06:58:18,534 [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.objectstore CRITICAL 2023-10-24 06:58:18,561 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] None delete error [Errno 13] Permission denied: 'tmpwnxe09ke' +galaxy.jobs DEBUG 2023-10-24 06:58:18,561 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 129 executed (91.711 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:58:20,574 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 130 +tpv.core.entities DEBUG 2023-10-24 06:58:20,610 [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={'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=None, 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 2023-10-24 06:58:20,611 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (130) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:58:20,616 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (130) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:58:20,630 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (130) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:58:20,647 [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 2023-10-24 06:58:20,654 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [130] queued (37.606 ms) +galaxy.jobs.handler INFO 2023-10-24 06:58:20,659 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (130) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:58:20,661 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 130 +galaxy.jobs DEBUG 2023-10-24 06:58:20,756 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [130] prepared (78.426 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:58:20,774 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] 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' '154:/galaxy/server/database/objects/6/a/1/dataset_6a15c4f5-800d-4dbe-9de0-3b9c99026370_files:/galaxy/server/database/objects/6/a/1/dataset_6a15c4f5-800d-4dbe-9de0-3b9c99026370.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:58:20,786 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (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.kubernetes ERROR 2023-10-24 06:58:29,815 [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://10.112.0.1:443/apis/batch/v1/namespaces/edge-23-10-24-06-08-1/jobs/gxy-5tt8n + +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-5tt8n": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:58:29,854 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (130/gxy-5tt8n) Terminated at user's request +galaxy.jobs.handler DEBUG 2023-10-24 06:58:30,892 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 131 +tpv.core.entities DEBUG 2023-10-24 06:58:30,929 [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={'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=None, 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 2023-10-24 06:58:30,930 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (131) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:58:30,935 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (131) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:58:30,950 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (131) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:58:30,967 [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 2023-10-24 06:58:30,973 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [131] queued (37.446 ms) +galaxy.jobs.handler INFO 2023-10-24 06:58:30,979 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (131) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:58:30,980 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 131 +galaxy.jobs DEBUG 2023-10-24 06:58:31,077 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [131] prepared (79.189 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:58:31,094 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/131/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/131/registry.xml' '/galaxy/server/database/jobs_directory/000/131/upload_params.json' '155:/galaxy/server/database/objects/d/3/c/dataset_d3cc82fb-bf61-4111-bc29-51ccee707c82_files:/galaxy/server/database/objects/d/3/c/dataset_d3cc82fb-bf61-4111-bc29-51ccee707c82.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:58:31,107 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (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; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 06:58:41,167 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 131: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:58:47,234 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 131 finished +galaxy.model.metadata DEBUG 2023-10-24 06:58:47,283 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 155 +galaxy.jobs INFO 2023-10-24 06:58:47,318 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 131 in /galaxy/server/database/jobs_directory/000/131 +galaxy.jobs DEBUG 2023-10-24 06:58:47,355 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 131 executed (103.296 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:58:48,409 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 132 +tpv.core.entities DEBUG 2023-10-24 06:58:48,448 [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={'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=None, 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 2023-10-24 06:58:48,448 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (132) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:58:48,453 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (132) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:58:48,467 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (132) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:58:48,482 [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 2023-10-24 06:58:48,490 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [132] queued (36.674 ms) +galaxy.jobs.handler INFO 2023-10-24 06:58:48,494 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (132) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:58:48,501 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 132 +galaxy.jobs DEBUG 2023-10-24 06:58:48,591 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [132] prepared (71.873 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 06:58:48,592 [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 2023-10-24 06:58:48,592 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0: python:3.7 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:58:48,620 [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/python:3.7--1,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 06:58:48,641 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/132/tool_script.sh] for tool command [cat '/galaxy/server/database/jobs_directory/000/132/configs/tmpbda3x3ay' && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/cf34c344508d/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/132/configs/tmp_68kvdhw' -Q '/galaxy/server/database/jobs_directory/000/132/configs/tmpbda3x3ay' -o '/galaxy/server/database/objects/4/0/b/dataset_40bbc802-7da5-42cd-a02f-7ec164644760.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:58:48,654 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (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 $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 06:58:48,665 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 06:58:48,665 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0: python:3.7 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:58:48,682 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/python:3.7--1,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 06:58:54,430 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 132: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:59:00,410 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 132 finished +galaxy.model.metadata DEBUG 2023-10-24 06:59:00,457 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 156 +galaxy.jobs INFO 2023-10-24 06:59:00,491 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 132 in /galaxy/server/database/jobs_directory/000/132 +galaxy.objectstore CRITICAL 2023-10-24 06:59:00,520 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] None delete error [Errno 13] Permission denied: 'tmp_68kvdhw' +galaxy.jobs DEBUG 2023-10-24 06:59:00,520 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 132 executed (93.976 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:59:02,835 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 133 +tpv.core.entities DEBUG 2023-10-24 06:59:02,870 [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={'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=None, 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 2023-10-24 06:59:02,870 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (133) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:59:02,875 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (133) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:59:02,888 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (133) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:59:02,904 [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 2023-10-24 06:59:02,913 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [133] queued (37.802 ms) +galaxy.jobs.handler INFO 2023-10-24 06:59:02,918 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (133) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:59:02,921 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 133 +galaxy.jobs DEBUG 2023-10-24 06:59:03,018 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [133] prepared (79.233 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:59:03,036 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/133/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/133/registry.xml' '/galaxy/server/database/jobs_directory/000/133/upload_params.json' '157:/galaxy/server/database/objects/d/b/d/dataset_dbd79a2c-6a46-4d9f-9e11-9d629c82d7de_files:/galaxy/server/database/objects/d/b/d/dataset_dbd79a2c-6a46-4d9f-9e11-9d629c82d7de.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:59:03,048 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (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; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 06:59:13,682 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 133: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:59:19,675 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 133 finished +galaxy.model.metadata DEBUG 2023-10-24 06:59:19,723 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 157 +galaxy.jobs INFO 2023-10-24 06:59:19,755 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 133 in /galaxy/server/database/jobs_directory/000/133 +galaxy.jobs DEBUG 2023-10-24 06:59:19,788 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 133 executed (96.201 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:59:20,343 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 134 +tpv.core.entities DEBUG 2023-10-24 06:59:20,381 [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={'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=None, 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 2023-10-24 06:59:20,381 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (134) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:59:20,386 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (134) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:59:20,399 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (134) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:59:20,414 [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 2023-10-24 06:59:20,422 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [134] queued (36.076 ms) +galaxy.jobs.handler INFO 2023-10-24 06:59:20,426 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (134) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:59:20,431 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 134 +galaxy.jobs DEBUG 2023-10-24 06:59:20,527 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [134] prepared (78.206 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 06:59:20,528 [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 2023-10-24 06:59:20,528 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0: python:3.7 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:59:20,565 [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/python:3.7--1,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 06:59:20,585 [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 [cat '/galaxy/server/database/jobs_directory/000/134/configs/tmpsh9bqowl' && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/cf34c344508d/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/134/configs/tmp59xo480q' -Q '/galaxy/server/database/jobs_directory/000/134/configs/tmpsh9bqowl' -o '/galaxy/server/database/objects/1/6/0/dataset_160a5ce3-5645-4742-9ce0-0de933b13228.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:59:20,598 [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 $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 06:59:20,610 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 06:59:20,610 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0: python:3.7 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:59:20,627 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/python:3.7--1,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 06:59:25,812 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 134: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:59:31,596 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 134 finished +galaxy.model.metadata DEBUG 2023-10-24 06:59:31,644 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 158 +galaxy.jobs INFO 2023-10-24 06:59:31,680 [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.objectstore CRITICAL 2023-10-24 06:59:31,723 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] None delete error [Errno 13] Permission denied: 'tmp59xo480q' +galaxy.jobs DEBUG 2023-10-24 06:59:31,723 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 134 executed (111.849 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:59:33,736 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 135 +tpv.core.entities DEBUG 2023-10-24 06:59:33,770 [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={'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=None, 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 2023-10-24 06:59:33,771 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (135) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:59:33,776 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (135) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:59:33,789 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (135) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:59:33,805 [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 2023-10-24 06:59:33,811 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [135] queued (35.358 ms) +galaxy.jobs.handler INFO 2023-10-24 06:59:33,814 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (135) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:59:33,819 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 135 +galaxy.jobs DEBUG 2023-10-24 06:59:33,921 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [135] prepared (85.263 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:59:33,940 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/135/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/135/registry.xml' '/galaxy/server/database/jobs_directory/000/135/upload_params.json' '159:/galaxy/server/database/objects/4/2/0/dataset_4205196f-f5fe-4d09-a48d-0ad19b421c6d_files:/galaxy/server/database/objects/4/2/0/dataset_4205196f-f5fe-4d09-a48d-0ad19b421c6d.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:59:33,953 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (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; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 06:59:45,114 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 135: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 06:59:51,105 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 135 finished +galaxy.model.metadata DEBUG 2023-10-24 06:59:51,168 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 159 +galaxy.jobs INFO 2023-10-24 06:59:51,214 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 135 in /galaxy/server/database/jobs_directory/000/135 +galaxy.jobs DEBUG 2023-10-24 06:59:51,251 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 135 executed (114.428 ms) +galaxy.jobs.handler DEBUG 2023-10-24 06:59:52,282 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 136 +tpv.core.entities DEBUG 2023-10-24 06:59:52,323 [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={'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=None, 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 2023-10-24 06:59:52,324 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (136) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:59:52,328 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (136) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:59:52,342 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (136) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:59:52,360 [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 2023-10-24 06:59:52,369 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [136] queued (40.781 ms) +galaxy.jobs.handler INFO 2023-10-24 06:59:52,375 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (136) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:59:52,377 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 136 +galaxy.jobs DEBUG 2023-10-24 06:59:52,465 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [136] prepared (69.691 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 06:59:52,466 [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 2023-10-24 06:59:52,466 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0: python:3.7 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:59:52,494 [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/python:3.7--1,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 06:59:52,514 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/136/tool_script.sh] for tool command [cat '/galaxy/server/database/jobs_directory/000/136/configs/tmpkgl6zl5q' && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/cf34c344508d/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/136/configs/tmp_mvqe1xq' -Q '/galaxy/server/database/jobs_directory/000/136/configs/tmpkgl6zl5q' --comment_char='#' -o '/galaxy/server/database/objects/9/d/9/dataset_9d97200a-860c-4cbf-b5d0-f148971d13cc.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:59:52,536 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (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; +if [ -f "/galaxy/server/database/jobs_directory/000/136/working/results0.tsv" ] ; then cp "/galaxy/server/database/jobs_directory/000/136/working/results0.tsv" "/galaxy/server/database/objects/8/f/7/dataset_8f744d3d-98e2-4a61-ba4a-0a4d07b57705.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 06:59:52,546 [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 2023-10-24 06:59:52,546 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0: python:3.7 +galaxy.tool_util.deps.containers INFO 2023-10-24 06:59:52,562 [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/python:3.7--1,type=docker]] +galaxy.jobs.runners.kubernetes ERROR 2023-10-24 06:59:57,154 [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://10.112.0.1:443/apis/batch/v1/namespaces/edge-23-10-24-06-08-1/jobs/gxy-qb9wr + +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-qb9wr": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:59:57,200 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (136/gxy-qb9wr) Terminated at user's request +galaxy.util WARNING 2023-10-24 06:59:57,261 [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/8/f/7/dataset_8f744d3d-98e2-4a61-ba4a-0a4d07b57705.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/7/dataset_8f744d3d-98e2-4a61-ba4a-0a4d07b57705.dat' +galaxy.objectstore CRITICAL 2023-10-24 06:59:57,281 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] None delete error [Errno 13] Permission denied: 'tmp_mvqe1xq' +galaxy.jobs.handler DEBUG 2023-10-24 06:59:59,530 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 137 +tpv.core.entities DEBUG 2023-10-24 06:59:59,565 [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={'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=None, 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 2023-10-24 06:59:59,565 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (137) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 06:59:59,570 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (137) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 06:59:59,583 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (137) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 06:59:59,596 [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 2023-10-24 06:59:59,603 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [137] queued (33.093 ms) +galaxy.jobs.handler INFO 2023-10-24 06:59:59,608 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (137) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 06:59:59,609 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 137 +galaxy.jobs DEBUG 2023-10-24 06:59:59,702 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [137] prepared (76.271 ms) +galaxy.jobs.command_factory INFO 2023-10-24 06:59:59,720 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/137/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/137/registry.xml' '/galaxy/server/database/jobs_directory/000/137/upload_params.json' '162:/galaxy/server/database/objects/2/f/9/dataset_2f9b7b40-979d-40cf-bbdf-eaa3499504a6_files:/galaxy/server/database/objects/2/f/9/dataset_2f9b7b40-979d-40cf-bbdf-eaa3499504a6.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 06:59:59,733 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (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; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 07:00:09,499 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 137: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 07:00:15,464 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 137 finished +galaxy.model.metadata DEBUG 2023-10-24 07:00:15,519 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 162 +galaxy.jobs INFO 2023-10-24 07:00:15,551 [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 2023-10-24 07:00:15,582 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 137 executed (95.895 ms) +galaxy.jobs.handler DEBUG 2023-10-24 07:00:17,037 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 138 +tpv.core.entities DEBUG 2023-10-24 07:00:17,074 [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={'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=None, 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 2023-10-24 07:00:17,075 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (138) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 07:00:17,081 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (138) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 07:00:17,094 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (138) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 07:00:17,107 [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 2023-10-24 07:00:17,115 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [138] queued (34.071 ms) +galaxy.jobs.handler INFO 2023-10-24 07:00:17,120 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (138) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 07:00:17,122 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 138 +galaxy.jobs DEBUG 2023-10-24 07:00:17,215 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [138] prepared (76.544 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 07:00:17,216 [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 2023-10-24 07:00:17,216 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0: python:3.7 +galaxy.tool_util.deps.containers INFO 2023-10-24 07:00:17,236 [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/python:3.7--1,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 07:00:17,255 [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 [cat '/galaxy/server/database/jobs_directory/000/138/configs/tmpef0c3bi0' && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/cf34c344508d/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/138/configs/tmpzpc6a817' -Q '/galaxy/server/database/jobs_directory/000/138/configs/tmpef0c3bi0' -o '/galaxy/server/database/objects/7/0/b/dataset_70b7a446-b831-422a-9599-13df75423eef.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 07:00:17,269 [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 $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 07:00:17,280 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 07:00:17,280 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0: python:3.7 +galaxy.tool_util.deps.containers INFO 2023-10-24 07:00:17,297 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/python:3.7--1,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 07:00:22,695 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 138: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 07:00:28,664 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 138 finished +galaxy.model.metadata DEBUG 2023-10-24 07:00:28,710 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 163 +galaxy.jobs INFO 2023-10-24 07:00:28,746 [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.objectstore CRITICAL 2023-10-24 07:00:28,776 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] None delete error [Errno 13] Permission denied: 'tmpef0c3bi0' +galaxy.jobs DEBUG 2023-10-24 07:00:28,776 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 138 executed (97.001 ms) +galaxy.jobs.handler DEBUG 2023-10-24 07:00:31,468 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 139 +tpv.core.entities DEBUG 2023-10-24 07:00:31,501 [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={'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=None, 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 2023-10-24 07:00:31,502 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (139) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 07:00:31,507 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (139) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 07:00:31,520 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (139) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 07:00:31,533 [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 2023-10-24 07:00:31,540 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [139] queued (33.058 ms) +galaxy.jobs.handler INFO 2023-10-24 07:00:31,545 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (139) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 07:00:31,546 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 139 +galaxy.jobs DEBUG 2023-10-24 07:00:31,656 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [139] prepared (92.551 ms) +galaxy.jobs.command_factory INFO 2023-10-24 07:00:31,676 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/139/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/139/registry.xml' '/galaxy/server/database/jobs_directory/000/139/upload_params.json' '164:/galaxy/server/database/objects/2/c/2/dataset_2c21b82c-f67f-4799-b331-eb443dd6101d_files:/galaxy/server/database/objects/2/c/2/dataset_2c21b82c-f67f-4799-b331-eb443dd6101d.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 07:00:31,688 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (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; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 07:00:41,912 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 139: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 07:00:47,835 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 139 finished +galaxy.model.metadata DEBUG 2023-10-24 07:00:47,883 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 164 +galaxy.jobs INFO 2023-10-24 07:00:47,918 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 139 in /galaxy/server/database/jobs_directory/000/139 +galaxy.jobs DEBUG 2023-10-24 07:00:47,970 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 139 executed (119.162 ms) +galaxy.jobs.handler DEBUG 2023-10-24 07:00:48,955 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 140 +tpv.core.entities DEBUG 2023-10-24 07:00:48,992 [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={'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=None, 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 2023-10-24 07:00:48,993 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (140) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 07:00:48,998 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (140) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 07:00:49,014 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (140) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 07:00:49,029 [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 2023-10-24 07:00:49,037 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [140] queued (38.845 ms) +galaxy.jobs.handler INFO 2023-10-24 07:00:49,042 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (140) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 07:00:49,044 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 140 +galaxy.jobs DEBUG 2023-10-24 07:00:49,128 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [140] prepared (67.096 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 07:00:49,129 [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 2023-10-24 07:00:49,129 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0: python:3.7 +galaxy.tool_util.deps.containers INFO 2023-10-24 07:00:49,161 [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/python:3.7--1,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 07:00:49,181 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/140/tool_script.sh] for tool command [cat '/galaxy/server/database/jobs_directory/000/140/configs/tmp49mxk32p' && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/cf34c344508d/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/140/configs/tmpu2ts7pk0' -Q '/galaxy/server/database/jobs_directory/000/140/configs/tmp49mxk32p' -o '/galaxy/server/database/objects/a/a/1/dataset_aa19a5dd-d765-4014-9169-0e369a58a3aa.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 07:00:49,194 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (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 $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 07:00:49,204 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 07:00:49,205 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0: python:3.7 +galaxy.tool_util.deps.containers INFO 2023-10-24 07:00:49,230 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/python:3.7--1,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 07:00:55,080 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 140: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 07:01:00,998 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 140 finished +galaxy.model.metadata DEBUG 2023-10-24 07:01:01,048 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 165 +galaxy.jobs INFO 2023-10-24 07:01:01,082 [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.objectstore CRITICAL 2023-10-24 07:01:01,117 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] None delete error [Errno 13] Permission denied: 'tmp49mxk32p' +galaxy.jobs DEBUG 2023-10-24 07:01:01,117 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 140 executed (102.056 ms) +galaxy.jobs.handler DEBUG 2023-10-24 07:01:03,408 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 141 +tpv.core.entities DEBUG 2023-10-24 07:01:03,450 [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={'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=None, 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 2023-10-24 07:01:03,451 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (141) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 07:01:03,456 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (141) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 07:01:03,470 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (141) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 07:01:03,485 [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 2023-10-24 07:01:03,492 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [141] queued (35.715 ms) +galaxy.jobs.handler INFO 2023-10-24 07:01:03,496 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (141) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 07:01:03,499 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 141 +galaxy.jobs DEBUG 2023-10-24 07:01:03,598 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [141] prepared (82.587 ms) +galaxy.jobs.command_factory INFO 2023-10-24 07:01:03,617 [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' '166:/galaxy/server/database/objects/4/0/d/dataset_40da69dc-21a9-419c-a984-99e342d70f3c_files:/galaxy/server/database/objects/4/0/d/dataset_40da69dc-21a9-419c-a984-99e342d70f3c.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 07:01:03,629 [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 $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 07:01:14,312 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 141: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 07:01:20,333 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 141 finished +galaxy.model.metadata DEBUG 2023-10-24 07:01:20,383 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 166 +galaxy.jobs INFO 2023-10-24 07:01:20,420 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 141 in /galaxy/server/database/jobs_directory/000/141 +galaxy.jobs DEBUG 2023-10-24 07:01:20,465 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 141 executed (115.522 ms) +galaxy.jobs.handler DEBUG 2023-10-24 07:01:21,953 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 142 +tpv.core.entities DEBUG 2023-10-24 07:01:21,993 [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={'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=None, 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 2023-10-24 07:01:21,994 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (142) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 07:01:21,999 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (142) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 07:01:22,014 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (142) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 07:01:22,029 [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 2023-10-24 07:01:22,036 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [142] queued (37.208 ms) +galaxy.jobs.handler INFO 2023-10-24 07:01:22,040 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (142) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 07:01:22,044 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 142 +galaxy.jobs DEBUG 2023-10-24 07:01:22,128 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [142] prepared (66.802 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 07:01:22,129 [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 2023-10-24 07:01:22,129 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0: python:3.7 +galaxy.tool_util.deps.containers INFO 2023-10-24 07:01:22,148 [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/python:3.7--1,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 07:01:22,168 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/142/tool_script.sh] for tool command [cat '/galaxy/server/database/jobs_directory/000/142/configs/tmpfu26v9t1' && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/cf34c344508d/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/142/configs/tmpz20jijqd' -Q '/galaxy/server/database/jobs_directory/000/142/configs/tmpfu26v9t1' --comment_char='#' -o '/galaxy/server/database/objects/2/d/2/dataset_2d2d134b-3f05-4259-874a-a8d0a68a6c1c.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 07:01:22,181 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (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 $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 07:01:22,192 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 07:01:22,192 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0: python:3.7 +galaxy.tool_util.deps.containers INFO 2023-10-24 07:01:22,209 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/python:3.7--1,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 07:01:28,475 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 142: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 07:01:34,333 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 142 finished +galaxy.model.metadata DEBUG 2023-10-24 07:01:34,382 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 167 +galaxy.jobs INFO 2023-10-24 07:01:34,418 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 142 in /galaxy/server/database/jobs_directory/000/142 +galaxy.objectstore CRITICAL 2023-10-24 07:01:34,447 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] None delete error [Errno 13] Permission denied: 'tmpz20jijqd' +galaxy.jobs DEBUG 2023-10-24 07:01:34,447 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 142 executed (96.241 ms) +galaxy.jobs.handler DEBUG 2023-10-24 07:01:38,419 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 143 +tpv.core.entities DEBUG 2023-10-24 07:01:38,452 [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={'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=None, 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 2023-10-24 07:01:38,453 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (143) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 07:01:38,457 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (143) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 07:01:38,471 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (143) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 07:01:38,486 [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 2023-10-24 07:01:38,493 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [143] queued (35.597 ms) +galaxy.jobs.handler INFO 2023-10-24 07:01:38,497 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (143) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 07:01:38,501 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 143 +galaxy.jobs DEBUG 2023-10-24 07:01:38,614 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [143] prepared (95.390 ms) +galaxy.jobs.command_factory INFO 2023-10-24 07:01:38,633 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] 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' '168:/galaxy/server/database/objects/e/5/6/dataset_e5646f80-8635-4eea-ba89-be835a6ec77e_files:/galaxy/server/database/objects/e/5/6/dataset_e5646f80-8635-4eea-ba89-be835a6ec77e.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 07:01:38,645 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (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 $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 07:01:48,713 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 143: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 07:01:54,624 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 143 finished +galaxy.model.metadata DEBUG 2023-10-24 07:01:54,680 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 168 +galaxy.jobs INFO 2023-10-24 07:01:54,718 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 143 in /galaxy/server/database/jobs_directory/000/143 +galaxy.jobs DEBUG 2023-10-24 07:01:54,754 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 143 executed (108.181 ms) +galaxy.jobs.handler DEBUG 2023-10-24 07:01:55,916 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 144 +tpv.core.entities DEBUG 2023-10-24 07:01:55,957 [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={'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=None, 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 2023-10-24 07:01:55,958 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (144) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 07:01:55,962 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (144) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 07:01:55,977 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (144) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 07:01:55,990 [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 2023-10-24 07:01:55,998 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [144] queued (35.757 ms) +galaxy.jobs.handler INFO 2023-10-24 07:01:56,003 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (144) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 07:01:56,008 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 144 +galaxy.jobs DEBUG 2023-10-24 07:01:56,083 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [144] prepared (56.253 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 07:01:56,084 [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 2023-10-24 07:01:56,084 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1: mulled-v2-975985c5f84877700b556bc77586e7e90986b693:e6883c0cde219a11f5cd7b8a2577fde5fc086eb2 +galaxy.tool_util.deps.containers INFO 2023-10-24 07:01:56,314 [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-v2-975985c5f84877700b556bc77586e7e90986b693:e6883c0cde219a11f5cd7b8a2577fde5fc086eb2-0,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 07:01:56,333 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/144/tool_script.sh] for tool command [python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/372967836e98/column_remove_by_header/column_remove_by_header.py' '/galaxy/server/database/objects/e/5/6/dataset_e5646f80-8635-4eea-ba89-be835a6ec77e.dat' '/galaxy/server/database/objects/8/1/f/dataset_81f936fb-efd2-4748-84f1-2141671dece9.dat' ' ' '' '#' 'a'] +galaxy.jobs.runners DEBUG 2023-10-24 07:01:56,347 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (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 $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 07:01:56,357 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 07:01:56,357 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1: mulled-v2-975985c5f84877700b556bc77586e7e90986b693:e6883c0cde219a11f5cd7b8a2577fde5fc086eb2 +galaxy.tool_util.deps.containers INFO 2023-10-24 07:01:56,374 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-975985c5f84877700b556bc77586e7e90986b693:e6883c0cde219a11f5cd7b8a2577fde5fc086eb2-0,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 07:02:06,946 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 144: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 07:02:12,699 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 144 finished +galaxy.model.metadata DEBUG 2023-10-24 07:02:12,748 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 169 +galaxy.jobs INFO 2023-10-24 07:02:12,781 [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 2023-10-24 07:02:12,820 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 144 executed (103.942 ms) +galaxy.jobs.handler DEBUG 2023-10-24 07:02:15,459 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 145 +tpv.core.entities DEBUG 2023-10-24 07:02:15,493 [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={'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=None, 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 2023-10-24 07:02:15,494 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (145) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 07:02:15,499 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (145) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 07:02:15,514 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (145) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 07:02:15,530 [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 2023-10-24 07:02:15,537 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [145] queued (37.651 ms) +galaxy.jobs.handler INFO 2023-10-24 07:02:15,541 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (145) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 07:02:15,545 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 145 +galaxy.jobs DEBUG 2023-10-24 07:02:15,657 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [145] prepared (94.973 ms) +galaxy.jobs.command_factory INFO 2023-10-24 07:02:15,677 [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 [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/145/registry.xml' '/galaxy/server/database/jobs_directory/000/145/upload_params.json' '170:/galaxy/server/database/objects/1/2/2/dataset_1229407f-2db8-459e-a147-5e72cc6ce2d7_files:/galaxy/server/database/objects/1/2/2/dataset_1229407f-2db8-459e-a147-5e72cc6ce2d7.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 07:02:15,690 [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 $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 07:02:25,232 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 145: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 07:02:30,950 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 145 finished +galaxy.model.metadata DEBUG 2023-10-24 07:02:31,003 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 170 +galaxy.jobs INFO 2023-10-24 07:02:31,044 [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 2023-10-24 07:02:31,081 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 145 executed (113.860 ms) +galaxy.jobs.handler DEBUG 2023-10-24 07:02:31,927 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 146 +tpv.core.entities DEBUG 2023-10-24 07:02:31,971 [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={'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=None, 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 2023-10-24 07:02:31,971 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (146) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 07:02:31,977 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (146) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 07:02:31,991 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (146) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 07:02:32,006 [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 2023-10-24 07:02:32,015 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [146] queued (38.657 ms) +galaxy.jobs.handler INFO 2023-10-24 07:02:32,019 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (146) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 07:02:32,024 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 146 +galaxy.jobs DEBUG 2023-10-24 07:02:32,094 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [146] prepared (52.841 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 07:02:32,094 [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 2023-10-24 07:02:32,095 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1: mulled-v2-975985c5f84877700b556bc77586e7e90986b693:e6883c0cde219a11f5cd7b8a2577fde5fc086eb2 +galaxy.tool_util.deps.containers INFO 2023-10-24 07:02:32,115 [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-v2-975985c5f84877700b556bc77586e7e90986b693:e6883c0cde219a11f5cd7b8a2577fde5fc086eb2-0,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 07:02:32,135 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/146/tool_script.sh] for tool command [python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/372967836e98/column_remove_by_header/column_remove_by_header.py' '/galaxy/server/database/objects/1/2/2/dataset_1229407f-2db8-459e-a147-5e72cc6ce2d7.dat' '/galaxy/server/database/objects/6/1/0/dataset_6104ce47-eeb0-432e-a8a9-3a4aca13845a.dat' ' ' '--keep' '#' 'KEY' 'a'] +galaxy.jobs.runners DEBUG 2023-10-24 07:02:32,149 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (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 $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 07:02:32,159 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 07:02:32,159 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1: mulled-v2-975985c5f84877700b556bc77586e7e90986b693:e6883c0cde219a11f5cd7b8a2577fde5fc086eb2 +galaxy.tool_util.deps.containers INFO 2023-10-24 07:02:32,176 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-975985c5f84877700b556bc77586e7e90986b693:e6883c0cde219a11f5cd7b8a2577fde5fc086eb2-0,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 07:02:37,364 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 146: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 07:02:43,163 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 146 finished +galaxy.model.metadata DEBUG 2023-10-24 07:02:43,215 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 171 +galaxy.jobs INFO 2023-10-24 07:02:43,251 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 146 in /galaxy/server/database/jobs_directory/000/146 +galaxy.jobs DEBUG 2023-10-24 07:02:43,287 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 146 executed (106.884 ms) +galaxy.jobs.handler DEBUG 2023-10-24 07:02:48,429 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 147 +tpv.core.entities DEBUG 2023-10-24 07:02:48,465 [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={'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=None, 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 2023-10-24 07:02:48,466 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (147) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 07:02:48,470 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (147) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 07:02:48,485 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (147) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 07:02:48,499 [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 2023-10-24 07:02:48,506 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [147] queued (35.712 ms) +galaxy.jobs.handler INFO 2023-10-24 07:02:48,509 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (147) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 07:02:48,514 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 147 +galaxy.jobs DEBUG 2023-10-24 07:02:48,608 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [147] prepared (78.294 ms) +galaxy.jobs.command_factory INFO 2023-10-24 07:02:48,626 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] 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' '172:/galaxy/server/database/objects/1/b/c/dataset_1bc16717-abea-48f5-8ce7-3882f2b14ae3_files:/galaxy/server/database/objects/1/b/c/dataset_1bc16717-abea-48f5-8ce7-3882f2b14ae3.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 07:02:48,639 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (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 $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 07:02:59,602 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 147: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 07:03:05,559 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 147 finished +galaxy.model.metadata DEBUG 2023-10-24 07:03:05,608 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 172 +galaxy.jobs INFO 2023-10-24 07:03:05,642 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 147 in /galaxy/server/database/jobs_directory/000/147 +galaxy.jobs DEBUG 2023-10-24 07:03:05,675 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 147 executed (99.385 ms) +galaxy.jobs.handler DEBUG 2023-10-24 07:03:06,033 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 148 +tpv.core.entities DEBUG 2023-10-24 07:03:06,072 [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={'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=None, 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 2023-10-24 07:03:06,073 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (148) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 07:03:06,078 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (148) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 07:03:06,093 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (148) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 07:03:06,108 [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 2023-10-24 07:03:06,116 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [148] queued (37.706 ms) +galaxy.jobs.handler INFO 2023-10-24 07:03:06,122 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (148) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 07:03:06,125 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 148 +galaxy.jobs DEBUG 2023-10-24 07:03:06,233 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [148] prepared (88.675 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 07:03:06,234 [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 2023-10-24 07:03:06,234 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.10: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:0b38f50a02650e4ae53cfaa6fa2c599511f9c2c0 +galaxy.tool_util.deps.containers INFO 2023-10-24 07:03:06,448 [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-b99184dc2d32592dd62a87fa4a796c61585788e6:0b38f50a02650e4ae53cfaa6fa2c599511f9c2c0-0,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 07:03:06,469 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/148/tool_script.sh] for tool command [bcftools 2>&1 | grep 'Version:' > /galaxy/server/database/jobs_directory/000/148/outputs/COMMAND_VERSION 2>&1; +export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/1/b/c/dataset_1bc16717-abea-48f5-8ce7-3882f2b14ae3.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools plugin mendelian --output-type 'v' input.vcf.gz --trio "NA00001,NA00002,NA00006" --delete 2> tmp_stderr > '/galaxy/server/database/objects/4/e/c/dataset_4ec2c165-0b2b-4b82-a548-597f3d26841b.dat' && cat tmp_stderr] +galaxy.jobs.runners DEBUG 2023-10-24 07:03:06,482 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (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 $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 07:03:06,492 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 07:03:06,492 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.10: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:0b38f50a02650e4ae53cfaa6fa2c599511f9c2c0 +galaxy.tool_util.deps.containers INFO 2023-10-24 07:03:06,508 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:0b38f50a02650e4ae53cfaa6fa2c599511f9c2c0-0,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 07:03:18,873 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 148: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 07:03:24,669 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 148 finished +galaxy.model.metadata DEBUG 2023-10-24 07:03:24,718 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 173 +galaxy.jobs INFO 2023-10-24 07:03:24,752 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 148 in /galaxy/server/database/jobs_directory/000/148 +galaxy.jobs DEBUG 2023-10-24 07:03:24,791 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 148 executed (105.623 ms) +galaxy.jobs.handler DEBUG 2023-10-24 07:03:26,626 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 149 +tpv.core.entities DEBUG 2023-10-24 07:03:26,662 [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={'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=None, 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 2023-10-24 07:03:26,663 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (149) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 07:03:26,668 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (149) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 07:03:26,682 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (149) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 07:03:26,697 [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 2023-10-24 07:03:26,704 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [149] queued (35.771 ms) +galaxy.jobs.handler INFO 2023-10-24 07:03:26,708 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (149) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 07:03:26,710 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 149 +galaxy.jobs DEBUG 2023-10-24 07:03:26,824 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [149] prepared (96.418 ms) +galaxy.jobs.command_factory INFO 2023-10-24 07:03:26,842 [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 [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/149/registry.xml' '/galaxy/server/database/jobs_directory/000/149/upload_params.json' '174:/galaxy/server/database/objects/e/3/e/dataset_e3e86e2d-0863-4e7b-8eae-3c99abc83b76_files:/galaxy/server/database/objects/e/3/e/dataset_e3e86e2d-0863-4e7b-8eae-3c99abc83b76.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 07:03:26,855 [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 $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 07:03:36,102 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 149: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 07:03:41,746 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 149 finished +galaxy.model.metadata DEBUG 2023-10-24 07:03:41,794 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 174 +galaxy.jobs INFO 2023-10-24 07:03:41,827 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 149 in /galaxy/server/database/jobs_directory/000/149 +galaxy.jobs DEBUG 2023-10-24 07:03:41,868 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 149 executed (106.767 ms) +galaxy.jobs.handler DEBUG 2023-10-24 07:03:43,081 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 150 +tpv.core.entities DEBUG 2023-10-24 07:03:43,120 [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={'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=None, 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 2023-10-24 07:03:43,121 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (150) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 07:03:43,126 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (150) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 07:03:43,143 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (150) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 07:03:43,159 [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 2023-10-24 07:03:43,167 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [150] queued (40.885 ms) +galaxy.jobs.handler INFO 2023-10-24 07:03:43,172 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (150) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 07:03:43,175 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 150 +galaxy.jobs DEBUG 2023-10-24 07:03:43,243 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [150] prepared (51.000 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 07:03:43,244 [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 2023-10-24 07:03:43,244 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.10: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:0b38f50a02650e4ae53cfaa6fa2c599511f9c2c0 +galaxy.tool_util.deps.containers INFO 2023-10-24 07:03:43,276 [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-b99184dc2d32592dd62a87fa4a796c61585788e6:0b38f50a02650e4ae53cfaa6fa2c599511f9c2c0-0,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 07:03:43,296 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/150/tool_script.sh] for tool command [bcftools 2>&1 | grep 'Version:' > /galaxy/server/database/jobs_directory/000/150/outputs/COMMAND_VERSION 2>&1; +export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/e/3/e/dataset_e3e86e2d-0863-4e7b-8eae-3c99abc83b76.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools plugin mendelian --output-type 'v' input.vcf.gz --trio "NA00001,NA00002,NA00006" --list x 2> tmp_stderr > '/galaxy/server/database/objects/4/1/1/dataset_41182423-f124-4411-87d0-0ad43dd66d14.dat' && cat tmp_stderr] +galaxy.jobs.runners DEBUG 2023-10-24 07:03:43,309 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (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 $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 07:03:43,319 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 07:03:43,319 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.10: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:0b38f50a02650e4ae53cfaa6fa2c599511f9c2c0 +galaxy.tool_util.deps.containers INFO 2023-10-24 07:03:43,351 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:0b38f50a02650e4ae53cfaa6fa2c599511f9c2c0-0,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 07:03:48,233 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 150: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 07:03:53,906 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 150 finished +galaxy.model.metadata DEBUG 2023-10-24 07:03:53,955 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 175 +galaxy.jobs INFO 2023-10-24 07:03:53,987 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 150 in /galaxy/server/database/jobs_directory/000/150 +galaxy.jobs DEBUG 2023-10-24 07:03:54,018 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 150 executed (96.302 ms) +galaxy.jobs.handler DEBUG 2023-10-24 07:03:57,513 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 151 +tpv.core.entities DEBUG 2023-10-24 07:03:57,548 [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={'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=None, 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 2023-10-24 07:03:57,549 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (151) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 07:03:57,554 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (151) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 07:03:57,567 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (151) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 07:03:57,581 [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 2023-10-24 07:03:57,587 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [151] queued (33.494 ms) +galaxy.jobs.handler INFO 2023-10-24 07:03:57,591 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (151) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 07:03:57,596 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 151 +galaxy.jobs DEBUG 2023-10-24 07:03:57,692 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [151] prepared (79.592 ms) +galaxy.jobs.command_factory INFO 2023-10-24 07:03:57,710 [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' '176:/galaxy/server/database/objects/6/e/a/dataset_6ea23985-6889-4ff4-9ea9-555b78f90230_files:/galaxy/server/database/objects/6/e/a/dataset_6ea23985-6889-4ff4-9ea9-555b78f90230.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 07:03:57,721 [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.handler DEBUG 2023-10-24 07:03:58,594 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 153, 152 +tpv.core.entities DEBUG 2023-10-24 07:03:58,634 [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={'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=None, 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 2023-10-24 07:03:58,634 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (152) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 07:03:58,639 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (152) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 07:03:58,652 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (152) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 07:03:58,668 [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 2023-10-24 07:03:58,674 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [152] queued (35.470 ms) +galaxy.jobs.handler INFO 2023-10-24 07:03:58,680 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (152) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 07:03:58,682 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 152 +tpv.core.entities DEBUG 2023-10-24 07:03:58,695 [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={'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=None, 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 2023-10-24 07:03:58,696 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (153) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 07:03:58,702 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (153) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 07:03:58,718 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (153) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 07:03:58,743 [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 2023-10-24 07:03:58,750 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [153] queued (47.107 ms) +galaxy.jobs.handler INFO 2023-10-24 07:03:58,755 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (153) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 07:03:58,758 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 153 +galaxy.jobs DEBUG 2023-10-24 07:03:58,793 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [152] prepared (86.964 ms) +galaxy.jobs.command_factory INFO 2023-10-24 07:03:58,824 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] 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' '177:/galaxy/server/database/objects/8/a/8/dataset_8a80c6dc-5582-4d46-addf-f0486328c556_files:/galaxy/server/database/objects/8/a/8/dataset_8a80c6dc-5582-4d46-addf-f0486328c556.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 07:03:58,839 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (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 $return_code" +galaxy.jobs DEBUG 2023-10-24 07:03:58,870 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [153] prepared (88.955 ms) +galaxy.jobs.command_factory INFO 2023-10-24 07:03:58,889 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/153/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/153/registry.xml' '/galaxy/server/database/jobs_directory/000/153/upload_params.json' '178:/galaxy/server/database/objects/8/7/5/dataset_87520b03-2013-489c-867a-4c0c2db23713_files:/galaxy/server/database/objects/8/7/5/dataset_87520b03-2013-489c-867a-4c0c2db23713.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 07:03:58,902 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (153) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 07:04:07,757 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 151: GALAXY_LIB="/galaxy/server/lib"; if [ "$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.runners DEBUG 2023-10-24 07:04:10,879 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] 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 . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2023-10-24 07:04:12,946 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 153: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 07:04:14,121 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 151 finished +galaxy.model.metadata DEBUG 2023-10-24 07:04:14,169 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 176 +galaxy.jobs INFO 2023-10-24 07:04:14,238 [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 2023-10-24 07:04:14,315 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 151 executed (178.674 ms) +galaxy.jobs.runners DEBUG 2023-10-24 07:04:17,695 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 152 finished +galaxy.model.metadata DEBUG 2023-10-24 07:04:17,740 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 177 +galaxy.jobs INFO 2023-10-24 07:04:17,770 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 152 in /galaxy/server/database/jobs_directory/000/152 +galaxy.jobs DEBUG 2023-10-24 07:04:17,802 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 152 executed (92.173 ms) +galaxy.jobs.runners DEBUG 2023-10-24 07:04:19,494 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 153 finished +galaxy.model.metadata DEBUG 2023-10-24 07:04:19,535 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 178 +galaxy.jobs INFO 2023-10-24 07:04:19,568 [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 DEBUG 2023-10-24 07:04:19,609 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 153 executed (102.290 ms) +galaxy.jobs.handler DEBUG 2023-10-24 07:04:20,455 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 154 +tpv.core.entities DEBUG 2023-10-24 07:04:20,508 [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={'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=None, 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 2023-10-24 07:04:20,508 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (154) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 07:04:20,514 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (154) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 07:04:20,529 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (154) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 07:04:20,544 [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 2023-10-24 07:04:20,553 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [154] queued (39.396 ms) +galaxy.jobs.handler INFO 2023-10-24 07:04:20,557 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (154) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 07:04:20,561 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 154 +galaxy.jobs DEBUG 2023-10-24 07:04:20,675 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [154] prepared (98.028 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 07:04:20,676 [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 2023-10-24 07:04:20,676 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/bcftools_csq/1.10: mulled-v2-f7a49c68bd00a9e0147f58c2f0ef0a7bd67e944b:12f91350ec8ab2357494c48ffc38c7c6aa3ef2ca +galaxy.tool_util.deps.containers INFO 2023-10-24 07:04:20,894 [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-f7a49c68bd00a9e0147f58c2f0ef0a7bd67e944b:12f91350ec8ab2357494c48ffc38c7c6aa3ef2ca-0,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 07:04:20,914 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/154/tool_script.sh] for tool command [bcftools 2>&1 | grep 'Version:' > /galaxy/server/database/jobs_directory/000/154/outputs/COMMAND_VERSION 2>&1; +export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/6/e/a/dataset_6ea23985-6889-4ff4-9ea9-555b78f90230.dat' > input.vcf.gz && bcftools index input.vcf.gz && ln -s '/galaxy/server/database/objects/8/a/8/dataset_8a80c6dc-5582-4d46-addf-f0486328c556.dat' ref.fa && samtools faidx ref.fa && bcftools csq --fasta-ref ref.fa --gff-annot '/galaxy/server/database/objects/8/7/5/dataset_87520b03-2013-489c-867a-4c0c2db23713.dat' --ncsq 16 --output-type 'v' input.vcf.gz > '/galaxy/server/database/objects/a/3/2/dataset_a32047c4-713c-422a-9afc-8b00efb3de21.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 07:04:20,927 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (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 $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 07:04:20,937 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 07:04:20,937 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/bcftools_csq/1.10: mulled-v2-f7a49c68bd00a9e0147f58c2f0ef0a7bd67e944b:12f91350ec8ab2357494c48ffc38c7c6aa3ef2ca +galaxy.tool_util.deps.containers INFO 2023-10-24 07:04:20,953 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-f7a49c68bd00a9e0147f58c2f0ef0a7bd67e944b:12f91350ec8ab2357494c48ffc38c7c6aa3ef2ca-0,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 07:04:33,228 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 154: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 07:04:39,066 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 154 finished +galaxy.model.metadata DEBUG 2023-10-24 07:04:39,117 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 179 +galaxy.jobs INFO 2023-10-24 07:04:39,153 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 154 in /galaxy/server/database/jobs_directory/000/154 +galaxy.jobs DEBUG 2023-10-24 07:04:39,185 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 154 executed (101.339 ms) +galaxy.jobs.handler DEBUG 2023-10-24 07:04:43,104 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 155, 156 +tpv.core.entities DEBUG 2023-10-24 07:04:43,145 [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={'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=None, 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 2023-10-24 07:04:43,146 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (155) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 07:04:43,151 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (155) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 07:04:43,166 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (155) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 07:04:43,182 [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 2023-10-24 07:04:43,190 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [155] queued (38.628 ms) +galaxy.jobs.handler INFO 2023-10-24 07:04:43,195 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (155) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 07:04:43,196 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 155 +tpv.core.entities DEBUG 2023-10-24 07:04:43,211 [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={'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=None, 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 2023-10-24 07:04:43,211 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (156) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 07:04:43,217 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (156) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 07:04:43,237 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (156) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 07:04:43,265 [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 2023-10-24 07:04:43,274 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [156] queued (56.562 ms) +galaxy.jobs.handler INFO 2023-10-24 07:04:43,278 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (156) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 07:04:43,284 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 156 +galaxy.jobs DEBUG 2023-10-24 07:04:43,319 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [155] prepared (102.165 ms) +galaxy.jobs.command_factory INFO 2023-10-24 07:04:43,346 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/155/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/155/registry.xml' '/galaxy/server/database/jobs_directory/000/155/upload_params.json' '180:/galaxy/server/database/objects/c/3/3/dataset_c33d11d1-7a53-432f-b42c-6dd60e09e9ae_files:/galaxy/server/database/objects/c/3/3/dataset_c33d11d1-7a53-432f-b42c-6dd60e09e9ae.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 07:04:43,359 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (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 $return_code" +galaxy.jobs DEBUG 2023-10-24 07:04:43,397 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [156] prepared (92.149 ms) +galaxy.jobs.command_factory INFO 2023-10-24 07:04:43,417 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/156/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/156/registry.xml' '/galaxy/server/database/jobs_directory/000/156/upload_params.json' '181:/galaxy/server/database/objects/0/6/b/dataset_06b34c7c-23aa-415c-9b08-96d727af3151_files:/galaxy/server/database/objects/0/6/b/dataset_06b34c7c-23aa-415c-9b08-96d727af3151.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 07:04:43,430 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (156) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 07:04:53,634 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 155: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 07:04:54,677 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] 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 2023-10-24 07:05:00,079 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 155 finished +galaxy.model.metadata DEBUG 2023-10-24 07:05:00,128 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 180 +galaxy.jobs INFO 2023-10-24 07:05:00,165 [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 2023-10-24 07:05:00,200 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 155 executed (103.937 ms) +galaxy.jobs.runners DEBUG 2023-10-24 07:05:01,006 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 156 finished +galaxy.model.metadata DEBUG 2023-10-24 07:05:01,053 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 181 +galaxy.jobs INFO 2023-10-24 07:05:01,086 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 156 in /galaxy/server/database/jobs_directory/000/156 +galaxy.jobs DEBUG 2023-10-24 07:05:01,120 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 156 executed (99.494 ms) +galaxy.jobs.handler DEBUG 2023-10-24 07:05:01,767 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 157 +tpv.core.entities DEBUG 2023-10-24 07:05:01,810 [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={'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=None, 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 2023-10-24 07:05:01,811 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (157) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 07:05:01,816 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (157) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 07:05:01,830 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (157) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 07:05:01,846 [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 2023-10-24 07:05:01,856 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [157] queued (39.639 ms) +galaxy.jobs.handler INFO 2023-10-24 07:05:01,861 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (157) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 07:05:01,863 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 157 +galaxy.jobs DEBUG 2023-10-24 07:05:01,945 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [157] prepared (64.819 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 07:05:01,946 [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 2023-10-24 07:05:01,946 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/vcfcommonsamples/vcfcommonsamples/1.0.0_rc3+galaxy0: vcflib:1.0.0_rc3 +galaxy.tool_util.deps.containers INFO 2023-10-24 07:05:02,228 [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/vcflib:1.0.0_rc3--py37hc088bd4_0,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 07:05:02,247 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/157/tool_script.sh] for tool command [vcfcommonsamples '/galaxy/server/database/objects/c/3/3/dataset_c33d11d1-7a53-432f-b42c-6dd60e09e9ae.dat' '/galaxy/server/database/objects/0/6/b/dataset_06b34c7c-23aa-415c-9b08-96d727af3151.dat' > '/galaxy/server/database/objects/d/0/7/dataset_d07a5a35-5d5d-4cea-a039-7793d457962f.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 07:05:02,261 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (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 $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 07:05:02,271 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 07:05:02,271 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/vcfcommonsamples/vcfcommonsamples/1.0.0_rc3+galaxy0: vcflib:1.0.0_rc3 +galaxy.tool_util.deps.containers INFO 2023-10-24 07:05:02,288 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/vcflib:1.0.0_rc3--py37hc088bd4_0,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 07:05:14,960 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 157: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 07:05:20,776 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 157 finished +galaxy.model.metadata DEBUG 2023-10-24 07:05:20,825 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 182 +galaxy.jobs INFO 2023-10-24 07:05:20,864 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 157 in /galaxy/server/database/jobs_directory/000/157 +galaxy.jobs DEBUG 2023-10-24 07:05:20,902 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 157 executed (109.491 ms) +galaxy.jobs.handler DEBUG 2023-10-24 07:05:24,596 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 158 +tpv.core.entities DEBUG 2023-10-24 07:05:24,633 [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={'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=None, 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 2023-10-24 07:05:24,634 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (158) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 07:05:24,639 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (158) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 07:05:24,654 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (158) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 07:05:24,671 [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 2023-10-24 07:05:24,679 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [158] queued (39.655 ms) +galaxy.jobs.handler INFO 2023-10-24 07:05:24,684 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (158) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 07:05:24,686 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 158 +galaxy.jobs DEBUG 2023-10-24 07:05:24,786 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [158] prepared (83.611 ms) +galaxy.jobs.command_factory INFO 2023-10-24 07:05:24,806 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] 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' '183:/galaxy/server/database/objects/f/5/2/dataset_f5235c93-79b7-4478-825f-0b38a2df2f42_files:/galaxy/server/database/objects/f/5/2/dataset_f5235c93-79b7-4478-825f-0b38a2df2f42.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 07:05:24,820 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (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 $return_code" +galaxy.jobs.runners DEBUG 2023-10-24 07:05:35,204 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 158: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 07:05:40,866 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 158 finished +galaxy.model.metadata DEBUG 2023-10-24 07:05:40,914 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 183 +galaxy.jobs INFO 2023-10-24 07:05:40,947 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 158 in /galaxy/server/database/jobs_directory/000/158 +galaxy.jobs DEBUG 2023-10-24 07:05:40,978 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 158 executed (94.971 ms) +galaxy.jobs.handler DEBUG 2023-10-24 07:05:42,104 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 159 +tpv.core.entities DEBUG 2023-10-24 07:05:42,141 [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={'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=None, 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 2023-10-24 07:05:42,142 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (159) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2023-10-24 07:05:42,146 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (159) Dispatching to k8s runner +galaxy.jobs DEBUG 2023-10-24 07:05:42,160 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (159) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2023-10-24 07:05:42,174 [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 2023-10-24 07:05:42,181 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [159] queued (34.891 ms) +galaxy.jobs.handler INFO 2023-10-24 07:05:42,185 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (159) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2023-10-24 07:05:42,189 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 159 +galaxy.jobs DEBUG 2023-10-24 07:05:42,261 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [159] prepared (54.937 ms) +galaxy.tool_util.deps.containers INFO 2023-10-24 07:05:42,262 [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 2023-10-24 07:05:42,262 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/vcfdistance/vcfdistance/1.0.0_rc3+galaxy0: vcflib:1.0.0_rc3 +galaxy.tool_util.deps.containers INFO 2023-10-24 07:05:42,282 [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/vcflib:1.0.0_rc3--py37hc088bd4_0,type=docker]] +galaxy.jobs.command_factory INFO 2023-10-24 07:05:42,302 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/159/tool_script.sh] for tool command [cat '/galaxy/server/database/objects/f/5/2/dataset_f5235c93-79b7-4478-825f-0b38a2df2f42.dat' | vcfdistance > '/galaxy/server/database/objects/1/0/8/dataset_108eea5c-bec9-4562-a432-15ed5afdfb6e.dat'] +galaxy.jobs.runners DEBUG 2023-10-24 07:05:42,315 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (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 $return_code" +galaxy.tool_util.deps.containers INFO 2023-10-24 07:05:42,325 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2023-10-24 07:05:42,325 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/vcfdistance/vcfdistance/1.0.0_rc3+galaxy0: vcflib:1.0.0_rc3 +galaxy.tool_util.deps.containers INFO 2023-10-24 07:05:42,341 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/vcflib:1.0.0_rc3--py37hc088bd4_0,type=docker]] +galaxy.jobs.runners DEBUG 2023-10-24 07:05:48,342 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 159: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2023-10-24 07:05:54,046 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 159 finished +galaxy.model.metadata DEBUG 2023-10-24 07:05:54,092 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 184 +galaxy.jobs INFO 2023-10-24 07:05:54,131 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 159 in /galaxy/server/database/jobs_directory/000/159 +galaxy.jobs DEBUG 2023-10-24 07:05:54,172 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 159 executed (109.262 ms) diff --git a/reports/anvil-edge/tool-tests/edge-23-10-24-06-08-1/jobs.txt b/reports/anvil-edge/tool-tests/edge-23-10-24-06-08-1/jobs.txt new file mode 100644 index 000000000..08434d17d --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-23-10-24-06-08-1/jobs.txt @@ -0,0 +1,159 @@ +11fb2a0834893de8 ok 2023-10-24T07:05:54.135026 toolshed.g2.bx.psu.edu/repos/devteam/vcfdistance/vcfdistance/1.0.0_rc3+galaxy0 +cc021280a2ddec1b ok 2023-10-24T07:05:40.950273 upload1 +c7d9fee5801aa918 ok 2023-10-24T07:05:20.867261 toolshed.g2.bx.psu.edu/repos/devteam/vcfcommonsamples/vcfcommonsamples/1.0.0_rc3+galaxy0 +081fda218d170895 ok 2023-10-24T07:05:01.090075 upload1 +fb8a865dfbb79992 ok 2023-10-24T07:05:00.168496 upload1 +0170cd6e6911e97e ok 2023-10-24T07:04:39.157174 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/bcftools_csq/1.10 +f6f155cd30b2fe54 ok 2023-10-24T07:04:19.571360 upload1 +70d4db306a0fab2b ok 2023-10-24T07:04:17.773667 upload1 +db8b8af119989393 ok 2023-10-24T07:04:14.242302 upload1 +4dafd9736a46b5aa ok 2023-10-24T07:03:53.990578 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.10 +c41381f06c649741 ok 2023-10-24T07:03:41.831183 upload1 +7b8a8352110e45b6 ok 2023-10-24T07:03:24.755505 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.10 +69510454f39def74 ok 2023-10-24T07:03:05.645078 upload1 +e2c00607622263d9 ok 2023-10-24T07:02:43.255167 toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1 +6d43fcd162a02898 ok 2023-10-24T07:02:31.047701 upload1 +097a88afa78b74af ok 2023-10-24T07:02:12.785049 toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1 +3b8c6b9f6fd7594a ok 2023-10-24T07:01:54.722367 upload1 +8073c888c3a180a0 ok 2023-10-24T07:01:34.421116 toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0 +1c70ec5bc2d319c3 ok 2023-10-24T07:01:20.424039 upload1 +8e26fadd3debc078 ok 2023-10-24T07:01:01.086250 toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0 +04deda8802bf0a5f ok 2023-10-24T07:00:47.921600 upload1 +5902f11b4b6256af ok 2023-10-24T07:00:28.749869 toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0 +7b20b7ac3e79d9df ok 2023-10-24T07:00:15.554498 upload1 +9c5885c0875e8135 error 2023-10-24T06:59:57.255203 toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0 +b24ef8d5e9b69a46 ok 2023-10-24T06:59:51.218096 upload1 +85f23abbadb9fa4e ok 2023-10-24T06:59:31.683521 toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0 +1565539e571bf243 ok 2023-10-24T06:59:19.758377 upload1 +cefc52d14cb4f186 ok 2023-10-24T06:59:00.494656 toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0 +478fd91263330e3d ok 2023-10-24T06:58:47.322233 upload1 +911c99275447de60 error 2023-10-24T06:58:29.896507 upload1 +1fba13c59ee144a3 ok 2023-10-24T06:58:18.537324 toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0 +26f3b5ab5b8463e6 ok 2023-10-24T06:58:04.643270 upload1 +606f27db86776ff6 ok 2023-10-24T06:58:03.616089 upload1 +0b46f4832cf85eda ok 2023-10-24T06:57:43.944849 toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0 +923804dda71f7317 ok 2023-10-24T06:57:31.336902 upload1 +e219d9fbc5abf3d2 ok 2023-10-24T06:57:30.186214 upload1 +2508872f2388dfce ok 2023-10-24T06:57:11.435078 toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0 +f5ec43b567333743 ok 2023-10-24T06:56:59.207764 upload1 +41a888e05d248b65 ok 2023-10-24T06:56:39.978340 toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0 +a4c7f04fd58da044 ok 2023-10-24T06:56:27.388496 upload1 +4f01926b6271168e ok 2023-10-24T06:56:26.319331 upload1 +c2817ae83258538f ok 2023-10-24T06:56:07.302671 toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0 +771c81d420c40696 ok 2023-10-24T06:55:48.568998 upload1 +c75606a77a9e6598 ok 2023-10-24T06:55:47.533133 upload1 +e3e10d2227fe51a8 ok 2023-10-24T06:55:25.720788 toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_parameter_iterator/scanpy_parameter_iterator/0.0.1+galaxy0 +eed4de4bbc4a1574 error 2023-10-24T06:54:44.082001 toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_exprs_freq/scater_plot_exprs_freq/1.12.2 +d48aa8293f429b21 ok 2023-10-24T06:53:56.158275 upload1 +c1e606af192f37db ok 2023-10-24T06:53:32.772252 toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2 +bc26de549bbb396e ok 2023-10-24T06:53:19.203987 upload1 +406a5736390cc0b2 ok 2023-10-24T06:53:18.228545 upload1 +bc85f495b65ed0b2 ok 2023-10-24T06:52:58.403320 toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2 +5a2866febb346be8 ok 2023-10-24T06:52:43.033034 upload1 +5d4f689fa8c33fb4 ok 2023-10-24T06:52:41.218953 upload1 +1b14fde99d7533f4 error 2023-10-24T06:52:19.846117 toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.3 +587dc591d413742a ok 2023-10-24T06:52:05.057545 upload1 +27b2002a21d335bb ok 2023-10-24T06:52:04.966355 upload1 +87a5c83e33288d48 ok 2023-10-24T06:51:44.147712 upload1 +84c1567a3601922d ok 2023-10-24T06:51:41.241887 upload1 +3e6ca2f14c25c690 ok 2023-10-24T06:51:22.293867 toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1 +0fe01ba1233b8e05 ok 2023-10-24T06:51:09.466123 upload1 +6cb0104eb5f2f3a0 ok 2023-10-24T06:51:06.598708 upload1 +a0e548e7ae2c7319 ok 2023-10-24T06:51:03.904132 upload1 +d06bda1d0dc205fb ok 2023-10-24T06:50:44.217522 toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1 +3e2b7763c606bc10 ok 2023-10-24T06:50:31.242373 upload1 +923133f6c61916cc ok 2023-10-24T06:50:30.348706 upload1 +8d849f168ffcc439 ok 2023-10-24T06:50:09.938567 toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1 +a06c3faa3e996663 ok 2023-10-24T06:49:56.686530 upload1 +119c61687da3b62f ok 2023-10-24T06:49:54.876201 upload1 +bcb59a5c2249df5d ok 2023-10-24T06:49:53.753597 upload1 +35e4ae728060a1bc ok 2023-10-24T06:49:31.315785 toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1 +72e0b1c8686ab46e ok 2023-10-24T06:49:15.839707 upload1 +b5c4717d6462b9cd ok 2023-10-24T06:49:13.318158 upload1 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toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +d054e2c56e0372b2 ok 2023-10-24T06:45:07.179269 upload1 +7a0fe7d625813b63 ok 2023-10-24T06:44:48.829675 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +bcf74409967b222c ok 2023-10-24T06:44:35.742261 upload1 +1a4dc9cafea277e5 ok 2023-10-24T06:44:17.574774 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +27db995cc6075875 ok 2023-10-24T06:44:05.393495 upload1 +b0ddf54a3dc91e9b ok 2023-10-24T06:43:47.294461 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +3080e1caaead61ad ok 2023-10-24T06:43:34.945915 upload1 +a0d28c4ceebadaff ok 2023-10-24T06:43:15.854691 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +614cec69f1f0adfc ok 2023-10-24T06:43:02.520242 upload1 +90d4582ed632427d ok 2023-10-24T06:42:44.247140 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +56880add842a3669 ok 2023-10-24T06:42:30.358085 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toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +78f45309268aaef0 ok 2023-10-24T06:39:06.372455 upload1 +b1b34c50f9999259 ok 2023-10-24T06:38:48.155887 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +7f451aa57262a321 ok 2023-10-24T06:38:36.065056 upload1 +70e6c596681d15ea ok 2023-10-24T06:38:16.771552 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +764fae55a12043c9 ok 2023-10-24T06:38:04.387957 upload1 +81990d627ca10816 ok 2023-10-24T06:37:46.352300 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +11d17061120b964f ok 2023-10-24T06:37:33.055016 upload1 +2cacb424dabb719d ok 2023-10-24T06:37:13.888407 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +2158b7cdd72d2947 ok 2023-10-24T06:37:00.879561 upload1 +694d325998e95736 ok 2023-10-24T06:36:42.510482 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +bc30ffaea2795f76 ok 2023-10-24T06:36:30.538812 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+ beta.kubernetes.io/instance-type=e2-custom-20-81920 + beta.kubernetes.io/os=linux + cloud.google.com/gke-boot-disk=pd-balanced + cloud.google.com/gke-container-runtime=containerd + cloud.google.com/gke-cpu-scaling-level=20 + 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/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-edge-23-10-24-06-08-default-pool-7d913280-zv8h + 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: 7932187416354021693 + csi.volume.kubernetes.io/nodeid: + {"cvmfs.csi.cern.ch":"gke-edge-23-10-24-06-08-default-pool-7d913280-zv8h","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: Tue, 24 Oct 2023 06:13:51 +0000 +Taints: +Unschedulable: false +Lease: + HolderIdentity: gke-edge-23-10-24-06-08-default-pool-7d913280-zv8h + AcquireTime: + RenewTime: Tue, 24 Oct 2023 07:06:49 +0000 +Conditions: + Type Status LastHeartbeatTime LastTransitionTime Reason Message + ---- ------ ----------------- ------------------ ------ ------- + ReadonlyFilesystem False Tue, 24 Oct 2023 07:04:01 +0000 Tue, 24 Oct 2023 06:13:54 +0000 FilesystemIsNotReadOnly Filesystem is not read-only + FrequentUnregisterNetDevice False Tue, 24 Oct 2023 07:04:01 +0000 Tue, 24 Oct 2023 06:13:54 +0000 NoFrequentUnregisterNetDevice node is functioning properly + CorruptDockerOverlay2 False Tue, 24 Oct 2023 07:04:01 +0000 Tue, 24 Oct 2023 06:13:54 +0000 NoCorruptDockerOverlay2 docker overlay2 is functioning properly + FrequentKubeletRestart False Tue, 24 Oct 2023 07:04:01 +0000 Tue, 24 Oct 2023 06:13:54 +0000 NoFrequentKubeletRestart kubelet is functioning properly + FrequentDockerRestart False Tue, 24 Oct 2023 07:04:01 +0000 Tue, 24 Oct 2023 06:13:54 +0000 NoFrequentDockerRestart docker is functioning properly + FrequentContainerdRestart False Tue, 24 Oct 2023 07:04:01 +0000 Tue, 24 Oct 2023 06:13:54 +0000 NoFrequentContainerdRestart containerd is functioning properly + KernelDeadlock False Tue, 24 Oct 2023 07:04:01 +0000 Tue, 24 Oct 2023 06:13:54 +0000 KernelHasNoDeadlock kernel has no deadlock + NetworkUnavailable False Tue, 24 Oct 2023 06:13:52 +0000 Tue, 24 Oct 2023 06:13:52 +0000 RouteCreated NodeController create implicit route + MemoryPressure False Tue, 24 Oct 2023 07:05:24 +0000 Tue, 24 Oct 2023 06:12:44 +0000 KubeletHasSufficientMemory kubelet has sufficient memory available + DiskPressure False Tue, 24 Oct 2023 07:05:24 +0000 Tue, 24 Oct 2023 06:12:44 +0000 KubeletHasNoDiskPressure kubelet has no disk pressure + PIDPressure False Tue, 24 Oct 2023 07:05:24 +0000 Tue, 24 Oct 2023 06:12:44 +0000 KubeletHasSufficientPID kubelet has sufficient PID available + Ready True Tue, 24 Oct 2023 07:05:24 +0000 Tue, 24 Oct 2023 06:13:52 +0000 KubeletReady kubelet is posting ready status. AppArmor enabled +Addresses: + InternalIP: 10.142.15.194 + ExternalIP: 34.138.180.48 + InternalDNS: gke-edge-23-10-24-06-08-default-pool-7d913280-zv8h.c.anvil-and-terra-development.internal + Hostname: gke-edge-23-10-24-06-08-default-pool-7d913280-zv8h.c.anvil-and-terra-development.internal +Capacity: + attachable-volumes-gce-pd: 127 + cpu: 20 + ephemeral-storage: 98831908Ki + hugepages-1Gi: 0 + hugepages-2Mi: 0 + memory: 82375736Ki + pods: 110 +Allocatable: + attachable-volumes-gce-pd: 127 + cpu: 19880m + ephemeral-storage: 47060071478 + hugepages-1Gi: 0 + hugepages-2Mi: 0 + memory: 75561016Ki + pods: 110 +System Info: + Machine ID: 46686247295629b2b11e210249dd98db + System UUID: 46686247-2956-29b2-b11e-210249dd98db + Boot ID: 97dcca5a-8d91-4c6c-866f-842a0622f1bd + Kernel Version: 5.10.176+ + OS Image: Container-Optimized OS from Google + Operating System: linux + Architecture: amd64 + Container Runtime Version: containerd://1.6.20 + Kubelet Version: v1.24.16-gke.500 + Kube-Proxy Version: v1.24.16-gke.500 +PodCIDR: 10.108.0.0/24 +PodCIDRs: 10.108.0.0/24 +ProviderID: gce://anvil-and-terra-development/us-east1-b/gke-edge-23-10-24-06-08-default-pool-7d913280-zv8h +Non-terminated Pods: (24 in total) + Namespace Name CPU Requests CPU Limits Memory Requests Memory Limits Age + --------- ---- ------------ ---------- --------------- ------------- --- + edge-23-10-24-06-08-1 edge-23-10-24-06-08-1-cvmfscsi-controllerplugin-9c9957b45-nlgvj 0 (0%) 0 (0%) 0 (0%) 0 (0%) 50m + edge-23-10-24-06-08-1 edge-23-10-24-06-08-1-cvmfscsi-nodeplugin-wvsps 0 (0%) 0 (0%) 0 (0%) 0 (0%) 45m + edge-23-10-24-06-08-1 edge-23-10-24-06-08-1-galaxy-celery-5597dfd99d-9lm7w 500m (2%) 2 (10%) 2G (2%) 8G (10%) 49m + edge-23-10-24-06-08-1 edge-23-10-24-06-08-1-galaxy-celery-beat-678bd7676c-9d8l9 500m (2%) 2 (10%) 2G (2%) 8G (10%) 49m + edge-23-10-24-06-08-1 edge-23-10-24-06-08-1-galaxy-galaxy-postgres-0 250m (1%) 0 (0%) 256Mi (0%) 0 (0%) 49m + edge-23-10-24-06-08-1 edge-23-10-24-06-08-1-galaxy-job-0-5b545b9bf9-ss9gt 500m (2%) 2 (10%) 2G (2%) 8G (10%) 49m + edge-23-10-24-06-08-1 edge-23-10-24-06-08-1-galaxy-nginx-7fbf587878-gg9vm 100m (0%) 2 (10%) 500M (0%) 3G (3%) 49m + edge-23-10-24-06-08-1 edge-23-10-24-06-08-1-galaxy-rabbitmq-server-server-0 1 (5%) 2 (10%) 2Gi (2%) 2Gi (2%) 49m + edge-23-10-24-06-08-1 edge-23-10-24-06-08-1-galaxy-web-5f95fb7ccf-fsfmt 500m (2%) 2 (10%) 2G (2%) 8G (10%) 49m + edge-23-10-24-06-08-1 edge-23-10-24-06-08-1-galaxy-workflow-796ffd55d5-qth5h 500m (2%) 2 (10%) 2G (2%) 8G (10%) 49m + edge-23-10-24-06-08-1 edge-23-10-24-06-08-1-nfs-0 0 (0%) 0 (0%) 0 (0%) 0 (0%) 50m + edge-23-10-24-06-08-1 edge-23-10-24-06-08-1-rabbitmq-5886bfc5d8-4hq8j 0 (0%) 0 (0%) 0 (0%) 0 (0%) 50m + edge-23-10-24-06-08-1 edge-23-10-24-06-08-1-rabbitmq-messaging-topology-operatorjh6wv 0 (0%) 0 (0%) 0 (0%) 0 (0%) 50m + kube-system event-exporter-gke-857959888b-87csb 0 (0%) 0 (0%) 0 (0%) 0 (0%) 54m + kube-system fluentbit-gke-h9kfl 100m (0%) 0 (0%) 200Mi (0%) 500Mi (0%) 53m + kube-system gke-metrics-agent-z2sjk 8m (0%) 0 (0%) 110Mi (0%) 110Mi (0%) 53m + kube-system konnectivity-agent-5db9c54-lk6nl 10m (0%) 0 (0%) 30Mi (0%) 125Mi (0%) 53m + kube-system konnectivity-agent-autoscaler-7d9fbfd578-thfwd 10m (0%) 0 (0%) 10M (0%) 0 (0%) 53m + kube-system kube-dns-864d87b455-l97zn 260m (1%) 0 (0%) 110Mi (0%) 210Mi (0%) 54m + kube-system kube-dns-autoscaler-9f89698b6-m6gsd 20m (0%) 0 (0%) 10Mi (0%) 0 (0%) 54m + kube-system kube-proxy-gke-edge-23-10-24-06-08-default-pool-7d913280-zv8h 100m (0%) 0 (0%) 0 (0%) 0 (0%) 51m + kube-system l7-default-backend-6dc845c45d-qz58l 10m (0%) 0 (0%) 20Mi (0%) 0 (0%) 53m + kube-system metrics-server-v0.5.2-6bf845b67f-lnx7b 48m (0%) 43m (0%) 105Mi (0%) 355Mi (0%) 52m + kube-system pdcsi-node-8vvbl 10m (0%) 0 (0%) 20Mi (0%) 100Mi (0%) 53m +Allocated resources: + (Total limits may be over 100 percent, i.e., overcommitted.) + Resource Requests Limits + -------- -------- ------ + cpu 4426m (22%) 14043m (70%) + memory 13560307584 (17%) 46615490048 (60%) + ephemeral-storage 35Gi (79%) 200Gi (456%) + hugepages-1Gi 0 (0%) 0 (0%) + hugepages-2Mi 0 (0%) 0 (0%) + attachable-volumes-gce-pd 0 0 +Events: + Type Reason Age From Message + ---- ------ ---- ---- ------- + Normal Starting 53m kube-proxy + Normal NodeAllocatableEnforced 55m kubelet Updated Node Allocatable limit across pods + Normal Starting 55m kubelet Starting kubelet. + Warning InvalidDiskCapacity 55m kubelet invalid capacity 0 on image filesystem + Normal NodeHasNoDiskPressure 54m (x7 over 55m) kubelet Node gke-edge-23-10-24-06-08-default-pool-7d913280-zv8h status is now: NodeHasNoDiskPressure + Normal NodeHasSufficientPID 54m (x7 over 55m) kubelet Node gke-edge-23-10-24-06-08-default-pool-7d913280-zv8h status is now: NodeHasSufficientPID + Normal NodeHasSufficientMemory 54m (x8 over 55m) kubelet Node gke-edge-23-10-24-06-08-default-pool-7d913280-zv8h status is now: NodeHasSufficientMemory + Normal RegisteredNode 52m node-controller Node gke-edge-23-10-24-06-08-default-pool-7d913280-zv8h event: Registered Node gke-edge-23-10-24-06-08-default-pool-7d913280-zv8h in Controller + Warning NodeRegistrationCheckerStart 52m node-registration-checker-monitor Tue Oct 24 06:10:52 UTC 2023 - ** Starting Node Registration Checker ** + Warning ContainerdStart 52m (x2 over 52m) systemd-monitor Starting containerd container runtime... + Warning DockerStart 52m (x3 over 52m) systemd-monitor Starting Docker Application Container Engine... + Warning KubeletStart 52m systemd-monitor Started Kubernetes kubelet. + Warning NodeSysctlChange 52m sysctl-monitor {"unmanaged": {"net.netfilter.nf_conntrack_buckets": "163840"}} + Warning NodeRegistrationCheckerDidNotRunChecks 48m node-registration-checker-monitor Tue Oct 24 06:17:53 UTC 2023 - ** Node ready and registered. ** diff --git a/reports/anvil-edge/tool-tests/edge-23-10-24-06-08-1/results.html b/reports/anvil-edge/tool-tests/edge-23-10-24-06-08-1/results.html new file mode 100644 index 000000000..28e26ed3f --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-23-10-24-06-08-1/results.html @@ -0,0 +1,291 @@ + + + + + + + Test Results (powered by Planemo) + + + + + + + + + + +
+
+
+
+ + + + + + + \ No newline at end of file diff --git a/reports/anvil-edge/tool-tests/edge-23-10-24-06-08-1/results.json b/reports/anvil-edge/tool-tests/edge-23-10-24-06-08-1/results.json new file mode 100644 index 000000000..e6eed0da5 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-23-10-24-06-08-1/results.json @@ -0,0 +1 @@ +{"version": "0.1", "suitename": "Galaxy Tool Tests", "results": {"total": 72, "errors": 4, "failures": 5, "skips": 1}, "tests": [{"id": "bcftools_csq/1.10-0", "has_data": true, "data": {"tool_id": "bcftools_csq", "tool_version": "1.10", "test_index": 0, "time_seconds": 43.697279930114746, "inputs": {"input_file": {"src": "hda", "id": "3dcbb2d7cdd8dc15"}, "sec_required|reference_source|fasta_ref": {"src": "hda", "id": "8525be4c85bdcda0"}, "sec_required|reference_source|reference_source_selector": "history", "sec_required|gff_annot": {"src": "hda", "id": "e9c073d6c5d36530"}, "output_type": "v"}, "job": {"model_class": "Job", "id": "0170cd6e6911e97e", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T07:04:39.157174", "create_time": "2023-10-24T07:04:20.208390", "galaxy_version": "23.1", "command_version": "Version: 1.10.2 (using htslib 1.10.2)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/bcftools_csq/1.10", "history_id": "b8e3c9423bdc89f6", "external_id": "gxy-xcpbr", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/6/e/a/dataset_6ea23985-6889-4ff4-9ea9-555b78f90230.dat' > input.vcf.gz && bcftools index input.vcf.gz && ln -s '/galaxy/server/database/objects/8/a/8/dataset_8a80c6dc-5582-4d46-addf-f0486328c556.dat' ref.fa && samtools faidx ref.fa && bcftools csq --fasta-ref ref.fa --gff-annot '/galaxy/server/database/objects/8/7/5/dataset_87520b03-2013-489c-867a-4c0c2db23713.dat' --ncsq 16 --output-type 'v' input.vcf.gz > '/galaxy/server/database/objects/a/3/2/dataset_a32047c4-713c-422a-9afc-8b00efb3de21.dat'", "traceback": null, "params": {"__input_ext": "\"vcf\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "sec_subset": "{\"invert_samples\": false, \"invert_samples_file\": false, \"samples\": \"\", \"samples_file\": null}", "sec_restrict": "{\"exclude\": null, \"include\": null, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}}", "sec_csq_opts": "{\"custom_tag\": \"\", \"local_csq\": false, \"ncsq\": \"16\", \"phase\": null}", "sec_required": "{\"gff_annot\": {\"values\": [{\"id\": 178, \"src\": \"hda\"}]}, \"reference_source\": {\"__current_case__\": 1, \"fasta_ref\": {\"values\": [{\"id\": 177, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}}"}, "inputs": {"input_file": {"id": "3dcbb2d7cdd8dc15", "src": "hda", "uuid": "6ea23985-6889-4ff4-9ea9-555b78f90230"}, "sec_required|reference_source|fasta_ref": {"id": "8525be4c85bdcda0", "src": "hda", "uuid": "8a80c6dc-5582-4d46-addf-f0486328c556"}, "sec_required|gff_annot": {"id": "e9c073d6c5d36530", "src": "hda", "uuid": "87520b03-2013-489c-867a-4c0c2db23713"}}, "outputs": {"output_file": {"id": "e82d291c83a9fea6", "src": "hda", "uuid": "a32047c4-713c-422a-9afc-8b00efb3de21"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Parsing /galaxy/server/database/objects/8/7/5/dataset_87520b03-2013-489c-867a-4c0c2db23713.dat ...\nIndexed 4 transcripts, 10 exons, 10 CDSs, 6 UTRs\nCalling...\n", "job_stdout": "", "job_stderr": "", "stderr": "Parsing /galaxy/server/database/objects/8/7/5/dataset_87520b03-2013-489c-867a-4c0c2db23713.dat ...\nIndexed 4 transcripts, 10 exons, 10 CDSs, 6 UTRs\nCalling...\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": "2023-10-24 07:04:27", "plugin": "core", "name": "end_epoch", "raw_value": "1698131067.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 07:04:27", "plugin": "core", "name": "start_epoch", "raw_value": "1698131067.0000000"}, {"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_csq/1.10-1", "has_data": true, "data": {"tool_id": "bcftools_csq", "tool_version": "1.10", "test_index": 1, "status": "skip"}}, {"id": "bcftools_plugin_mendelian/1.10-0", "has_data": true, "data": {"tool_id": "bcftools_plugin_mendelian", "tool_version": "1.10", "test_index": 0, "time_seconds": 38.25355505943298, "inputs": {"input_file": {"src": "hda", "id": "4c5ab01d79d17dc6"}, "sec_plugin|trios|mother": "NA00001", "sec_plugin|trios|father": "NA00002", "sec_plugin|trios|child": "NA00006", "sec_plugin|trios|trios_src": "trio", "sec_plugin|mode": "delete", "output_type": "v"}, "job": {"model_class": "Job", "id": "7b8a8352110e45b6", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T07:03:24.755505", "create_time": "2023-10-24T07:03:05.920064", "galaxy_version": "23.1", "command_version": "Version: 1.10.2 (using htslib 1.10.2)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.10", "history_id": "b8e3c9423bdc89f6", "external_id": "gxy-9k9gb", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/1/b/c/dataset_1bc16717-abea-48f5-8ce7-3882f2b14ae3.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools plugin mendelian --output-type 'v' input.vcf.gz --trio \"NA00001,NA00002,NA00006\" --delete 2> tmp_stderr > '/galaxy/server/database/objects/4/e/c/dataset_4ec2c165-0b2b-4b82-a548-597f3d26841b.dat' && cat tmp_stderr", "traceback": null, "params": {"__input_ext": "\"vcf\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "sec_plugin": "{\"mode\": \"delete\", \"trios\": {\"__current_case__\": 0, \"child\": \"NA00006\", \"father\": \"NA00002\", \"mother\": \"NA00001\", \"trios_src\": \"trio\"}}", "sec_restrict": "{\"exclude\": null, \"include\": null, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}}"}, "inputs": {"input_file": {"id": "4c5ab01d79d17dc6", "src": "hda", "uuid": "1bc16717-abea-48f5-8ce7-3882f2b14ae3"}}, "outputs": {"output_file": {"id": "629c8721dcd03043", "src": "hda", "uuid": "4ec2c165-0b2b-4b82-a548-597f3d26841b"}}, "output_collections": {}, "tool_stdout": "# [1]nOK\t[2]nBad\t[3]nSkipped\t[4]Trio (mother,father,child)\n20\t13\t0\tNA00001,NA00002,NA00006\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "# [1]nOK\t[2]nBad\t[3]nSkipped\t[4]Trio (mother,father,child)\n20\t13\t0\tNA00001,NA00002,NA00006\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": "2023-10-24 07:03:12", "plugin": "core", "name": "end_epoch", "raw_value": "1698130992.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 07:03:12", "plugin": "core", "name": "start_epoch", "raw_value": "1698130992.0000000"}, {"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_plugin_mendelian/1.10-1", "has_data": true, "data": {"tool_id": "bcftools_plugin_mendelian", "tool_version": "1.10", "test_index": 1, "time_seconds": 28.8156795501709, "inputs": {"input_file": {"src": "hda", "id": "aacf167083658b09"}, "sec_plugin|trios|mother": "NA00001", "sec_plugin|trios|father": "NA00002", "sec_plugin|trios|child": "NA00006", "sec_plugin|trios|trios_src": "trio", "sec_plugin|mode": "x", "output_type": "v"}, "job": {"model_class": "Job", "id": "4dafd9736a46b5aa", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T07:03:53.990578", "create_time": "2023-10-24T07:03:42.083601", "galaxy_version": "23.1", "command_version": "Version: 1.10.2 (using htslib 1.10.2)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.10", "history_id": "b8e3c9423bdc89f6", "external_id": "gxy-n9hcf", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/e/3/e/dataset_e3e86e2d-0863-4e7b-8eae-3c99abc83b76.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools plugin mendelian --output-type 'v' input.vcf.gz --trio \"NA00001,NA00002,NA00006\" --list x 2> tmp_stderr > '/galaxy/server/database/objects/4/1/1/dataset_41182423-f124-4411-87d0-0ad43dd66d14.dat' && cat tmp_stderr", "traceback": null, "params": {"__input_ext": "\"vcf\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "sec_plugin": "{\"mode\": \"x\", \"trios\": {\"__current_case__\": 0, \"child\": \"NA00006\", \"father\": \"NA00002\", \"mother\": \"NA00001\", \"trios_src\": \"trio\"}}", "sec_restrict": "{\"exclude\": null, \"include\": null, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}}"}, "inputs": {"input_file": {"id": "aacf167083658b09", "src": "hda", "uuid": "e3e86e2d-0863-4e7b-8eae-3c99abc83b76"}}, "outputs": {"output_file": {"id": "6446a223a28eb7b4", "src": "hda", "uuid": "41182423-f124-4411-87d0-0ad43dd66d14"}}, "output_collections": {}, "tool_stdout": "# [1]nOK\t[2]nBad\t[3]nSkipped\t[4]Trio (mother,father,child)\n20\t13\t0\tNA00001,NA00002,NA00006\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "# [1]nOK\t[2]nBad\t[3]nSkipped\t[4]Trio (mother,father,child)\n20\t13\t0\tNA00001,NA00002,NA00006\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": "2023-10-24 07:03:44", "plugin": "core", "name": "end_epoch", "raw_value": "1698131024.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 07:03:44", "plugin": "core", "name": "start_epoch", "raw_value": "1698131024.0000000"}, {"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": "column_remove_by_header/0.0.1-0", "has_data": true, "data": {"tool_id": "column_remove_by_header", "tool_version": "0.0.1", "test_index": 0, "time_seconds": 36.93518090248108, "inputs": {"input_tabular": {"src": "hda", "id": "42f5463204ed888d"}, "headers_0|name": "a", "keep_columns": false, "strip_characters": "#"}, "job": {"model_class": "Job", "id": "097a88afa78b74af", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T07:02:12.785049", "create_time": "2023-10-24T07:01:55.045939", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1", "history_id": "b8e3c9423bdc89f6", "external_id": "gxy-gwdff", "command_line": "python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/372967836e98/column_remove_by_header/column_remove_by_header.py' '/galaxy/server/database/objects/e/5/6/dataset_e5646f80-8635-4eea-ba89-be835a6ec77e.dat' '/galaxy/server/database/objects/8/1/f/dataset_81f936fb-efd2-4748-84f1-2141671dece9.dat' '\t' '' '#' 'a'", "traceback": null, "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "strip_characters": "\"#\"", "keep_columns": "false", "headers": "[{\"__index__\": 0, \"name\": \"a\"}]"}, "inputs": {"input_tabular": {"id": "42f5463204ed888d", "src": "hda", "uuid": "e5646f80-8635-4eea-ba89-be835a6ec77e"}}, "outputs": {"output_tabular": {"id": "ef4fa31d162801f1", "src": "hda", "uuid": "81f936fb-efd2-4748-84f1-2141671dece9"}}, "output_collections": {}, "tool_stdout": "Kept 3 of 4 columns.\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "Kept 3 of 4 columns.\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": "2023-10-24 07:02:02", "plugin": "core", "name": "end_epoch", "raw_value": "1698130922.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 07:02:02", "plugin": "core", "name": "start_epoch", "raw_value": "1698130922.0000000"}, {"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": "column_remove_by_header/0.0.1-1", "has_data": true, "data": {"tool_id": "column_remove_by_header", "tool_version": "0.0.1", "test_index": 1, "time_seconds": 30.463411569595337, "inputs": {"input_tabular": {"src": "hda", "id": "27cf0dc2ae19b90b"}, "headers_0|name": "KEY", "headers_1|name": "a", "keep_columns": true, "strip_characters": "#"}, "job": {"model_class": "Job", "id": "e2c00607622263d9", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T07:02:43.255167", "create_time": "2023-10-24T07:02:31.561835", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1", "history_id": "b8e3c9423bdc89f6", "external_id": "gxy-jzfcg", "command_line": "python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/372967836e98/column_remove_by_header/column_remove_by_header.py' '/galaxy/server/database/objects/1/2/2/dataset_1229407f-2db8-459e-a147-5e72cc6ce2d7.dat' '/galaxy/server/database/objects/6/1/0/dataset_6104ce47-eeb0-432e-a8a9-3a4aca13845a.dat' '\t' '--keep' '#' 'KEY' 'a'", "traceback": null, "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "strip_characters": "\"#\"", "keep_columns": "true", "headers": "[{\"__index__\": 0, \"name\": \"KEY\"}, {\"__index__\": 1, \"name\": \"a\"}]"}, "inputs": {"input_tabular": {"id": "27cf0dc2ae19b90b", "src": "hda", "uuid": "1229407f-2db8-459e-a147-5e72cc6ce2d7"}}, "outputs": {"output_tabular": {"id": "9c18ca452cad57fc", "src": "hda", "uuid": "6104ce47-eeb0-432e-a8a9-3a4aca13845a"}}, "output_collections": {}, "tool_stdout": "Kept 2 of 4 columns.\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "Kept 2 of 4 columns.\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": "2023-10-24 07:02:33", "plugin": "core", "name": "end_epoch", "raw_value": "1698130953.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 07:02:33", "plugin": "core", "name": "start_epoch", "raw_value": "1698130953.0000000"}, {"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": "deeptools_bigwig_compare/3.3.2.0.0-0", "has_data": true, "data": {"tool_id": "deeptools_bigwig_compare", "tool_version": "3.3.2.0.0", "test_index": 0, "time_seconds": 64.87193584442139, "inputs": {"bigwigFile1": {"src": "hda", "id": "77276f690f763f22"}, "bigwigFile2": {"src": "hda", "id": "77276f690f763f22"}, "comparison|comparison_select": "ratio", "outFileFormat": "bigwig", "advancedOpt|showAdvancedOpt": "no"}, "job": {"model_class": "Job", "id": "9c4723942930224c", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T06:27:41.876681", "create_time": "2023-10-24T06:26:57.062805", "galaxy_version": "23.1", "command_version": "bigwigCompare 3.3.2", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/3.3.2.0.0", "history_id": "b8e3c9423bdc89f6", "external_id": "gxy-grbxv", "command_line": "bigwigCompare --numberOfProcessors \"${GALAXY_SLOTS:-4}\" --bigwig1 '/galaxy/server/database/objects/4/7/2/dataset_472dff6b-09b1-42fc-bc84-bddeaffd01d7.dat' --bigwig2 '/galaxy/server/database/objects/4/7/2/dataset_472dff6b-09b1-42fc-bc84-bddeaffd01d7.dat' --outFileName '/galaxy/server/database/objects/1/6/f/dataset_16f915b4-2906-49e3-a927-34ae8bb2136b.dat' --outFileFormat 'bigwig' --operation ratio --pseudocount 1 1", "traceback": null, "params": {"comparison": "{\"__current_case__\": 1, \"comparison_select\": \"ratio\", \"pseudocount\": \"1 1\"}", "outFileFormat": "\"bigwig\"", "region": "\"\"", "advancedOpt": 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'/galaxy/server/database/objects/7/9/1/dataset_791fcede-e78a-48eb-9af5-10c8a8c3f59b.dat' solexa '/galaxy/server/database/objects/5/3/4/dataset_5346666b-a0db-43a9-a06e-8e03852a8b42.dat' cssanger None summarize_input --fix-id", "traceback": null, "params": {"__input_ext": "\"fastq\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "options_type": "{\"__current_case__\": 1, \"fix_id\": true, \"force_quality_encoding\": \"None\", \"options_type_selector\": \"advanced\", \"output_type\": \"cssanger\", \"summarize_input\": \"summarize_input\"}", "input_type": "\"solexa\""}, "inputs": {"input_file": {"id": "764fae55a12043c9", "src": "hda", "uuid": "791fcede-e78a-48eb-9af5-10c8a8c3f59b"}}, "outputs": {"output_file": {"id": "70e6c596681d15ea", "src": "hda", "uuid": "5346666b-a0db-43a9-a06e-8e03852a8b42"}}, "output_collections": {}, "tool_stdout": "Groomed 2 solexa reads into cssanger reads.\nConverted between Solexa and PHRED scores.\nBased upon quality and sequence, the input data is valid for: solexa, solexa.gz, solexa.bz2, sanger, sanger.gz, sanger.bz2\nInput ASCII range: ';'(59) - '~'(126)\nInput decimal range: -5 - 62\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "Groomed 2 solexa reads into cssanger reads.\nConverted between Solexa and PHRED scores.\nBased upon quality and sequence, the input data is valid for: solexa, solexa.gz, solexa.bz2, sanger, sanger.gz, sanger.bz2\nInput ASCII range: ';'(59) - '~'(126)\nInput decimal range: -5 - 62\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": "2023-10-24 06:38:06", "plugin": "core", "name": "end_epoch", "raw_value": "1698129486.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 06:38:06", "plugin": "core", "name": "start_epoch", "raw_value": "1698129486.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "fastq_groomer/1.1.5-2", "has_data": true, "data": {"tool_id": "fastq_groomer", "tool_version": "1.1.5", "test_index": 2, "time_seconds": 22.671237468719482, "inputs": {"input_file": {"src": "hda", "id": "c9eeda56cd2b8988"}, "input_type": "sanger", "options_type|fix_id": false, "options_type|options_type_selector": "advanced"}, "job": {"model_class": "Job", "id": "a946c2d814bbae50", "state": "error", "exit_code": null, "update_time": "2023-10-24T06:29:27.643636", "create_time": "2023-10-24T06:29:21.607663", "galaxy_version": "23.1", "command_version": null, "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", "history_id": "b8e3c9423bdc89f6", "external_id": "gxy-sg9z7", "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/7/3/1/dataset_731f009c-9d5f-47be-87c7-f1653c70dd28.dat' sanger '/galaxy/server/database/objects/8/c/8/dataset_8c875dbd-9a4a-4696-ada1-babebafcd667.dat' sanger ascii summarize_input --no-fix-id", "traceback": null, "params": {"input_type": "\"sanger\"", "options_type": "{\"__current_case__\": 1, \"fix_id\": false, \"force_quality_encoding\": \"ascii\", \"options_type_selector\": \"advanced\", \"output_type\": \"sanger\", \"summarize_input\": \"summarize_input\"}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"fastq\""}, "inputs": {"input_file": {"id": "c9eeda56cd2b8988", "src": "hda", "uuid": "731f009c-9d5f-47be-87c7-f1653c70dd28"}}, "outputs": {"output_file": {"id": "a946c2d814bbae50", "src": "hda", "uuid": "8c875dbd-9a4a-4696-ada1-babebafcd667"}}, "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": []}, "status": "success"}}, {"id": "fastq_groomer/1.1.5-20", "has_data": true, "data": {"tool_id": "fastq_groomer", "tool_version": "1.1.5", "test_index": 20, "time_seconds": 31.05567693710327, "inputs": {"input_file": {"src": "hda", "id": "7f451aa57262a321"}, "input_type": "cssanger", "options_type|output_type": "cssanger", "options_type|force_quality_encoding": "None", "options_type|summarize_input": "summarize_input", "options_type|options_type_selector": "advanced"}, "job": {"model_class": "Job", "id": "b1b34c50f9999259", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T06:38:48.155887", "create_time": "2023-10-24T06:38:36.633737", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", "history_id": "b8e3c9423bdc89f6", "external_id": "gxy-2cdbf", "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/6/a/f/dataset_6af18c03-bef4-4fe2-83ca-aa31eda56680.dat' cssanger '/galaxy/server/database/objects/c/9/6/dataset_c965df51-d317-4f27-b962-2bee2d0a5ddc.dat' cssanger None summarize_input --fix-id", "traceback": null, "params": {"__input_ext": "\"fastq\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "options_type": "{\"__current_case__\": 1, \"fix_id\": true, \"force_quality_encoding\": \"None\", \"options_type_selector\": \"advanced\", \"output_type\": \"cssanger\", \"summarize_input\": \"summarize_input\"}", "input_type": "\"cssanger\""}, "inputs": {"input_file": {"id": "7f451aa57262a321", "src": "hda", "uuid": "6af18c03-bef4-4fe2-83ca-aa31eda56680"}}, "outputs": {"output_file": {"id": "b1b34c50f9999259", "src": "hda", "uuid": "c965df51-d317-4f27-b962-2bee2d0a5ddc"}}, "output_collections": {}, "tool_stdout": "Groomed 2 cssanger reads into cssanger reads.\nBased upon quality and sequence, the input data is valid for: cssanger, cssanger.gz, cssanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "Groomed 2 cssanger reads into cssanger reads.\nBased upon quality and sequence, the input data is valid for: cssanger, cssanger.gz, cssanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\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": "2023-10-24 06:38:38", "plugin": "core", "name": "end_epoch", "raw_value": "1698129518.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 06:38:38", "plugin": "core", "name": "start_epoch", "raw_value": "1698129518.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "fastq_groomer/1.1.5-21", "has_data": true, "data": {"tool_id": "fastq_groomer", "tool_version": "1.1.5", "test_index": 21, "time_seconds": 30.68277883529663, "inputs": {"input_file": {"src": "hda", "id": "78f45309268aaef0"}, "input_type": "cssanger", "options_type|output_type": "sanger", "options_type|force_quality_encoding": "None", "options_type|summarize_input": "summarize_input", "options_type|options_type_selector": "advanced"}, "job": {"model_class": "Job", "id": "126ca59d605c9933", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T06:39:18.651246", "create_time": "2023-10-24T06:39:06.609028", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", "history_id": "b8e3c9423bdc89f6", "external_id": "gxy-jsw5j", "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/6/8/4/dataset_68410e5e-51d4-4de1-8e40-67ec016871c9.dat' cssanger '/galaxy/server/database/objects/d/f/7/dataset_df7c9849-cb1c-4f43-8b33-dc4433ab4f69.dat' sanger None summarize_input --fix-id", "traceback": null, "params": {"__input_ext": "\"fastq\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "options_type": "{\"__current_case__\": 1, \"fix_id\": true, \"force_quality_encoding\": \"None\", \"options_type_selector\": \"advanced\", \"output_type\": \"sanger\", \"summarize_input\": \"summarize_input\"}", "input_type": "\"cssanger\""}, "inputs": {"input_file": {"id": "78f45309268aaef0", "src": "hda", "uuid": "68410e5e-51d4-4de1-8e40-67ec016871c9"}}, "outputs": {"output_file": {"id": "126ca59d605c9933", "src": "hda", "uuid": "df7c9849-cb1c-4f43-8b33-dc4433ab4f69"}}, "output_collections": {}, "tool_stdout": "Groomed 2 cssanger reads into sanger reads.\nBased upon quality and sequence, the input data is valid for: cssanger, cssanger.gz, cssanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "Groomed 2 cssanger reads into sanger reads.\nBased upon quality and sequence, the input data is valid for: cssanger, cssanger.gz, cssanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\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": "2023-10-24 06:39:08", "plugin": "core", "name": "end_epoch", "raw_value": "1698129548.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 06:39:07", "plugin": "core", "name": "start_epoch", "raw_value": "1698129547.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "fastq_groomer/1.1.5-22", "has_data": true, "data": {"tool_id": "fastq_groomer", "tool_version": "1.1.5", "test_index": 22, "time_seconds": 31.106141567230225, "inputs": {"input_file": {"src": "hda", "id": "46b31e3e9e797ce1"}, "input_type": "cssanger", "options_type|output_type": "illumina", "options_type|force_quality_encoding": "None", "options_type|summarize_input": "summarize_input", "options_type|options_type_selector": "advanced"}, "job": {"model_class": "Job", "id": "8c0471b1c07aa6f6", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T06:39:50.064011", "create_time": "2023-10-24T06:39:38.313225", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", "history_id": "b8e3c9423bdc89f6", "external_id": "gxy-rb45s", "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/c/4/a/dataset_c4a2498a-928f-4245-a05b-7d01405e627f.dat' cssanger '/galaxy/server/database/objects/e/5/4/dataset_e54f6384-5bdd-4d7c-9ad1-6d946e3b4591.dat' illumina None summarize_input --fix-id", "traceback": null, "params": {"__input_ext": "\"fastq\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "options_type": "{\"__current_case__\": 1, \"fix_id\": true, \"force_quality_encoding\": \"None\", \"options_type_selector\": \"advanced\", \"output_type\": \"illumina\", \"summarize_input\": \"summarize_input\"}", "input_type": "\"cssanger\""}, "inputs": {"input_file": {"id": "46b31e3e9e797ce1", "src": "hda", "uuid": "c4a2498a-928f-4245-a05b-7d01405e627f"}}, "outputs": {"output_file": {"id": "8c0471b1c07aa6f6", "src": "hda", "uuid": "e54f6384-5bdd-4d7c-9ad1-6d946e3b4591"}}, "output_collections": {}, "tool_stdout": "Groomed 2 cssanger reads into illumina reads.\nBased upon quality and sequence, the input data is valid for: cssanger, cssanger.gz, cssanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "Groomed 2 cssanger reads into illumina reads.\nBased upon quality and sequence, the input data is valid for: cssanger, cssanger.gz, cssanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\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": "2023-10-24 06:39:39", "plugin": "core", "name": "end_epoch", "raw_value": "1698129579.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 06:39:39", "plugin": "core", "name": "start_epoch", "raw_value": "1698129579.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "fastq_groomer/1.1.5-23", "has_data": true, "data": {"tool_id": "fastq_groomer", "tool_version": "1.1.5", "test_index": 23, "time_seconds": 31.17434525489807, "inputs": {"input_file": {"src": "hda", "id": "d7d107607e2429b2"}, "input_type": "cssanger", "options_type|output_type": "solexa", "options_type|force_quality_encoding": "None", "options_type|summarize_input": "summarize_input", "options_type|options_type_selector": "advanced"}, "job": {"model_class": "Job", "id": "a33a3839028e1680", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T06:40:21.229365", "create_time": "2023-10-24T06:40:08.752333", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", "history_id": "b8e3c9423bdc89f6", "external_id": "gxy-4wz8d", "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/8/c/9/dataset_8c9d95a3-c000-4eae-8db7-aa17ff1d4aa3.dat' cssanger '/galaxy/server/database/objects/9/1/4/dataset_914e8f4c-27d6-4054-9adf-6ca4dde67cef.dat' solexa None summarize_input --fix-id", "traceback": null, "params": {"__input_ext": "\"fastq\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "options_type": "{\"__current_case__\": 1, \"fix_id\": true, \"force_quality_encoding\": \"None\", \"options_type_selector\": \"advanced\", \"output_type\": \"solexa\", \"summarize_input\": \"summarize_input\"}", "input_type": "\"cssanger\""}, "inputs": {"input_file": {"id": "d7d107607e2429b2", "src": "hda", "uuid": "8c9d95a3-c000-4eae-8db7-aa17ff1d4aa3"}}, "outputs": {"output_file": {"id": "a33a3839028e1680", "src": "hda", "uuid": "914e8f4c-27d6-4054-9adf-6ca4dde67cef"}}, "output_collections": {}, "tool_stdout": "Groomed 2 cssanger reads into solexa reads.\nConverted between Solexa and PHRED scores.\nBased upon quality and sequence, the input data is valid for: cssanger, cssanger.gz, cssanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "Groomed 2 cssanger reads into solexa reads.\nConverted between Solexa and PHRED scores.\nBased upon quality and sequence, the input data is valid for: cssanger, cssanger.gz, cssanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\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": "2023-10-24 06:40:11", "plugin": "core", "name": "end_epoch", "raw_value": "1698129611.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 06:40:11", "plugin": "core", "name": "start_epoch", "raw_value": "1698129611.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "fastq_groomer/1.1.5-24", "has_data": true, "data": {"tool_id": "fastq_groomer", "tool_version": "1.1.5", "test_index": 24, "time_seconds": 31.960021018981934, "inputs": {"input_file": {"src": "hda", "id": "0156de56552e9e55"}, "input_type": "cssanger", "options_type|output_type": "cssanger", "options_type|force_quality_encoding": "None", "options_type|summarize_input": "summarize_input", "options_type|options_type_selector": "advanced"}, "job": {"model_class": "Job", "id": "7153690388b50ea2", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T06:40:53.679779", "create_time": "2023-10-24T06:40:41.304557", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", "history_id": "b8e3c9423bdc89f6", "external_id": "gxy-59xtl", "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/1/4/4/dataset_1441990d-e1b4-4c9e-976b-14ab75683299.dat' cssanger '/galaxy/server/database/objects/1/2/6/dataset_126e020d-c002-4709-a115-ee92710b3f5c.dat' cssanger None summarize_input --fix-id", "traceback": null, "params": {"__input_ext": "\"fastq\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "options_type": "{\"__current_case__\": 1, \"fix_id\": true, \"force_quality_encoding\": \"None\", \"options_type_selector\": \"advanced\", \"output_type\": \"cssanger\", \"summarize_input\": \"summarize_input\"}", "input_type": "\"cssanger\""}, "inputs": {"input_file": {"id": "0156de56552e9e55", "src": "hda", "uuid": "1441990d-e1b4-4c9e-976b-14ab75683299"}}, "outputs": {"output_file": {"id": "7153690388b50ea2", "src": "hda", "uuid": "126e020d-c002-4709-a115-ee92710b3f5c"}}, "output_collections": {}, "tool_stdout": "Groomed 2 cssanger reads into cssanger reads.\nBased upon quality and sequence, the input data is valid for: cssanger, cssanger.gz, cssanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "Groomed 2 cssanger reads into cssanger reads.\nBased upon quality and sequence, the input data is valid for: cssanger, cssanger.gz, cssanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": 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"job_stderr": "", "stderr": "", "stdout": "Groomed 2 sanger reads into sanger reads.\nBased upon quality and sequence, the input data is valid for: sanger, sanger.gz, sanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\n", "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": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 06:29:48", "plugin": "core", "name": "start_epoch", "raw_value": "1698128988.0000000"}, {"title": "Job End Time", "value": "2023-10-24 06:29:48", "plugin": "core", "name": "end_epoch", "raw_value": "1698128988.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, 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solexa, solexa.gz, solexa.bz2, sanger, sanger.gz, sanger.bz2\nInput ASCII range: ';'(59) - '~'(126)\nInput decimal range: -5 - 62\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "Groomed 2 solexa reads into solexa reads.\nBased upon quality and sequence, the input data is valid for: solexa, solexa.gz, solexa.bz2, sanger, sanger.gz, sanger.bz2\nInput ASCII range: ';'(59) - '~'(126)\nInput decimal range: -5 - 62\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": "2023-10-24 06:44:07", "plugin": "core", "name": "end_epoch", "raw_value": "1698129847.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 06:44:07", "plugin": "core", "name": "start_epoch", "raw_value": "1698129847.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "fastq_groomer/1.1.5-32", "has_data": true, "data": {"tool_id": "fastq_groomer", "tool_version": "1.1.5", "test_index": 32, "time_seconds": 31.454225778579712, "inputs": {"input_file": {"src": "hda", "id": "bcf74409967b222c"}, "input_type": "solexa", "options_type|output_type": "solexa", "options_type|force_quality_encoding": "decimal", "options_type|summarize_input": "summarize_input", "options_type|options_type_selector": "advanced"}, "job": {"model_class": "Job", "id": "7a0fe7d625813b63", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T06:44:48.829675", "create_time": "2023-10-24T06:44:35.959736", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", "history_id": "b8e3c9423bdc89f6", "external_id": "gxy-gszjj", "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/b/1/e/dataset_b1e624eb-301a-4a80-8c3a-2e20f7c2306c.dat' solexa '/galaxy/server/database/objects/5/3/f/dataset_53f3bf70-0101-4542-a3bd-7233e004098a.dat' solexa decimal summarize_input --fix-id", "traceback": null, "params": {"__input_ext": "\"fastq\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "options_type": "{\"__current_case__\": 1, \"fix_id\": true, \"force_quality_encoding\": \"decimal\", \"options_type_selector\": \"advanced\", \"output_type\": \"solexa\", \"summarize_input\": \"summarize_input\"}", "input_type": "\"solexa\""}, "inputs": {"input_file": {"id": "bcf74409967b222c", "src": "hda", "uuid": "b1e624eb-301a-4a80-8c3a-2e20f7c2306c"}}, "outputs": {"output_file": {"id": "7a0fe7d625813b63", "src": "hda", "uuid": "53f3bf70-0101-4542-a3bd-7233e004098a"}}, "output_collections": {}, "tool_stdout": "Groomed 2 solexa reads into solexa reads.\nBased upon quality and sequence, the input data is valid for: solexa, solexa.gz, solexa.bz2, sanger, sanger.gz, sanger.bz2\nInput ASCII range: ';'(59) - '~'(126)\nInput decimal range: -5 - 62\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "Groomed 2 solexa reads into solexa reads.\nBased upon quality and sequence, the input data is valid for: solexa, solexa.gz, solexa.bz2, sanger, sanger.gz, sanger.bz2\nInput ASCII range: ';'(59) - '~'(126)\nInput decimal range: -5 - 62\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": "2023-10-24 06:44:37", "plugin": "core", "name": "end_epoch", "raw_value": "1698129877.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 06:44:37", "plugin": "core", "name": "start_epoch", "raw_value": "1698129877.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "fastq_groomer/1.1.5-33", "has_data": true, "data": {"tool_id": "fastq_groomer", "tool_version": "1.1.5", "test_index": 33, "time_seconds": 31.128181219100952, "inputs": {"input_file": {"src": "hda", "id": "d054e2c56e0372b2"}, "input_type": "sanger", "options_type|options_type_selector": "basic"}, "job": {"model_class": "Job", "id": "a49c0e63ede3772c", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T06:45:20.428941", "create_time": "2023-10-24T06:45:07.587874", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", "history_id": "b8e3c9423bdc89f6", "external_id": "gxy-7z5f7", "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/5/0/7/dataset_507aeea3-1a79-4c7f-85b3-60d7c32e2270.dat' sanger.gz '/galaxy/server/database/objects/4/5/9/dataset_45939652-a97e-457d-bcb6-c5e2262df31b.dat' sanger ascii summarize_input", "traceback": null, "params": {"__input_ext": "\"fastq.gz\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "options_type": "{\"__current_case__\": 0, \"options_type_selector\": \"basic\"}", "input_type": "\"sanger\""}, "inputs": {"input_file": {"id": "d054e2c56e0372b2", "src": "hda", "uuid": "507aeea3-1a79-4c7f-85b3-60d7c32e2270"}}, "outputs": {"output_file": {"id": "a49c0e63ede3772c", "src": "hda", "uuid": "45939652-a97e-457d-bcb6-c5e2262df31b"}}, "output_collections": {}, "tool_stdout": "Groomed 2 sanger.gz reads into sanger reads.\nBased upon quality and sequence, the input data is valid for: sanger, sanger.gz, sanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "Groomed 2 sanger.gz reads into sanger reads.\nBased upon quality and sequence, the input data is valid for: sanger, sanger.gz, sanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\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": "2023-10-24 06:45:10", "plugin": "core", "name": "end_epoch", "raw_value": "1698129910.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 06:45:09", "plugin": "core", "name": "start_epoch", "raw_value": "1698129909.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "fastq_groomer/1.1.5-34", "has_data": true, "data": {"tool_id": "fastq_groomer", "tool_version": "1.1.5", "test_index": 34, "time_seconds": 31.9081027507782, "inputs": {"input_file": {"src": "hda", "id": "366bbd0d88d92503"}, "input_type": "cssanger", "options_type|options_type_selector": "basic"}, "job": {"model_class": "Job", "id": "3ab6baa328705356", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T06:45:52.545287", "create_time": "2023-10-24T06:45:40.141976", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", "history_id": "b8e3c9423bdc89f6", "external_id": "gxy-cpm52", "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/f/d/e/dataset_fde9b032-0028-421a-85b9-922e8ad5986b.dat' cssanger.bz2 '/galaxy/server/database/objects/2/b/a/dataset_2baef198-7c70-4196-b100-76ac2912afdd.dat' cssanger ascii summarize_input", "traceback": null, "params": {"__input_ext": "\"fastq.bz2\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "options_type": "{\"__current_case__\": 0, \"options_type_selector\": \"basic\"}", "input_type": "\"cssanger\""}, "inputs": {"input_file": {"id": "366bbd0d88d92503", "src": "hda", "uuid": "fde9b032-0028-421a-85b9-922e8ad5986b"}}, "outputs": {"output_file": {"id": "3ab6baa328705356", "src": "hda", "uuid": "2baef198-7c70-4196-b100-76ac2912afdd"}}, "output_collections": {}, "tool_stdout": "Groomed 2 cssanger.bz2 reads into cssanger reads.\nBased upon quality and sequence, the input data is valid for: cssanger, cssanger.gz, cssanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "Groomed 2 cssanger.bz2 reads into cssanger reads.\nBased upon quality and sequence, the input data is valid for: cssanger, cssanger.gz, cssanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\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": "2023-10-24 06:45:42", "plugin": "core", "name": "end_epoch", "raw_value": "1698129942.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 06:45:42", "plugin": "core", "name": "start_epoch", "raw_value": "1698129942.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "fastq_groomer/1.1.5-4", "has_data": true, "data": {"tool_id": "fastq_groomer", "tool_version": "1.1.5", "test_index": 4, "time_seconds": 31.504658937454224, "inputs": {"input_file": {"src": "hda", "id": "423354c57717f009"}, "input_type": "cssanger", "options_type|options_type_selector": "basic"}, "job": {"model_class": "Job", "id": "f39862b462167507", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T06:30:29.445852", "create_time": "2023-10-24T06:30:17.729931", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", "history_id": "b8e3c9423bdc89f6", "external_id": "gxy-fcc9t", "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/f/f/a/dataset_ffa08cf2-7ee4-418e-bfdb-62f03829572d.dat' cssanger '/galaxy/server/database/objects/2/b/1/dataset_2b16b589-e1fd-47a9-82a3-2189df275673.dat' cssanger ascii summarize_input", "traceback": null, "params": {"input_type": "\"cssanger\"", "options_type": "{\"__current_case__\": 0, \"options_type_selector\": \"basic\"}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"fastq\""}, "inputs": {"input_file": {"id": "423354c57717f009", "src": "hda", "uuid": "ffa08cf2-7ee4-418e-bfdb-62f03829572d"}}, "outputs": {"output_file": {"id": "f39862b462167507", "src": "hda", "uuid": "2b16b589-e1fd-47a9-82a3-2189df275673"}}, "output_collections": {}, "tool_stdout": "Groomed 2 cssanger reads into cssanger reads.\nBased upon quality and sequence, the input data is valid for: cssanger, cssanger.gz, cssanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "Groomed 2 cssanger reads into cssanger reads.\nBased upon quality and sequence, the input data is valid for: cssanger, cssanger.gz, cssanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\n", "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": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 06:30:19", "plugin": "core", "name": "start_epoch", "raw_value": "1698129019.0000000"}, {"title": "Job End Time", "value": "2023-10-24 06:30:19", "plugin": "core", "name": "end_epoch", "raw_value": "1698129019.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "fastq_groomer/1.1.5-5", "has_data": true, "data": {"tool_id": "fastq_groomer", "tool_version": "1.1.5", "test_index": 5, "time_seconds": 31.09030318260193, "inputs": {"input_file": {"src": "hda", "id": "a3cd12807abe778e"}, "input_type": "illumina", "options_type|options_type_selector": "basic"}, "job": {"model_class": "Job", "id": "ec00b3778f885404", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T06:31:00.844470", "create_time": "2023-10-24T06:30:48.140637", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", "history_id": "b8e3c9423bdc89f6", "external_id": "gxy-dsqg2", "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/e/4/8/dataset_e48ec717-63ce-4f27-8c05-6c32341d007c.dat' illumina '/galaxy/server/database/objects/c/a/3/dataset_ca3af834-2bb2-4939-918c-f8e321d88ff4.dat' sanger ascii summarize_input", "traceback": null, "params": {"input_type": "\"illumina\"", "options_type": "{\"__current_case__\": 0, \"options_type_selector\": \"basic\"}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"fastq\""}, "inputs": {"input_file": {"id": "a3cd12807abe778e", "src": "hda", "uuid": "e48ec717-63ce-4f27-8c05-6c32341d007c"}}, "outputs": {"output_file": {"id": "ec00b3778f885404", "src": "hda", "uuid": "ca3af834-2bb2-4939-918c-f8e321d88ff4"}}, "output_collections": {}, "tool_stdout": "Groomed 2 illumina reads into sanger reads.\nBased upon quality and sequence, the input data is valid for: illumina, illumina.gz, illumina.bz2, solexa, solexa.gz, solexa.bz2, sanger, sanger.gz, sanger.bz2\nInput ASCII range: '@'(64) - '~'(126)\nInput decimal range: 0 - 62\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "Groomed 2 illumina reads into sanger reads.\nBased upon quality and sequence, the input data is valid for: illumina, illumina.gz, illumina.bz2, solexa, solexa.gz, solexa.bz2, sanger, sanger.gz, sanger.bz2\nInput ASCII range: '@'(64) - '~'(126)\nInput decimal range: 0 - 62\n", "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": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 06:30:50", "plugin": "core", "name": "start_epoch", "raw_value": "1698129050.0000000"}, {"title": "Job End Time", "value": "2023-10-24 06:30:50", "plugin": "core", "name": "end_epoch", "raw_value": "1698129050.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "fastq_groomer/1.1.5-6", "has_data": true, "data": {"tool_id": "fastq_groomer", "tool_version": "1.1.5", "test_index": 6, "time_seconds": 30.229788541793823, "inputs": {"input_file": {"src": "hda", "id": "171a1ad371d14de3"}, "input_type": "solexa", "options_type|options_type_selector": "basic"}, "job": {"model_class": "Job", "id": "d38e788f8d55d88b", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T06:31:31.065364", "create_time": "2023-10-24T06:31:19.347394", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", "history_id": "b8e3c9423bdc89f6", "external_id": "gxy-pzcgm", "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/f/4/2/dataset_f42b6dd4-4090-433e-abb5-1c210f4171fa.dat' solexa '/galaxy/server/database/objects/3/0/d/dataset_30d706a9-fed7-4e1e-af9d-a39780741c06.dat' sanger ascii summarize_input", "traceback": null, "params": {"input_type": "\"solexa\"", "options_type": "{\"__current_case__\": 0, \"options_type_selector\": \"basic\"}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"fastq\""}, "inputs": {"input_file": {"id": "171a1ad371d14de3", "src": "hda", "uuid": "f42b6dd4-4090-433e-abb5-1c210f4171fa"}}, "outputs": {"output_file": {"id": "d38e788f8d55d88b", "src": "hda", "uuid": "30d706a9-fed7-4e1e-af9d-a39780741c06"}}, "output_collections": {}, "tool_stdout": "Groomed 2 solexa reads into sanger reads.\nConverted between Solexa and PHRED scores.\nBased upon quality and sequence, the input data is valid for: solexa, solexa.gz, solexa.bz2, sanger, sanger.gz, sanger.bz2\nInput ASCII range: ';'(59) - '~'(126)\nInput decimal range: -5 - 62\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "Groomed 2 solexa reads into sanger reads.\nConverted between Solexa and PHRED scores.\nBased upon quality and sequence, the input data is valid for: solexa, solexa.gz, solexa.bz2, sanger, sanger.gz, sanger.bz2\nInput ASCII range: ';'(59) - '~'(126)\nInput decimal range: -5 - 62\n", "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": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 06:31:21", "plugin": "core", "name": "start_epoch", "raw_value": "1698129081.0000000"}, {"title": "Job End Time", "value": "2023-10-24 06:31:21", "plugin": "core", "name": "end_epoch", "raw_value": "1698129081.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "fastq_groomer/1.1.5-7", "has_data": true, "data": {"tool_id": "fastq_groomer", "tool_version": "1.1.5", "test_index": 7, "time_seconds": 30.192665815353394, "inputs": {"input_file": {"src": "hda", "id": "72c953527d942c36"}, "input_type": "sanger", "options_type|options_type_selector": "basic"}, "job": {"model_class": "Job", "id": "eeb6a031c51d4f9f", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T06:32:01.452630", "create_time": "2023-10-24T06:31:49.712561", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", "history_id": "b8e3c9423bdc89f6", "external_id": "gxy-xswh8", "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/a/9/f/dataset_a9f318ad-988c-4626-beaf-7083a35c6122.dat' sanger '/galaxy/server/database/objects/b/5/8/dataset_b58a1a9d-d6ff-49c0-9df7-ead5a67d552b.dat' sanger ascii summarize_input", "traceback": null, "params": {"__input_ext": "\"fastq\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "options_type": "{\"__current_case__\": 0, \"options_type_selector\": \"basic\"}", "input_type": "\"sanger\""}, "inputs": {"input_file": {"id": "72c953527d942c36", "src": "hda", "uuid": "a9f318ad-988c-4626-beaf-7083a35c6122"}}, "outputs": {"output_file": {"id": "eeb6a031c51d4f9f", "src": "hda", "uuid": "b58a1a9d-d6ff-49c0-9df7-ead5a67d552b"}}, "output_collections": {}, "tool_stdout": "Groomed 2 sanger reads into sanger reads.\nBased upon quality and sequence, the input data is valid for: illumina, illumina.gz, illumina.bz2, solexa, solexa.gz, solexa.bz2, sanger, sanger.gz, sanger.bz2\nInput ASCII range: '@'(64) - '~'(126)\nInput decimal range: 31 - 93\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "Groomed 2 sanger reads into sanger reads.\nBased upon quality and sequence, the input data is valid for: illumina, illumina.gz, illumina.bz2, solexa, solexa.gz, solexa.bz2, sanger, sanger.gz, sanger.bz2\nInput ASCII range: '@'(64) - '~'(126)\nInput decimal range: 31 - 93\n", "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": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 06:31:51", "plugin": "core", "name": "start_epoch", "raw_value": "1698129111.0000000"}, {"title": "Job End Time", "value": "2023-10-24 06:31:51", "plugin": "core", "name": "end_epoch", "raw_value": "1698129111.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "fastq_groomer/1.1.5-8", "has_data": true, "data": {"tool_id": "fastq_groomer", "tool_version": "1.1.5", "test_index": 8, "time_seconds": 32.18229651451111, "inputs": {"input_file": {"src": "hda", "id": "21e944d65e4acb48"}, "input_type": "illumina", "options_type|output_type": "illumina", "options_type|force_quality_encoding": "None", "options_type|summarize_input": "summarize_input", "options_type|options_type_selector": "advanced"}, "job": {"model_class": "Job", "id": "3f5a2398326409f8", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T06:32:33.756081", "create_time": "2023-10-24T06:32:21.253337", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", "history_id": "b8e3c9423bdc89f6", "external_id": "gxy-kbjhv", "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/4/4/2/dataset_4426d7ac-37c1-46d2-b6bc-be44649b218b.dat' illumina '/galaxy/server/database/objects/f/3/1/dataset_f310ade4-c065-42db-af0c-003891584872.dat' illumina None summarize_input --fix-id", "traceback": null, "params": {"__input_ext": "\"fastq\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "options_type": "{\"__current_case__\": 1, \"fix_id\": true, \"force_quality_encoding\": \"None\", \"options_type_selector\": \"advanced\", \"output_type\": \"illumina\", \"summarize_input\": \"summarize_input\"}", "input_type": "\"illumina\""}, "inputs": {"input_file": {"id": "21e944d65e4acb48", "src": "hda", "uuid": "4426d7ac-37c1-46d2-b6bc-be44649b218b"}}, "outputs": {"output_file": {"id": "3f5a2398326409f8", "src": "hda", "uuid": "f310ade4-c065-42db-af0c-003891584872"}}, "output_collections": {}, "tool_stdout": "Groomed 2 illumina reads into illumina reads.\nBased upon quality and sequence, the input data is valid for: illumina, illumina.gz, illumina.bz2, solexa, solexa.gz, solexa.bz2, sanger, sanger.gz, sanger.bz2\nInput ASCII range: '@'(64) - '~'(126)\nInput decimal range: 0 - 62\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "Groomed 2 illumina reads into illumina reads.\nBased upon quality and sequence, the input data is valid for: illumina, illumina.gz, illumina.bz2, solexa, solexa.gz, solexa.bz2, sanger, sanger.gz, sanger.bz2\nInput ASCII range: '@'(64) - '~'(126)\nInput decimal range: 0 - 62\n", "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": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 06:32:22", "plugin": "core", "name": "start_epoch", "raw_value": "1698129142.0000000"}, {"title": "Job End Time", "value": "2023-10-24 06:32:22", "plugin": "core", "name": "end_epoch", "raw_value": "1698129142.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "fastq_groomer/1.1.5-9", "has_data": true, "data": {"tool_id": "fastq_groomer", "tool_version": "1.1.5", "test_index": 9, "time_seconds": 31.379063367843628, "inputs": {"input_file": {"src": "hda", "id": "2b9a4d316151f6e0"}, "input_type": "illumina", "options_type|output_type": "sanger", "options_type|force_quality_encoding": "None", "options_type|summarize_input": "summarize_input", "options_type|options_type_selector": "advanced"}, "job": {"model_class": "Job", "id": "ed3a5a05a54f0477", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T06:33:05.161794", "create_time": "2023-10-24T06:32:53.186084", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", "history_id": "b8e3c9423bdc89f6", "external_id": "gxy-t4pkw", "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/2/e/c/dataset_2ec3cb50-2bfe-4273-8b69-f289645d10bf.dat' illumina '/galaxy/server/database/objects/f/d/1/dataset_fd12f761-f765-49f9-9a5a-6d6ae1a7ce4b.dat' sanger None summarize_input --fix-id", "traceback": null, "params": {"__input_ext": "\"fastq\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "options_type": "{\"__current_case__\": 1, \"fix_id\": true, \"force_quality_encoding\": \"None\", \"options_type_selector\": \"advanced\", \"output_type\": \"sanger\", \"summarize_input\": \"summarize_input\"}", "input_type": "\"illumina\""}, "inputs": {"input_file": {"id": "2b9a4d316151f6e0", "src": "hda", "uuid": "2ec3cb50-2bfe-4273-8b69-f289645d10bf"}}, "outputs": {"output_file": {"id": "ed3a5a05a54f0477", "src": "hda", "uuid": "fd12f761-f765-49f9-9a5a-6d6ae1a7ce4b"}}, "output_collections": {}, "tool_stdout": "Groomed 2 illumina reads into sanger reads.\nBased upon quality and sequence, the input data is valid for: illumina, illumina.gz, illumina.bz2, solexa, solexa.gz, solexa.bz2, sanger, sanger.gz, sanger.bz2\nInput ASCII range: '@'(64) - '~'(126)\nInput decimal range: 0 - 62\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "Groomed 2 illumina reads into sanger reads.\nBased upon quality and sequence, the input data is valid for: illumina, illumina.gz, illumina.bz2, solexa, solexa.gz, solexa.bz2, sanger, sanger.gz, sanger.bz2\nInput ASCII range: '@'(64) - '~'(126)\nInput decimal range: 0 - 62\n", "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": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 06:32:54", "plugin": "core", "name": "start_epoch", "raw_value": "1698129174.0000000"}, {"title": "Job End Time", "value": "2023-10-24 06:32:54", "plugin": "core", "name": "end_epoch", "raw_value": "1698129174.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "kallisto_pseudo/0.46.0.1-0", "has_data": true, "data": {"tool_id": "kallisto_pseudo", "tool_version": "0.46.0.1", "test_index": 0, "time_seconds": 41.195722818374634, "inputs": {"reference_transcriptome|reference": {"src": "hda", "id": "bcb59a5c2249df5d"}, "reference_transcriptome|reference_transcriptome_source": "history", "single_paired|collection|fastq_umi|forward": {"src": "hda", "id": "119c61687da3b62f"}, "single_paired|collection|fastq_umi|reverse": {"src": "hda", "id": "a06c3faa3e996663"}, "single_paired|collection|fastq_umi|umi": "yes", "single_paired|collection|collection_selector": "datasets", "single_paired|single_paired_selector": "paired"}, "job": {"model_class": "Job", "id": "35e4ae728060a1bc", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T06:49:31.315785", "create_time": "2023-10-24T06:49:16.131063", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1", "history_id": "b8e3c9423bdc89f6", "external_id": "gxy-686rm", "command_line": "ln -s '/galaxy/server/database/objects/a/5/9/dataset_a59b2029-0a5f-4401-8235-04d685c5f4b8.dat' reference.fa && kallisto index reference.fa -i reference.kallisto && kallisto pseudo -i 'reference.kallisto' --threads ${GALAXY_SLOTS:-1} -o . --batch '/galaxy/server/database/jobs_directory/000/90/configs/tmpd61o5l4x' --umi && if [ -f run_info.json ] ; then cat run_info.json ; fi && mkdir outputs && if [ -f matrix.ec ] ; then mv matrix.ec outputs/Matrix.ec ; fi && if [ -f matrix.tcc.mtx ] ; then mv matrix.tcc.mtx outputs/Matrix.tabular ; fi && if [ -f matrix.cells ] ; then mv matrix.cells outputs/Matrix.cells ; fi && if [ -f pseudoalignments.tsv ] ; then mv pseudoalignments.tsv outputs/Pseudoalignments.tabular ; fi && if [ -f pseudoalignments.ec ] ; then mv pseudoalignments.ec outputs/Pseudoalignments.ec ; fi", "traceback": null, "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "single_paired": "{\"__current_case__\": 1, \"collection\": {\"__current_case__\": 0, \"collection_selector\": \"datasets\", \"fastq_umi\": {\"__current_case__\": 0, \"forward\": {\"values\": [{\"id\": 92, \"src\": \"hda\"}]}, \"reverse\": {\"values\": [{\"id\": 93, \"src\": \"hda\"}]}, \"umi\": \"yes\"}}, \"single_paired_selector\": \"paired\"}", "reference_transcriptome": "{\"__current_case__\": 1, \"reference\": {\"values\": [{\"id\": 91, \"src\": \"hda\"}]}, \"reference_transcriptome_source\": \"history\"}"}, "inputs": {"reference_transcriptome|reference": {"id": "bcb59a5c2249df5d", "src": "hda", "uuid": "a59b2029-0a5f-4401-8235-04d685c5f4b8"}, "single_paired|collection|fastq_umi|forward": {"id": "119c61687da3b62f", "src": "hda", "uuid": "0de2cba0-ec4b-42cc-bf7f-6ffd984f4a82"}, "single_paired|collection|fastq_umi|forward1": {"id": "119c61687da3b62f", "src": "hda", "uuid": "0de2cba0-ec4b-42cc-bf7f-6ffd984f4a82"}, "single_paired|collection|fastq_umi|reverse": {"id": "a06c3faa3e996663", "src": "hda", "uuid": "a8ce847e-295c-47a5-b440-a91f5ea028e0"}, "single_paired|collection|fastq_umi|reverse1": {"id": "a06c3faa3e996663", "src": "hda", "uuid": "a8ce847e-295c-47a5-b440-a91f5ea028e0"}}, "outputs": {"sample": {"id": "8d849f168ffcc439", "src": "hda", "uuid": "dc9884eb-2265-4429-9c59-d2f6cf701605"}, "__new_primary_file_sample|Matrix.cells__": {"id": "923133f6c61916cc", "src": "hda", "uuid": "3a991224-0010-4299-a0a2-8ac4c238aca5"}, "__new_primary_file_sample|Matrix.ec__": {"id": "3e2b7763c606bc10", "src": "hda", "uuid": "bd4d350f-c79d-48a6-bab8-5ba832d0e47c"}, "__new_primary_file_sample|Matrix.tabular__": {"id": "d06bda1d0dc205fb", "src": "hda", "uuid": "df15f4cf-41f0-4713-b994-5c8ea8926846"}}, "output_collections": {}, "tool_stdout": "{\n\t\"n_targets\": 1,\n\t\"n_bootstraps\": 0,\n\t\"n_processed\": 200,\n\t\"n_pseudoaligned\": 200,\n\t\"n_unique\": 200,\n\t\"p_pseudoaligned\": 100.0,\n\t\"p_unique\": 100.0,\n\t\"kallisto_version\": \"0.46.0\",\n\t\"index_version\": 10,\n\t\"start_time\": \"Tue Oct 24 06:49:21 2023\",\n\t\"call\": \"kallisto pseudo -i reference.kallisto --threads 1 -o . --batch /galaxy/server/database/jobs_directory/000/90/configs/tmpd61o5l4x --umi\"\n}\n", "tool_stderr": "\n[build] loading fasta file reference.fa\n[build] k-mer length: 31\n[build] counting k-mers ... done.\n[build] building target de Bruijn graph ... done \n[build] creating equivalence classes ... done\n[build] target de Bruijn graph has 1 contigs and contains 16269 k-mers \n\n\n[index] k-mer length: 31\n[index] number of targets: 1\n[index] number of k-mers: 16,269\n[index] number of equivalence classes: 1\n[quant] running in single-end mode\n[quant] will process file 1: /galaxy/server/database/objects/a/8/c/dataset_a8ce847e-295c-47a5-b440-a91f5ea028e0.dat\n[quant] will process file 1: /galaxy/server/database/objects/a/8/c/dataset_a8ce847e-295c-47a5-b440-a91f5ea028e0.dat\n[quant] finding pseudoalignments for all files ... done\n[quant] processed 200 reads, 200 reads pseudoaligned, 200 unique UMIs mapped\n\n", "job_stdout": "", "job_stderr": "", "stderr": "\n[build] loading fasta file reference.fa\n[build] k-mer length: 31\n[build] counting k-mers ... done.\n[build] building target de Bruijn graph ... done \n[build] creating equivalence classes ... done\n[build] target de Bruijn graph has 1 contigs and contains 16269 k-mers \n\n\n[index] k-mer length: 31\n[index] number of targets: 1\n[index] number of k-mers: 16,269\n[index] number of equivalence classes: 1\n[quant] running in single-end mode\n[quant] will process file 1: /galaxy/server/database/objects/a/8/c/dataset_a8ce847e-295c-47a5-b440-a91f5ea028e0.dat\n[quant] will process file 1: /galaxy/server/database/objects/a/8/c/dataset_a8ce847e-295c-47a5-b440-a91f5ea028e0.dat\n[quant] finding pseudoalignments for all files ... done\n[quant] processed 200 reads, 200 reads pseudoaligned, 200 unique UMIs mapped\n\n", "stdout": "{\n\t\"n_targets\": 1,\n\t\"n_bootstraps\": 0,\n\t\"n_processed\": 200,\n\t\"n_pseudoaligned\": 200,\n\t\"n_unique\": 200,\n\t\"p_pseudoaligned\": 100.0,\n\t\"p_unique\": 100.0,\n\t\"kallisto_version\": \"0.46.0\",\n\t\"index_version\": 10,\n\t\"start_time\": \"Tue Oct 24 06:49:21 2023\",\n\t\"call\": \"kallisto pseudo -i reference.kallisto --threads 1 -o . --batch /galaxy/server/database/jobs_directory/000/90/configs/tmpd61o5l4x --umi\"\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": "2023-10-24 06:49:21", "plugin": "core", "name": "end_epoch", "raw_value": "1698130161.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 06:49:21", "plugin": "core", "name": "start_epoch", "raw_value": "1698130161.0000000"}, {"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": "kallisto_pseudo/0.46.0.1-1", "has_data": true, "data": {"tool_id": "kallisto_pseudo", "tool_version": "0.46.0.1", "test_index": 1, "time_seconds": 38.07896113395691, "inputs": {"reference_transcriptome|reference": {"src": "hda", "id": "a0e548e7ae2c7319"}, "reference_transcriptome|reference_transcriptome_source": "history", "single_paired|collection|reads": {"src": "hdca", "id": "b8e3c9423bdc89f6"}, "single_paired|collection|collection_selector": "collection", "single_paired|single_paired_selector": "paired"}, "job": {"model_class": "Job", "id": "8d849f168ffcc439", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T06:50:09.938567", "create_time": "2023-10-24T06:49:57.334972", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1", "history_id": "b8e3c9423bdc89f6", "external_id": "gxy-bhdzp", "command_line": "ln -s '/galaxy/server/database/objects/9/8/c/dataset_98cdf8c1-5f2c-4fbe-9699-86c7f45c44cb.dat' reference.fa && kallisto index reference.fa -i reference.kallisto && kallisto pseudo -i 'reference.kallisto' --threads ${GALAXY_SLOTS:-1} -o . '/galaxy/server/database/objects/b/d/3/dataset_bd3e4057-f67d-4507-a4e4-272e21e063e0.dat' '/galaxy/server/database/objects/3/8/7/dataset_387d13f6-4b53-460a-ac1a-cd5598ca80a4.dat' && if [ -f run_info.json ] ; then cat run_info.json ; fi && mkdir outputs && if [ -f matrix.ec ] ; then mv matrix.ec outputs/Matrix.ec ; fi && if [ -f matrix.tcc.mtx ] ; then mv matrix.tcc.mtx outputs/Matrix.tabular ; fi && if [ -f matrix.cells ] ; then mv matrix.cells outputs/Matrix.cells ; fi && if [ -f pseudoalignments.tsv ] ; then mv pseudoalignments.tsv outputs/Pseudoalignments.tabular ; fi && if [ -f pseudoalignments.ec ] ; then mv pseudoalignments.ec outputs/Pseudoalignments.ec ; fi", "traceback": null, "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "single_paired": "{\"__current_case__\": 1, \"collection\": {\"__current_case__\": 1, \"collection_selector\": \"collection\", \"reads\": {\"values\": [{\"id\": 1, \"src\": \"hdca\"}]}}, \"single_paired_selector\": \"paired\"}", "reference_transcriptome": "{\"__current_case__\": 1, \"reference\": {\"values\": [{\"id\": 98, \"src\": \"hda\"}]}, \"reference_transcriptome_source\": \"history\"}"}, "inputs": {"reference_transcriptome|reference": {"id": "a0e548e7ae2c7319", "src": "hda", "uuid": "98cdf8c1-5f2c-4fbe-9699-86c7f45c44cb"}, "single_paired|collection|reads1": {"id": "6cb0104eb5f2f3a0", "src": "hda", "uuid": "bd3e4057-f67d-4507-a4e4-272e21e063e0"}, "single_paired|collection|reads2": {"id": "0fe01ba1233b8e05", "src": "hda", "uuid": "387d13f6-4b53-460a-ac1a-cd5598ca80a4"}}, "outputs": {"sample": {"id": "3e6ca2f14c25c690", "src": "hda", "uuid": "ec718470-eb40-48f0-a553-d947ee082371"}, "__new_primary_file_sample|Matrix.cells__": {"id": "84c1567a3601922d", "src": "hda", "uuid": "c27706df-f303-4bff-b88f-1e49ba0da29e"}, "__new_primary_file_sample|Matrix.ec__": {"id": "87a5c83e33288d48", "src": "hda", "uuid": "f1cf7bd8-1051-450a-b169-73c89f8e702e"}, "__new_primary_file_sample|Matrix.tabular__": {"id": "27b2002a21d335bb", "src": "hda", "uuid": "a6e31994-8691-42b0-a2bf-df30d6cffbb2"}, "__new_primary_file_sample|Pseudoalignments.ec__": {"id": "587dc591d413742a", "src": "hda", "uuid": "91d4641a-5b47-44a1-b821-0841768c800b"}, "__new_primary_file_sample|Pseudoalignments.tabular__": {"id": "1b14fde99d7533f4", "src": "hda", "uuid": "dd52295e-5895-40dc-a7eb-85144bf7439e"}}, "output_collections": {}, "tool_stdout": "{\n\t\"n_targets\": 1,\n\t\"n_bootstraps\": 0,\n\t\"n_processed\": 100,\n\t\"n_pseudoaligned\": 0,\n\t\"n_unique\": 0,\n\t\"p_pseudoaligned\": 0.0,\n\t\"p_unique\": 0.0,\n\t\"kallisto_version\": \"0.46.0\",\n\t\"index_version\": 10,\n\t\"start_time\": \"Tue Oct 24 06:49:59 2023\",\n\t\"call\": \"kallisto pseudo -i reference.kallisto --threads 1 -o . /galaxy/server/database/objects/b/d/3/dataset_bd3e4057-f67d-4507-a4e4-272e21e063e0.dat /galaxy/server/database/objects/3/8/7/dataset_387d13f6-4b53-460a-ac1a-cd5598ca80a4.dat\"\n}\n", "tool_stderr": "\n[build] loading fasta file reference.fa\n[build] k-mer length: 31\n[build] counting k-mers ... done.\n[build] building target de Bruijn graph ... done \n[build] creating equivalence classes ... done\n[build] target de Bruijn graph has 1 contigs and contains 16269 k-mers \n\n\n[quant] fragment length distribution will be estimated from the data\n[index] k-mer length: 31\n[index] number of targets: 1\n[index] number of k-mers: 16,269\n[index] number of equivalence classes: 1\n[quant] running in paired-end mode\n[quant] will process pair 1: /galaxy/server/database/objects/b/d/3/dataset_bd3e4057-f67d-4507-a4e4-272e21e063e0.dat\n /galaxy/server/database/objects/3/8/7/dataset_387d13f6-4b53-460a-ac1a-cd5598ca80a4.dat\n[quant] finding pseudoalignments for the reads ... done\n[quant] processed 100 reads, 100 reads pseudoaligned\n\n", "job_stdout": "", "job_stderr": "", "stderr": "\n[build] loading fasta file reference.fa\n[build] k-mer length: 31\n[build] counting k-mers ... done.\n[build] building target de Bruijn graph ... done \n[build] creating equivalence classes ... done\n[build] target de Bruijn graph has 1 contigs and contains 16269 k-mers \n\n\n[quant] fragment length distribution will be estimated from the data\n[index] k-mer length: 31\n[index] number of targets: 1\n[index] number of k-mers: 16,269\n[index] number of equivalence classes: 1\n[quant] running in paired-end mode\n[quant] will process pair 1: /galaxy/server/database/objects/b/d/3/dataset_bd3e4057-f67d-4507-a4e4-272e21e063e0.dat\n /galaxy/server/database/objects/3/8/7/dataset_387d13f6-4b53-460a-ac1a-cd5598ca80a4.dat\n[quant] finding pseudoalignments for the reads ... done\n[quant] processed 100 reads, 100 reads pseudoaligned\n\n", "stdout": "{\n\t\"n_targets\": 1,\n\t\"n_bootstraps\": 0,\n\t\"n_processed\": 100,\n\t\"n_pseudoaligned\": 0,\n\t\"n_unique\": 0,\n\t\"p_pseudoaligned\": 0.0,\n\t\"p_unique\": 0.0,\n\t\"kallisto_version\": \"0.46.0\",\n\t\"index_version\": 10,\n\t\"start_time\": \"Tue Oct 24 06:49:59 2023\",\n\t\"call\": \"kallisto pseudo -i reference.kallisto --threads 1 -o . /galaxy/server/database/objects/b/d/3/dataset_bd3e4057-f67d-4507-a4e4-272e21e063e0.dat /galaxy/server/database/objects/3/8/7/dataset_387d13f6-4b53-460a-ac1a-cd5598ca80a4.dat\"\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": "2023-10-24 06:49:59", "plugin": "core", "name": "end_epoch", "raw_value": "1698130199.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 06:49:58", "plugin": "core", "name": "start_epoch", "raw_value": "1698130198.0000000"}, {"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": "kallisto_pseudo/0.46.0.1-2", "has_data": true, "data": {"tool_id": "kallisto_pseudo", "tool_version": "0.46.0.1", "test_index": 2, "time_seconds": 34.018917083740234, "inputs": {"reference_transcriptome|reference": {"src": "hda", "id": "5d4f689fa8c33fb4"}, "reference_transcriptome|reference_transcriptome_source": "history", "single_paired|reads": {"src": "hda", "id": "5a2866febb346be8"}, "single_paired|single_paired_selector": "single"}, "job": {"model_class": "Job", "id": "d06bda1d0dc205fb", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T06:50:44.217522", "create_time": "2023-10-24T06:50:31.571372", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1", "history_id": "b8e3c9423bdc89f6", "external_id": "gxy-4szgr", "command_line": "ln -s '/galaxy/server/database/objects/5/3/b/dataset_53bd9e37-5be2-4968-8e86-9954f5afd12d.dat' reference.fa && kallisto index reference.fa -i reference.kallisto && kallisto pseudo -i 'reference.kallisto' --threads ${GALAXY_SLOTS:-1} -o . --single --fragment-length 200 --sd 20 '/galaxy/server/database/objects/6/1/2/dataset_612a1a9e-c5b4-46a4-a199-27deb0969203.dat' && if [ -f run_info.json ] ; then cat run_info.json ; fi && mkdir outputs && if [ -f matrix.ec ] ; then mv matrix.ec outputs/Matrix.ec ; fi && if [ -f matrix.tcc.mtx ] ; then mv matrix.tcc.mtx outputs/Matrix.tabular ; fi && if [ -f matrix.cells ] ; then mv matrix.cells outputs/Matrix.cells ; fi && if [ -f pseudoalignments.tsv ] ; then mv pseudoalignments.tsv outputs/Pseudoalignments.tabular ; fi && if [ -f pseudoalignments.ec ] ; then mv pseudoalignments.ec outputs/Pseudoalignments.ec ; fi", "traceback": null, "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "single_paired": "{\"__current_case__\": 0, \"fragment_length\": \"200\", \"reads\": {\"values\": [{\"id\": 108, \"src\": \"hda\"}]}, \"sd\": \"20\", \"single_paired_selector\": \"single\"}", "reference_transcriptome": "{\"__current_case__\": 1, \"reference\": {\"values\": [{\"id\": 107, \"src\": \"hda\"}]}, \"reference_transcriptome_source\": \"history\"}"}, "inputs": {"reference_transcriptome|reference": {"id": "5d4f689fa8c33fb4", "src": "hda", "uuid": "53bd9e37-5be2-4968-8e86-9954f5afd12d"}, "single_paired|reads": {"id": "5a2866febb346be8", "src": "hda", "uuid": "612a1a9e-c5b4-46a4-a199-27deb0969203"}, "single_paired|reads1": {"id": "5a2866febb346be8", "src": "hda", "uuid": "612a1a9e-c5b4-46a4-a199-27deb0969203"}}, "outputs": {"sample": {"id": "bc85f495b65ed0b2", "src": "hda", "uuid": "e09dfdbe-7bb3-420f-a47b-b2bd4c04fe47"}, "__new_primary_file_sample|Matrix.cells__": {"id": "406a5736390cc0b2", "src": "hda", "uuid": "621ddbc3-a5eb-4b9b-80e5-ab77eb254d6b"}, "__new_primary_file_sample|Matrix.ec__": {"id": "bc26de549bbb396e", "src": "hda", "uuid": "b255eb85-21a1-42af-b8b6-b2092683a728"}, "__new_primary_file_sample|Matrix.tabular__": {"id": "c1e606af192f37db", "src": "hda", "uuid": "6044e8b3-a381-4b43-b9a5-f283b0ebb086"}, "__new_primary_file_sample|Pseudoalignments.ec__": {"id": "d48aa8293f429b21", "src": "hda", "uuid": "1d3d6254-93ef-4f0f-9d99-2a02deb334fc"}, "__new_primary_file_sample|Pseudoalignments.tabular__": {"id": "eed4de4bbc4a1574", "src": "hda", "uuid": "680891e8-f33d-4efb-9a5e-afab27855de7"}}, "output_collections": {}, "tool_stdout": "{\n\t\"n_targets\": 1,\n\t\"n_bootstraps\": 0,\n\t\"n_processed\": 100,\n\t\"n_pseudoaligned\": 0,\n\t\"n_unique\": 0,\n\t\"p_pseudoaligned\": 0.0,\n\t\"p_unique\": 0.0,\n\t\"kallisto_version\": \"0.46.0\",\n\t\"index_version\": 10,\n\t\"start_time\": \"Tue Oct 24 06:50:33 2023\",\n\t\"call\": \"kallisto pseudo -i reference.kallisto --threads 1 -o . --single --fragment-length 200 --sd 20 /galaxy/server/database/objects/6/1/2/dataset_612a1a9e-c5b4-46a4-a199-27deb0969203.dat\"\n}\n", "tool_stderr": "\n[build] loading fasta file reference.fa\n[build] k-mer length: 31\n[build] counting k-mers ... done.\n[build] building target de Bruijn graph ... done \n[build] creating equivalence classes ... done\n[build] target de Bruijn graph has 1 contigs and contains 16269 k-mers \n\n\n[quant] fragment length distribution is truncated gaussian with mean = 200, sd = 20\n[index] k-mer length: 31\n[index] number of targets: 1\n[index] number of k-mers: 16,269\n[index] number of equivalence classes: 1\n[quant] running in single-end mode\n[quant] will process file 1: /galaxy/server/database/objects/6/1/2/dataset_612a1a9e-c5b4-46a4-a199-27deb0969203.dat\n[quant] finding pseudoalignments for the reads ... done\n[quant] processed 100 reads, 100 reads pseudoaligned\n\n", "job_stdout": "", "job_stderr": "", "stderr": "\n[build] loading fasta file reference.fa\n[build] k-mer length: 31\n[build] counting k-mers ... done.\n[build] building target de Bruijn graph ... done \n[build] creating equivalence classes ... done\n[build] target de Bruijn graph has 1 contigs and contains 16269 k-mers \n\n\n[quant] fragment length distribution is truncated gaussian with mean = 200, sd = 20\n[index] k-mer length: 31\n[index] number of targets: 1\n[index] number of k-mers: 16,269\n[index] number of equivalence classes: 1\n[quant] running in single-end mode\n[quant] will process file 1: /galaxy/server/database/objects/6/1/2/dataset_612a1a9e-c5b4-46a4-a199-27deb0969203.dat\n[quant] finding pseudoalignments for the reads ... done\n[quant] processed 100 reads, 100 reads pseudoaligned\n\n", "stdout": "{\n\t\"n_targets\": 1,\n\t\"n_bootstraps\": 0,\n\t\"n_processed\": 100,\n\t\"n_pseudoaligned\": 0,\n\t\"n_unique\": 0,\n\t\"p_pseudoaligned\": 0.0,\n\t\"p_unique\": 0.0,\n\t\"kallisto_version\": \"0.46.0\",\n\t\"index_version\": 10,\n\t\"start_time\": \"Tue Oct 24 06:50:33 2023\",\n\t\"call\": \"kallisto pseudo -i reference.kallisto --threads 1 -o . --single --fragment-length 200 --sd 20 /galaxy/server/database/objects/6/1/2/dataset_612a1a9e-c5b4-46a4-a199-27deb0969203.dat\"\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": "2023-10-24 06:50:33", "plugin": "core", "name": "end_epoch", "raw_value": "1698130233.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 06:50:33", "plugin": "core", "name": "start_epoch", "raw_value": "1698130233.0000000"}, {"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": "kallisto_pseudo/0.46.0.1-3", "has_data": true, "data": {"tool_id": "kallisto_pseudo", "tool_version": "0.46.0.1", "test_index": 3, "time_seconds": 37.91775369644165, "inputs": {"reference_transcriptome|reference": {"src": "hda", "id": "e3e10d2227fe51a8"}, "reference_transcriptome|reference_transcriptome_source": "history", "single_paired|collection|fastq_umi|forward": {"src": "hda", "id": "c75606a77a9e6598"}, "single_paired|collection|fastq_umi|reverse": {"src": "hda", "id": "771c81d420c40696"}, "single_paired|collection|fastq_umi|umi": "no", "single_paired|collection|collection_selector": "datasets", "single_paired|single_paired_selector": "paired"}, "job": {"model_class": "Job", "id": "3e6ca2f14c25c690", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T06:51:22.293867", "create_time": "2023-10-24T06:51:09.997086", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1", "history_id": "b8e3c9423bdc89f6", "external_id": "gxy-5q5z6", "command_line": "ln -s '/galaxy/server/database/objects/b/e/4/dataset_be469919-acd0-4060-b657-5998fb931cfb.dat' reference.fa && kallisto index reference.fa -i reference.kallisto && kallisto pseudo -i 'reference.kallisto' --threads ${GALAXY_SLOTS:-1} -o . '/galaxy/server/database/objects/6/5/4/dataset_65473a5f-5ba4-43e3-a8e9-5a70b600b221.dat' '/galaxy/server/database/objects/1/2/9/dataset_1296f066-0260-492c-8a72-ff004ef505f2.dat' && if [ -f run_info.json ] ; then cat run_info.json ; fi && mkdir outputs && if [ -f matrix.ec ] ; then mv matrix.ec outputs/Matrix.ec ; fi && if [ -f matrix.tcc.mtx ] ; then mv matrix.tcc.mtx outputs/Matrix.tabular ; fi && if [ -f matrix.cells ] ; then mv matrix.cells outputs/Matrix.cells ; fi && if [ -f pseudoalignments.tsv ] ; then mv pseudoalignments.tsv outputs/Pseudoalignments.tabular ; fi && if [ -f pseudoalignments.ec ] ; then mv pseudoalignments.ec outputs/Pseudoalignments.ec ; fi", "traceback": null, "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "single_paired": "{\"__current_case__\": 1, \"collection\": {\"__current_case__\": 0, \"collection_selector\": \"datasets\", \"fastq_umi\": {\"__current_case__\": 1, \"forward\": {\"values\": [{\"id\": 116, \"src\": \"hda\"}]}, \"reverse\": {\"values\": [{\"id\": 117, \"src\": \"hda\"}]}, \"umi\": \"no\"}}, \"single_paired_selector\": \"paired\"}", "reference_transcriptome": "{\"__current_case__\": 1, \"reference\": {\"values\": [{\"id\": 115, \"src\": \"hda\"}]}, \"reference_transcriptome_source\": \"history\"}"}, "inputs": {"reference_transcriptome|reference": {"id": "e3e10d2227fe51a8", "src": "hda", "uuid": "be469919-acd0-4060-b657-5998fb931cfb"}, "single_paired|collection|fastq_umi|forward": {"id": "c75606a77a9e6598", "src": "hda", "uuid": "65473a5f-5ba4-43e3-a8e9-5a70b600b221"}, "single_paired|collection|fastq_umi|forward1": {"id": "c75606a77a9e6598", "src": "hda", "uuid": "65473a5f-5ba4-43e3-a8e9-5a70b600b221"}, "single_paired|collection|fastq_umi|reverse": {"id": "771c81d420c40696", "src": "hda", "uuid": "1296f066-0260-492c-8a72-ff004ef505f2"}, "single_paired|collection|fastq_umi|reverse1": {"id": "771c81d420c40696", "src": "hda", "uuid": "1296f066-0260-492c-8a72-ff004ef505f2"}}, "outputs": {"sample": {"id": "c2817ae83258538f", "src": "hda", "uuid": "ffe121be-4649-42a1-947e-d796067a59c2"}, "__new_primary_file_sample|Matrix.cells__": {"id": "4f01926b6271168e", "src": "hda", "uuid": "4cf9b9e3-5d5b-4d88-89a8-71ae0dde5fc5"}, "__new_primary_file_sample|Matrix.ec__": {"id": "a4c7f04fd58da044", "src": "hda", "uuid": "434217a4-0070-421b-8691-0b2c74040b9f"}, "__new_primary_file_sample|Matrix.tabular__": {"id": "41a888e05d248b65", "src": "hda", "uuid": "f9326bb7-b359-4cad-b0bc-01db69bc6885"}, "__new_primary_file_sample|Pseudoalignments.ec__": {"id": "f5ec43b567333743", "src": "hda", "uuid": "070ea975-5462-476e-9e1e-402cf8241e60"}, "__new_primary_file_sample|Pseudoalignments.tabular__": {"id": "2508872f2388dfce", "src": "hda", "uuid": "a799181c-615a-486e-ba3e-b3c99fdec028"}}, "output_collections": {}, "tool_stdout": "{\n\t\"n_targets\": 1,\n\t\"n_bootstraps\": 0,\n\t\"n_processed\": 200,\n\t\"n_pseudoaligned\": 0,\n\t\"n_unique\": 0,\n\t\"p_pseudoaligned\": 0.0,\n\t\"p_unique\": 0.0,\n\t\"kallisto_version\": \"0.46.0\",\n\t\"index_version\": 10,\n\t\"start_time\": \"Tue Oct 24 06:51:11 2023\",\n\t\"call\": \"kallisto pseudo -i reference.kallisto --threads 1 -o . /galaxy/server/database/objects/6/5/4/dataset_65473a5f-5ba4-43e3-a8e9-5a70b600b221.dat /galaxy/server/database/objects/1/2/9/dataset_1296f066-0260-492c-8a72-ff004ef505f2.dat\"\n}\n", "tool_stderr": "\n[build] loading fasta file reference.fa\n[build] k-mer length: 31\n[build] counting k-mers ... done.\n[build] building target de Bruijn graph ... done \n[build] creating equivalence classes ... done\n[build] target de Bruijn graph has 15 contigs and contains 16670 k-mers \n\n\n[quant] fragment length distribution will be estimated from the data\n[index] k-mer length: 31\n[index] number of targets: 1\n[index] number of k-mers: 16,670\n[index] number of equivalence classes: 1\n[quant] running in paired-end mode\n[quant] will process pair 1: /galaxy/server/database/objects/6/5/4/dataset_65473a5f-5ba4-43e3-a8e9-5a70b600b221.dat\n /galaxy/server/database/objects/1/2/9/dataset_1296f066-0260-492c-8a72-ff004ef505f2.dat\n[quant] finding pseudoalignments for the reads ... done\n[quant] processed 200 reads, 200 reads pseudoaligned\n\n", "job_stdout": "", "job_stderr": "", "stderr": "\n[build] loading fasta file reference.fa\n[build] k-mer length: 31\n[build] counting k-mers ... done.\n[build] building target de Bruijn graph ... done \n[build] creating equivalence classes ... done\n[build] target de Bruijn graph has 15 contigs and contains 16670 k-mers \n\n\n[quant] fragment length distribution will be estimated from the data\n[index] k-mer length: 31\n[index] number of targets: 1\n[index] number of k-mers: 16,670\n[index] number of equivalence classes: 1\n[quant] running in paired-end mode\n[quant] will process pair 1: /galaxy/server/database/objects/6/5/4/dataset_65473a5f-5ba4-43e3-a8e9-5a70b600b221.dat\n /galaxy/server/database/objects/1/2/9/dataset_1296f066-0260-492c-8a72-ff004ef505f2.dat\n[quant] finding pseudoalignments for the reads ... done\n[quant] processed 200 reads, 200 reads pseudoaligned\n\n", "stdout": "{\n\t\"n_targets\": 1,\n\t\"n_bootstraps\": 0,\n\t\"n_processed\": 200,\n\t\"n_pseudoaligned\": 0,\n\t\"n_unique\": 0,\n\t\"p_pseudoaligned\": 0.0,\n\t\"p_unique\": 0.0,\n\t\"kallisto_version\": \"0.46.0\",\n\t\"index_version\": 10,\n\t\"start_time\": \"Tue Oct 24 06:51:11 2023\",\n\t\"call\": \"kallisto pseudo -i reference.kallisto --threads 1 -o . /galaxy/server/database/objects/6/5/4/dataset_65473a5f-5ba4-43e3-a8e9-5a70b600b221.dat /galaxy/server/database/objects/1/2/9/dataset_1296f066-0260-492c-8a72-ff004ef505f2.dat\"\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": "2023-10-24 06:51:11", "plugin": "core", "name": "end_epoch", "raw_value": "1698130271.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 06:51:11", "plugin": "core", "name": "start_epoch", "raw_value": "1698130271.0000000"}, {"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": "kallisto_pseudo/0.46.0.1-4", "has_data": true, "data": {"tool_id": "kallisto_pseudo", "tool_version": "0.46.0.1", "test_index": 4, "time_seconds": 20.099539041519165, "inputs": {"single_paired|collection|fastq_umi|forward": {"src": "hda", "id": "e219d9fbc5abf3d2"}, "single_paired|collection|fastq_umi|reverse": {"src": "hda", "id": "923804dda71f7317"}, "single_paired|collection|fastq_umi|umi": "yes", "single_paired|collection|collection_selector": "datasets", "single_paired|single_paired_selector": "paired"}, "execution_problem": "parameter 'index': an invalid option (None) was selected, please verify", "dynamic_param_error": true, "status": "error"}}, {"id": "miniasm/0.3+galaxy0-0", "has_data": true, "data": {"tool_id": "miniasm", "tool_version": "0.3+galaxy0", "test_index": 0, "time_seconds": 118.1543619632721, "inputs": {"readFile": {"src": "hda", "id": "b8e3c9423bdc89f6"}, "paf": {"src": "hda", "id": "7ba13d1e0fea166b"}}, "job": {"model_class": "Job", "id": "7ce505be939b23e0", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T06:26:00.804699", "create_time": "2023-10-24T06:24:49.291856", "galaxy_version": "23.1", "command_version": "0.3-r179", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3+galaxy0", "history_id": "b8e3c9423bdc89f6", "external_id": "gxy-bm5zh", "command_line": "miniasm -f '/galaxy/server/database/objects/9/6/b/dataset_96bf6207-9ec4-46ab-91b3-c5d3b12b4a5a.dat' -m '100' -i '0.05' -s '1000' -c '3' -o '1000' -h '1000' -I '0.08' -g '1000' -d '50000' -e '4' -n '3' -F '0.8' '/galaxy/server/database/objects/d/a/8/dataset_da87cc5f-3019-40ec-b718-dad37a80f901.dat' > '/galaxy/server/database/objects/b/d/a/dataset_bda10934-e73b-4721-8bcd-12e513151db6.dat'", "traceback": null, "params": {"__input_ext": "\"fastqsanger\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "graph": "{\"finalDropRatio\": \"0.8\", \"maxBubDist\": \"50000\", \"maxGapDiff\": \"1000\", \"minUtgSize\": \"4\", \"nRounds\": \"3\"}", "overlapping": "{\"intThres\": \"0.08\", \"maxHang\": \"1000\", \"minOvlp\": \"1000\"}", "preselection": "{\"minCov\": \"3\", \"minIden\": \"0.05\", \"minMatch\": \"100\", \"minSpan\": \"1000\"}"}, "inputs": {"paf": {"id": "7ba13d1e0fea166b", "src": "hda", "uuid": "da87cc5f-3019-40ec-b718-dad37a80f901"}, "readFile": {"id": "b8e3c9423bdc89f6", "src": "hda", "uuid": "96bf6207-9ec4-46ab-91b3-c5d3b12b4a5a"}}, "outputs": {"gfa": {"id": "7ce505be939b23e0", "src": "hda", "uuid": "bda10934-e73b-4721-8bcd-12e513151db6"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "[M::main] ===> Step 1: reading read mappings <===\n[M::ma_hit_read::0.197*1.00] read 100000 hits; stored 187742 hits and 12067 sequences (111354001 bp)\n[M::main] ===> Step 2: 1-pass (crude) read selection <===\n[M::ma_hit_sub::0.221*1.00] 9155 query sequences remain after sub\n[M::ma_hit_cut::0.224*1.00] 161122 hits remain after cut\n[M::ma_hit_flt::0.227*1.00] 156936 hits remain after filtering; crude coverage after filtering: 11.85\n[M::main] ===> Step 3: 2-pass (fine) read selection <===\n[M::ma_hit_sub::0.238*1.00] 9023 query sequences remain after sub\n[M::ma_hit_cut::0.241*1.00] 152071 hits remain after cut\n[M::ma_hit_contained::0.246*1.00] 1536 sequences and 8359 hits remain after containment removal\n[M::main] ===> Step 4: graph cleaning <===\n[M::ma_sg_gen] read 8236 arcs\n[M::main] ===> Step 4.1: transitive reduction <===\n[M::asg_arc_del_trans] transitively reduced 4182 arcs\n[M::asg_arc_del_multi] removed 0 multi-arcs\n[M::asg_arc_del_asymm] removed 362 asymmetric arcs\n[M::main] ===> Step 4.2: initial tip cutting and bubble popping <===\n[M::asg_cut_tip] cut 260 tips\n[M::asg_pop_bubble] popped 105 bubbles and trimmed 4 tips\n[M::main] ===> Step 4.3: cutting short overlaps (3 rounds in total) <===\n[M::asg_arc_del_multi] removed 0 multi-arcs\n[M::asg_arc_del_asymm] removed 29 asymmetric arcs\n[M::asg_arc_del_short] removed 37 short overlaps\n[M::asg_cut_tip] cut 104 tips\n[M::asg_pop_bubble] popped 1 bubbles and trimmed 0 tips\n[M::asg_arc_del_multi] removed 0 multi-arcs\n[M::asg_arc_del_asymm] removed 1 asymmetric arcs\n[M::asg_arc_del_short] removed 1 short overlaps\n[M::asg_cut_tip] cut 3 tips\n[M::asg_pop_bubble] popped 0 bubbles and trimmed 0 tips\n[M::asg_arc_del_short] removed 0 short overlaps\n[M::main] ===> Step 4.4: removing short internal sequences and bi-loops <===\n[M::asg_cut_internal] cut 0 internal sequences\n[M::asg_cut_biloop] cut 0 small bi-loops\n[M::asg_cut_tip] cut 0 tips\n[M::asg_pop_bubble] popped 0 bubbles and trimmed 0 tips\n[M::main] ===> Step 4.5: aggressively cutting short overlaps <===\n[M::asg_arc_del_short] removed 0 short overlaps\n[M::main] ===> Step 5: generating unitigs <===\n[M::main] Version: 0.3-r179\n[M::main] CMD: miniasm -f /galaxy/server/database/objects/9/6/b/dataset_96bf6207-9ec4-46ab-91b3-c5d3b12b4a5a.dat -m 100 -i 0.05 -s 1000 -c 3 -o 1000 -h 1000 -I 0.08 -g 1000 -d 50000 -e 4 -n 3 -F 0.8 /galaxy/server/database/objects/d/a/8/dataset_da87cc5f-3019-40ec-b718-dad37a80f901.dat\n[M::main] Real time: 0.257 sec; CPU: 0.254 sec\n", "job_stdout": "", "job_stderr": "", "stderr": "[M::main] ===> Step 1: reading read mappings <===\n[M::ma_hit_read::0.197*1.00] read 100000 hits; stored 187742 hits and 12067 sequences (111354001 bp)\n[M::main] ===> Step 2: 1-pass (crude) read selection <===\n[M::ma_hit_sub::0.221*1.00] 9155 query sequences remain after sub\n[M::ma_hit_cut::0.224*1.00] 161122 hits remain after cut\n[M::ma_hit_flt::0.227*1.00] 156936 hits remain after filtering; crude coverage after filtering: 11.85\n[M::main] ===> Step 3: 2-pass (fine) read selection <===\n[M::ma_hit_sub::0.238*1.00] 9023 query sequences remain after sub\n[M::ma_hit_cut::0.241*1.00] 152071 hits remain after cut\n[M::ma_hit_contained::0.246*1.00] 1536 sequences and 8359 hits remain after containment removal\n[M::main] ===> Step 4: graph cleaning <===\n[M::ma_sg_gen] read 8236 arcs\n[M::main] ===> Step 4.1: transitive reduction <===\n[M::asg_arc_del_trans] transitively reduced 4182 arcs\n[M::asg_arc_del_multi] removed 0 multi-arcs\n[M::asg_arc_del_asymm] removed 362 asymmetric arcs\n[M::main] ===> Step 4.2: initial tip cutting and bubble popping <===\n[M::asg_cut_tip] cut 260 tips\n[M::asg_pop_bubble] popped 105 bubbles and trimmed 4 tips\n[M::main] ===> Step 4.3: cutting short overlaps (3 rounds in total) <===\n[M::asg_arc_del_multi] removed 0 multi-arcs\n[M::asg_arc_del_asymm] removed 29 asymmetric arcs\n[M::asg_arc_del_short] removed 37 short overlaps\n[M::asg_cut_tip] cut 104 tips\n[M::asg_pop_bubble] popped 1 bubbles and trimmed 0 tips\n[M::asg_arc_del_multi] removed 0 multi-arcs\n[M::asg_arc_del_asymm] removed 1 asymmetric arcs\n[M::asg_arc_del_short] removed 1 short overlaps\n[M::asg_cut_tip] cut 3 tips\n[M::asg_pop_bubble] popped 0 bubbles and trimmed 0 tips\n[M::asg_arc_del_short] removed 0 short overlaps\n[M::main] ===> Step 4.4: removing short internal sequences and bi-loops <===\n[M::asg_cut_internal] cut 0 internal sequences\n[M::asg_cut_biloop] cut 0 small bi-loops\n[M::asg_cut_tip] cut 0 tips\n[M::asg_pop_bubble] popped 0 bubbles and trimmed 0 tips\n[M::main] ===> Step 4.5: aggressively cutting short overlaps <===\n[M::asg_arc_del_short] removed 0 short overlaps\n[M::main] ===> Step 5: generating unitigs <===\n[M::main] Version: 0.3-r179\n[M::main] CMD: miniasm -f /galaxy/server/database/objects/9/6/b/dataset_96bf6207-9ec4-46ab-91b3-c5d3b12b4a5a.dat -m 100 -i 0.05 -s 1000 -c 3 -o 1000 -h 1000 -I 0.08 -g 1000 -d 50000 -e 4 -n 3 -F 0.8 /galaxy/server/database/objects/d/a/8/dataset_da87cc5f-3019-40ec-b718-dad37a80f901.dat\n[M::main] Real time: 0.257 sec; CPU: 0.254 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": "2023-10-24 06:25:49", "plugin": "core", "name": "end_epoch", "raw_value": "1698128749.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 06:25:49", "plugin": "core", "name": "start_epoch", "raw_value": "1698128749.0000000"}, {"title": "Memory Allocated (MB)", "value": "34359", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "34359.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "miniasm/0.3+galaxy0-1", "has_data": true, "data": {"tool_id": "miniasm", "tool_version": "0.3+galaxy0", "test_index": 1, "time_seconds": 34.45402431488037, "inputs": {"readFile": {"src": "hda", "id": "eab495b33e44fb49"}, "paf": {"src": "hda", "id": "c776b22589890bd5"}, "preselection|minMatch": "99", "preselection|minIden": "0.04", "preselection|minSpan": "999", "preselection|minCov": "2", "overlapping|minOvlp": "999", "overlapping|maxHang": "999", "overlapping|intThres": "0.7", "graph|maxGapDiff": "999", "graph|maxBubDist": "45000", "graph|minUtgSize": "3", "graph|nRounds": "2", "graph|finalDropRatio": "0.7"}, "job": {"model_class": "Job", "id": "8a580ec698d11313", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T06:26:35.478512", "create_time": "2023-10-24T06:26:22.721332", "galaxy_version": "23.1", "command_version": "0.3-r179", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3+galaxy0", "history_id": "b8e3c9423bdc89f6", "external_id": "gxy-s29nj", "command_line": "miniasm -f '/galaxy/server/database/objects/1/9/c/dataset_19c452e5-5cbf-4d01-9715-7a67e96dc63f.dat' -m '99' -i '0.04' -s '999' -c '2' -o '999' -h '999' -I '0.7' -g '999' -d '45000' -e '3' -n '2' -F '0.7' '/galaxy/server/database/objects/4/3/9/dataset_439051bb-ee13-4445-ba66-22f93ba24532.dat' > '/galaxy/server/database/objects/2/8/3/dataset_28398346-6e29-471c-b18b-e451dfbc5ed4.dat'", "traceback": null, "params": {"__input_ext": "\"fastqsanger\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "graph": "{\"finalDropRatio\": \"0.7\", \"maxBubDist\": \"45000\", \"maxGapDiff\": \"999\", \"minUtgSize\": \"3\", \"nRounds\": \"2\"}", "overlapping": "{\"intThres\": \"0.7\", \"maxHang\": \"999\", \"minOvlp\": \"999\"}", "preselection": "{\"minCov\": \"2\", \"minIden\": \"0.04\", \"minMatch\": \"99\", \"minSpan\": \"999\"}"}, "inputs": {"paf": {"id": "c776b22589890bd5", "src": "hda", "uuid": "439051bb-ee13-4445-ba66-22f93ba24532"}, "readFile": {"id": "eab495b33e44fb49", "src": "hda", "uuid": "19c452e5-5cbf-4d01-9715-7a67e96dc63f"}}, "outputs": {"gfa": {"id": "8a580ec698d11313", "src": "hda", "uuid": "28398346-6e29-471c-b18b-e451dfbc5ed4"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "[M::main] ===> Step 1: reading read mappings <===\n[M::ma_hit_read::0.201*1.00] read 100000 hits; stored 187766 hits and 12068 sequences (111355211 bp)\n[M::main] ===> Step 2: 1-pass (crude) read selection <===\n[M::ma_hit_sub::0.225*1.00] 10122 query sequences remain after sub\n[M::ma_hit_cut::0.228*1.00] 171862 hits remain after cut\n[M::ma_hit_flt::0.232*1.00] 165533 hits remain after filtering; crude coverage after filtering: 11.51\n[M::main] ===> Step 3: 2-pass (fine) read selection <===\n[M::ma_hit_sub::0.244*1.00] 9994 query sequences remain after sub\n[M::ma_hit_cut::0.247*1.00] 163595 hits remain after cut\n[M::ma_hit_contained::0.253*1.00] 1772 sequences and 10061 hits remain after containment removal\n[M::main] ===> Step 4: graph cleaning <===\n[M::ma_sg_gen] read 9758 arcs\n[M::main] ===> Step 4.1: transitive reduction <===\n[M::asg_arc_del_trans] transitively reduced 4694 arcs\n[M::asg_arc_del_multi] removed 0 multi-arcs\n[M::asg_arc_del_asymm] removed 484 asymmetric arcs\n[M::main] ===> Step 4.2: initial tip cutting and bubble popping <===\n[M::asg_cut_tip] cut 282 tips\n[M::asg_pop_bubble] popped 173 bubbles and trimmed 6 tips\n[M::main] ===> Step 4.3: cutting short overlaps (2 rounds in total) <===\n[M::asg_arc_del_multi] removed 0 multi-arcs\n[M::asg_arc_del_asymm] removed 26 asymmetric arcs\n[M::asg_arc_del_short] removed 38 short overlaps\n[M::asg_cut_tip] cut 53 tips\n[M::asg_pop_bubble] popped 8 bubbles and trimmed 0 tips\n[M::asg_arc_del_multi] removed 0 multi-arcs\n[M::asg_arc_del_asymm] removed 2 asymmetric arcs\n[M::asg_arc_del_short] removed 2 short overlaps\n[M::asg_cut_tip] cut 2 tips\n[M::asg_pop_bubble] popped 0 bubbles and trimmed 0 tips\n[M::main] ===> Step 4.4: removing short internal sequences and bi-loops <===\n[M::asg_cut_internal] cut 0 internal sequences\n[M::asg_cut_biloop] cut 0 small bi-loops\n[M::asg_cut_tip] cut 0 tips\n[M::asg_pop_bubble] popped 0 bubbles and trimmed 0 tips\n[M::main] ===> Step 4.5: aggressively cutting short overlaps <===\n[M::asg_arc_del_short] removed 0 short overlaps\n[M::main] ===> Step 5: generating unitigs <===\n[M::main] Version: 0.3-r179\n[M::main] CMD: miniasm -f /galaxy/server/database/objects/1/9/c/dataset_19c452e5-5cbf-4d01-9715-7a67e96dc63f.dat -m 99 -i 0.04 -s 999 -c 2 -o 999 -h 999 -I 0.7 -g 999 -d 45000 -e 3 -n 2 -F 0.7 /galaxy/server/database/objects/4/3/9/dataset_439051bb-ee13-4445-ba66-22f93ba24532.dat\n[M::main] Real time: 0.266 sec; CPU: 0.264 sec\n", "job_stdout": "", "job_stderr": "", "stderr": "[M::main] ===> Step 1: reading read mappings <===\n[M::ma_hit_read::0.201*1.00] read 100000 hits; stored 187766 hits and 12068 sequences (111355211 bp)\n[M::main] ===> Step 2: 1-pass (crude) read selection <===\n[M::ma_hit_sub::0.225*1.00] 10122 query sequences remain after sub\n[M::ma_hit_cut::0.228*1.00] 171862 hits remain after cut\n[M::ma_hit_flt::0.232*1.00] 165533 hits remain after filtering; crude coverage after filtering: 11.51\n[M::main] ===> Step 3: 2-pass (fine) read selection <===\n[M::ma_hit_sub::0.244*1.00] 9994 query sequences remain after sub\n[M::ma_hit_cut::0.247*1.00] 163595 hits remain after cut\n[M::ma_hit_contained::0.253*1.00] 1772 sequences and 10061 hits remain after containment removal\n[M::main] ===> Step 4: graph cleaning <===\n[M::ma_sg_gen] read 9758 arcs\n[M::main] ===> Step 4.1: transitive reduction <===\n[M::asg_arc_del_trans] transitively reduced 4694 arcs\n[M::asg_arc_del_multi] removed 0 multi-arcs\n[M::asg_arc_del_asymm] removed 484 asymmetric arcs\n[M::main] ===> Step 4.2: initial tip cutting and bubble popping <===\n[M::asg_cut_tip] cut 282 tips\n[M::asg_pop_bubble] popped 173 bubbles and trimmed 6 tips\n[M::main] ===> Step 4.3: cutting short overlaps (2 rounds in total) <===\n[M::asg_arc_del_multi] removed 0 multi-arcs\n[M::asg_arc_del_asymm] removed 26 asymmetric arcs\n[M::asg_arc_del_short] removed 38 short overlaps\n[M::asg_cut_tip] cut 53 tips\n[M::asg_pop_bubble] popped 8 bubbles and trimmed 0 tips\n[M::asg_arc_del_multi] removed 0 multi-arcs\n[M::asg_arc_del_asymm] removed 2 asymmetric arcs\n[M::asg_arc_del_short] removed 2 short overlaps\n[M::asg_cut_tip] cut 2 tips\n[M::asg_pop_bubble] popped 0 bubbles and trimmed 0 tips\n[M::main] ===> Step 4.4: removing short internal sequences and bi-loops <===\n[M::asg_cut_internal] cut 0 internal sequences\n[M::asg_cut_biloop] cut 0 small bi-loops\n[M::asg_cut_tip] cut 0 tips\n[M::asg_pop_bubble] popped 0 bubbles and trimmed 0 tips\n[M::main] ===> Step 4.5: aggressively cutting short overlaps <===\n[M::asg_arc_del_short] removed 0 short overlaps\n[M::main] ===> Step 5: generating unitigs <===\n[M::main] Version: 0.3-r179\n[M::main] CMD: miniasm -f /galaxy/server/database/objects/1/9/c/dataset_19c452e5-5cbf-4d01-9715-7a67e96dc63f.dat -m 99 -i 0.04 -s 999 -c 2 -o 999 -h 999 -I 0.7 -g 999 -d 45000 -e 3 -n 2 -F 0.7 /galaxy/server/database/objects/4/3/9/dataset_439051bb-ee13-4445-ba66-22f93ba24532.dat\n[M::main] Real time: 0.266 sec; CPU: 0.264 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": "2023-10-24 06:26:24", "plugin": "core", "name": "end_epoch", "raw_value": "1698128784.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 06:26:24", "plugin": "core", "name": "start_epoch", "raw_value": "1698128784.0000000"}, {"title": "Memory Allocated (MB)", "value": "34359", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "34359.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "mummer_mummerplot/4.0.0beta2+galaxy1-0", "has_data": true, "data": {"tool_id": "mummer_mummerplot", "tool_version": "4.0.0beta2+galaxy1", "test_index": 0, "time_seconds": 71.98010754585266, "inputs": {"delta": {"src": "hda", "id": "ad5589c2cdb72625"}, "reference_sequence": {"src": "hda", "id": "cbf3b94326c7a59b"}, "query_sequence": {"src": "hda", "id": "169d1f3e546c1de8"}, "sequences|seq_input": "no", "extra_outs": "all"}, "job": {"model_class": "Job", "id": "d7d727c9f1eb3290", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T06:47:03.160903", "create_time": "2023-10-24T06:46:20.076355", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0beta2+galaxy1", "history_id": "b8e3c9423bdc89f6", "external_id": "gxy-mjqzf", "command_line": "ln -s /galaxy/server/database/objects/3/c/3/dataset_3c33843b-1aa1-487d-a705-7371a5b5282b.dat reference.fa && ln -s /galaxy/server/database/objects/9/d/4/dataset_9d47488c-ba8c-47e1-aa2f-89e29be7a192.dat query.fa && mummerplot -b '20' -s 'small' -terminal png -title 'Title' '/galaxy/server/database/objects/e/f/7/dataset_ef7eaa53-713b-44ea-835b-99f63d32f046.dat' && gnuplot < out.gp", "traceback": null, "params": {"__input_ext": "\"txt\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "extra_outs": "\"all\"", "range": "{\"__current_case__\": 1, \"custom\": \"no\"}", "title": "\"Title\"", "snp": "false", "size": "\"small\"", "labels": "{\"IDs\": \"no\", \"__current_case__\": 1}", "fat": "false", "filter": "false", "coverage": "\"\"", "color": "\"\"", "breaklen": "\"20\"", "sequences": "{\"__current_case__\": 1, \"seq_input\": \"no\"}"}, "inputs": {"delta": {"id": "ad5589c2cdb72625", "src": "hda", "uuid": "ef7eaa53-713b-44ea-835b-99f63d32f046"}, "reference_sequence": {"id": "cbf3b94326c7a59b", "src": "hda", "uuid": "3c33843b-1aa1-487d-a705-7371a5b5282b"}, "query_sequence": {"id": "169d1f3e546c1de8", "src": "hda", "uuid": "9d47488c-ba8c-47e1-aa2f-89e29be7a192"}}, "outputs": {"gnuplot": {"id": "d7d727c9f1eb3290", "src": "hda", "uuid": "278d583c-60b4-43a8-aa41-6b0a8a3d3bd2"}, "fplot": {"id": "6f0947d15d2daeca", "src": "hda", "uuid": "f6c2124c-7b9a-4330-9fa4-75f8126a2cdf"}, "rplot": {"id": "39ee6c7f2ab69e67", "src": "hda", "uuid": "3d92f148-2d50-4bd0-bd0c-8235f8f68b87"}, "hplot": {"id": "3a730335f958c592", "src": "hda", "uuid": "5ac96cc3-1ebe-4c02-9ba2-8065ec2af4bf"}, "output_png": {"id": "4db4a831b783ae03", "src": "hda", "uuid": "ac29144d-c809-4919-914c-2f0c7134b3e5"}}, "output_collections": {}, "tool_stdout": "gnuplot 5.2 patchlevel 7\n", "tool_stderr": "Reading delta file /galaxy/server/database/objects/e/f/7/dataset_ef7eaa53-713b-44ea-835b-99f63d32f046.dat\nWriting plot files out.fplot, out.rplot, out.hplot\nWriting gnuplot script out.gp\nRendering plot out.png\nWARNING: Unable to run 'false out.gp', Inappropriate ioctl for device\n", "job_stdout": "", "job_stderr": "", "stderr": "Reading delta file /galaxy/server/database/objects/e/f/7/dataset_ef7eaa53-713b-44ea-835b-99f63d32f046.dat\nWriting plot files out.fplot, out.rplot, out.hplot\nWriting gnuplot script out.gp\nRendering plot out.png\nWARNING: Unable to run 'false out.gp', Inappropriate ioctl for device\n", "stdout": "gnuplot 5.2 patchlevel 7\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": "2023-10-24 06:46:45", "plugin": "core", "name": "end_epoch", "raw_value": "1698130005.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 06:46:45", "plugin": "core", "name": "start_epoch", "raw_value": "1698130005.0000000"}, {"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": "poretools_qualpos/0.6.1a1.1-0", "has_data": true, "data": {"tool_id": "poretools_qualpos", "tool_version": "0.6.1a1.1", "test_index": 0, "time_seconds": 66.21052098274231, "inputs": {"input": {"src": "hda", "id": "c266cf408fb9957c"}, "extension": "png"}, "job": {"model_class": "Job", "id": "39ee6c7f2ab69e67", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T06:48:14.771948", "create_time": "2023-10-24T06:47:29.992860", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualpos/poretools_qualpos/0.6.1a1.1", "history_id": "b8e3c9423bdc89f6", "external_id": "gxy-fv25w", "command_line": "export MPLBACKEND=\"agg\" && poretools qualpos '/galaxy/server/database/objects/7/9/0/dataset_79087b2d-7192-4f7a-8acd-939f28a6999a.dat' --saveas qualpos.png --min-length 0 --max-length 1000000000 --bin-width 1000 && mv qualpos.png '/galaxy/server/database/objects/6/4/b/dataset_64b1076b-c6ce-4a77-b0ab-fd148486cb42.dat'", "traceback": null, "params": {"__input_ext": "\"fast5.tar\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "bin_width": "\"1000\"", "max_length": "\"1000000000\"", "min_length": "\"0\"", "theme_bw": "false", "extension": "\"png\""}, "inputs": {"input": {"id": "c266cf408fb9957c", "src": "hda", "uuid": "79087b2d-7192-4f7a-8acd-939f28a6999a"}}, "outputs": {"output": {"id": "b5c4717d6462b9cd", "src": "hda", "uuid": "64b1076b-c6ce-4a77-b0ab-fd148486cb42"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "INFO:poreminion:Processing data...\nINFO:poreminion:Constructing box plot...\nINFO:poreminion:Writing plot to file...\n", "job_stdout": "", "job_stderr": "", "stderr": "INFO:poreminion:Processing data...\nINFO:poreminion:Constructing box plot...\nINFO:poreminion:Writing plot to file...\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": "2023-10-24 06:47:57", "plugin": "core", "name": "end_epoch", "raw_value": "1698130077.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 06:47:56", "plugin": "core", "name": "start_epoch", "raw_value": "1698130076.0000000"}, {"title": "Memory Allocated (MB)", "value": "12240", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12240.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "poretools_qualpos/0.6.1a1.1-1", "has_data": true, "data": {"tool_id": "poretools_qualpos", "tool_version": "0.6.1a1.1", "test_index": 1, "time_seconds": 34.56123208999634, "inputs": {"input": {"src": "hda", "id": "72e0b1c8686ab46e"}, "extension": "pdf"}, "job": {"model_class": "Job", "id": "4db4a831b783ae03", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T06:48:49.351351", "create_time": "2023-10-24T06:48:34.767751", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualpos/poretools_qualpos/0.6.1a1.1", "history_id": "b8e3c9423bdc89f6", "external_id": "gxy-t6zmp", "command_line": "export MPLBACKEND=\"agg\" && poretools qualpos '/galaxy/server/database/objects/1/8/8/dataset_18874cc2-5ca5-4f68-9786-c48b4cfe72f7.dat' --saveas qualpos.pdf --min-length 0 --max-length 1000000000 --bin-width 1000 && mv qualpos.pdf '/galaxy/server/database/objects/0/1/7/dataset_0179b3aa-fd69-417e-ba94-207181e88dd5.dat'", "traceback": null, "params": {"__input_ext": "\"fast5.tar\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "bin_width": "\"1000\"", "max_length": "\"1000000000\"", "min_length": "\"0\"", "theme_bw": "false", "extension": "\"pdf\""}, "inputs": {"input": {"id": "72e0b1c8686ab46e", "src": "hda", "uuid": "18874cc2-5ca5-4f68-9786-c48b4cfe72f7"}}, "outputs": {"output": {"id": "35e4ae728060a1bc", "src": "hda", "uuid": "0179b3aa-fd69-417e-ba94-207181e88dd5"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "INFO:poreminion:Processing data...\nINFO:poreminion:Constructing box plot...\nINFO:poreminion:Writing plot to file...\n", "job_stdout": "", "job_stderr": "", "stderr": "INFO:poreminion:Processing data...\nINFO:poreminion:Constructing box plot...\nINFO:poreminion:Writing plot to file...\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}, {"title": "Job End Time", "value": "2023-10-24 06:48:38", "plugin": "core", "name": "end_epoch", "raw_value": "1698130118.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 06:48:36", "plugin": "core", "name": "start_epoch", "raw_value": "1698130116.0000000"}, {"title": "Memory Allocated (MB)", "value": "12240", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12240.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "query_tabular/3.3.0-0", "has_data": true, "data": {"tool_id": "query_tabular", "tool_version": "3.3.0", "test_index": 0, "time_seconds": 39.83084297180176, "inputs": {"tables_0|table": {"src": "hda", "id": "8e26fadd3debc078"}, "tables_0|input_opts|linefilters_0|filter|comment_char": "35", "tables_0|input_opts|linefilters_0|filter|filter_type": "comment", "tables_0|tbl_opts|table_name": "customers", "tables_0|tbl_opts|col_names": "CustomerID,FirstName,LastName,Email,DOB,Phone", "tables_1|table": {"src": "hda", "id": "1c70ec5bc2d319c3"}, "tables_1|input_opts|linefilters_0|filter|comment_char": "35", "tables_1|input_opts|linefilters_0|filter|filter_type": "comment", "tables_1|tbl_opts|table_name": "sales", "tables_1|tbl_opts|col_names": "CustomerID,Date,SaleAmount", "sqlquery": "SELECT FirstName,LastName,sum(SaleAmount) as \"TotalSales\" FROM customers join sales on customers.CustomerID = sales.CustomerID GROUP BY customers.CustomerID ORDER BY TotalSales DESC"}, "job": {"model_class": "Job", "id": "c2817ae83258538f", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T06:56:07.302671", "create_time": "2023-10-24T06:55:49.056495", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0", "history_id": "b8e3c9423bdc89f6", "external_id": "gxy-pwpnf", "command_line": "cat '/galaxy/server/database/jobs_directory/000/118/configs/tmpi_296pfs' && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/cf34c344508d/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/118/configs/tmp23_aahur' -Q '/galaxy/server/database/jobs_directory/000/118/configs/tmpi_296pfs' --comment_char='#' -o '/galaxy/server/database/objects/7/d/3/dataset_7d3c0066-63b5-4d1d-9334-f80cb6051ca6.dat'", "traceback": null, "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addqueries": "{\"queries\": []}", "query_result": "{\"__current_case__\": 0, \"header\": \"yes\", \"header_prefix\": \"35\"}", "sqlquery": "\"SELECT FirstName,LastName,sum(SaleAmount) as \\\"TotalSales\\\" FROM customers join sales on customers.CustomerID = sales.CustomerID GROUP BY customers.CustomerID ORDER BY TotalSales DESC\"", "save_db": "false", "modify_database": "{\"sql_stmts\": []}", "tables": "[{\"__index__\": 0, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"__current_case__\": 1, \"comment_char\": \"35\", \"filter_type\": \"comment\"}}]}, \"table\": {\"values\": [{\"id\": 140, \"src\": \"hda\"}]}, \"tbl_opts\": {\"col_names\": \"CustomerID,FirstName,LastName,Email,DOB,Phone\", \"column_names_from_first_line\": false, \"indexes\": [], \"load_named_columns\": false, \"pkey_autoincr\": \"\", \"table_name\": \"customers\"}}, {\"__index__\": 1, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"__current_case__\": 1, \"comment_char\": \"35\", \"filter_type\": \"comment\"}}]}, \"table\": {\"values\": [{\"id\": 141, \"src\": \"hda\"}]}, \"tbl_opts\": {\"col_names\": \"CustomerID,Date,SaleAmount\", \"column_names_from_first_line\": false, \"indexes\": [], \"load_named_columns\": false, \"pkey_autoincr\": \"\", \"table_name\": \"sales\"}}]", "add_to_database": "{\"withdb\": null}", "workdb": "\"workdb.sqlite\""}, "inputs": {"tables_0|table": {"id": "8e26fadd3debc078", "src": "hda", "uuid": "50b2313b-26ae-48e9-8c30-6ab5bb930854"}, "tables_1|table": {"id": "1c70ec5bc2d319c3", "src": "hda", "uuid": "fd676cb1-e39f-4f01-b34c-6c8881ee0e1e"}}, "outputs": {"output": {"id": "8073c888c3a180a0", "src": "hda", "uuid": "7d3c0066-63b5-4d1d-9334-f80cb6051ca6"}}, "output_collections": {}, "tool_stdout": "\nSELECT FirstName,LastName,sum(SaleAmount) as \"TotalSales\" FROM customers join sales on customers.CustomerID = sales.CustomerID GROUP BY customers.CustomerID ORDER BY TotalSales DESC\n ", "tool_stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/5/0/b/dataset_50b2313b-26ae-48e9-8c30-6ab5bb930854.dat', 'table_name': 'customers', 'column_names': 'CustomerID,FirstName,LastName,Email,DOB,Phone', 'filters': [{'filter': 'regex', 'pattern': '^(#).*$', 'action': 'exclude_match'}]}, {'file_path': '/galaxy/server/database/objects/f/d/6/dataset_fd676cb1-e39f-4f01-b34c-6c8881ee0e1e.dat', 'table_name': 'sales', 'column_names': 'CustomerID,Date,SaleAmount', 'filters': [{'filter': 'regex', 'pattern': '^(#).*$', 'action': 'exclude_match'}]}]}\n\nSQL: \nSELECT FirstName,LastName,sum(SaleAmount) as \"TotalSales\" FROM customers join sales on customers.CustomerID = sales.CustomerID GROUP BY customers.CustomerID ORDER BY TotalSales DESC\n \nrowcount: None\n", "job_stdout": "", "job_stderr": "", "stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/5/0/b/dataset_50b2313b-26ae-48e9-8c30-6ab5bb930854.dat', 'table_name': 'customers', 'column_names': 'CustomerID,FirstName,LastName,Email,DOB,Phone', 'filters': [{'filter': 'regex', 'pattern': '^(#).*$', 'action': 'exclude_match'}]}, {'file_path': '/galaxy/server/database/objects/f/d/6/dataset_fd676cb1-e39f-4f01-b34c-6c8881ee0e1e.dat', 'table_name': 'sales', 'column_names': 'CustomerID,Date,SaleAmount', 'filters': [{'filter': 'regex', 'pattern': '^(#).*$', 'action': 'exclude_match'}]}]}\n\nSQL: \nSELECT FirstName,LastName,sum(SaleAmount) as \"TotalSales\" FROM customers join sales on customers.CustomerID = sales.CustomerID GROUP BY customers.CustomerID ORDER BY TotalSales DESC\n \nrowcount: None\n", "stdout": "\nSELECT FirstName,LastName,sum(SaleAmount) as \"TotalSales\" FROM customers join sales on customers.CustomerID = sales.CustomerID GROUP BY customers.CustomerID ORDER BY TotalSales DESC\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": "2023-10-24 06:55:56", "plugin": "core", "name": "end_epoch", "raw_value": "1698130556.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 06:55:56", "plugin": "core", "name": "start_epoch", "raw_value": "1698130556.0000000"}, {"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": "query_tabular/3.3.0-1", "has_data": true, "data": {"tool_id": "query_tabular", "tool_version": "3.3.0", "test_index": 1, "time_seconds": 32.59616470336914, "inputs": {"tables_0|table": {"src": "hda", "id": "3b8c6b9f6fd7594a"}, "tables_0|input_opts|linefilters_0|filter|comment_char": "35", "tables_0|input_opts|linefilters_0|filter|filter_type": "comment", "tables_0|tbl_opts|col_names": ",FirstName,LastName,,DOB,", "tables_1|table": {"src": "hda", "id": "097a88afa78b74af"}, "tables_1|input_opts|linefilters_0|filter|skip_lines": "1", "tables_1|input_opts|linefilters_0|filter|filter_type": "skip", "sqlquery": "SELECT FirstName,LastName,sum(t2.c3) as \"TotalSales\" FROM t1 join t2 on t1.c1 = t2.c1 GROUP BY t1.c1 ORDER BY TotalSales DESC;"}, "job": {"model_class": "Job", "id": "41a888e05d248b65", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T06:56:39.978340", "create_time": "2023-10-24T06:56:27.669426", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0", "history_id": "b8e3c9423bdc89f6", "external_id": "gxy-bvqlc", "command_line": "cat '/galaxy/server/database/jobs_directory/000/121/configs/tmpm44nhpdj' && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/cf34c344508d/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/121/configs/tmpfxjqlhvh' -Q '/galaxy/server/database/jobs_directory/000/121/configs/tmpm44nhpdj' --comment_char='#' -o '/galaxy/server/database/objects/f/0/6/dataset_f06c33b5-5254-4c9a-ac23-3f4cdb3325cb.dat'", "traceback": null, "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addqueries": "{\"queries\": []}", "query_result": "{\"__current_case__\": 0, \"header\": \"yes\", \"header_prefix\": \"35\"}", "sqlquery": "\"SELECT FirstName,LastName,sum(t2.c3) as \\\"TotalSales\\\" FROM t1 join t2 on t1.c1 = t2.c1 GROUP BY t1.c1 ORDER BY TotalSales DESC;\"", "save_db": "false", "modify_database": "{\"sql_stmts\": []}", "tables": "[{\"__index__\": 0, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"__current_case__\": 1, \"comment_char\": \"35\", \"filter_type\": \"comment\"}}]}, \"table\": {\"values\": [{\"id\": 143, \"src\": \"hda\"}]}, \"tbl_opts\": {\"col_names\": \",FirstName,LastName,,DOB,\", \"column_names_from_first_line\": false, \"indexes\": [], \"load_named_columns\": false, \"pkey_autoincr\": \"\", \"table_name\": \"\"}}, {\"__index__\": 1, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"__current_case__\": 0, \"filter_type\": \"skip\", \"skip_lines\": \"1\"}}]}, \"table\": {\"values\": [{\"id\": 144, \"src\": \"hda\"}]}, \"tbl_opts\": {\"col_names\": \"\", \"column_names_from_first_line\": false, \"indexes\": [], \"load_named_columns\": false, \"pkey_autoincr\": \"\", \"table_name\": \"\"}}]", "add_to_database": "{\"withdb\": null}", "workdb": "\"workdb.sqlite\""}, "inputs": {"tables_0|table": {"id": "3b8c6b9f6fd7594a", "src": "hda", "uuid": "ac65080c-e627-4585-bd34-3b4bfbd1514c"}, "tables_1|table": {"id": "097a88afa78b74af", "src": "hda", "uuid": "0704719f-85f2-4978-84bd-ab22d4cfc233"}}, "outputs": {"output": {"id": "6d43fcd162a02898", "src": "hda", "uuid": "f06c33b5-5254-4c9a-ac23-3f4cdb3325cb"}}, "output_collections": {}, "tool_stdout": "\nSELECT FirstName,LastName,sum(t2.c3) as \"TotalSales\" FROM t1 join t2 on t1.c1 = t2.c1 GROUP BY t1.c1 ORDER BY TotalSales DESC;\n ", "tool_stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/a/c/6/dataset_ac65080c-e627-4585-bd34-3b4bfbd1514c.dat', 'table_name': 't1', 'column_names': ',FirstName,LastName,,DOB,', 'filters': [{'filter': 'regex', 'pattern': '^(#).*$', 'action': 'exclude_match'}]}, {'file_path': '/galaxy/server/database/objects/0/7/0/dataset_0704719f-85f2-4978-84bd-ab22d4cfc233.dat', 'table_name': 't2', 'column_names': '', 'filters': [{'filter': 'skip', 'count': 1}]}]}\n\nSQL: \nSELECT FirstName,LastName,sum(t2.c3) as \"TotalSales\" FROM t1 join t2 on t1.c1 = t2.c1 GROUP BY t1.c1 ORDER BY TotalSales DESC;\n \nrowcount: None\n", "job_stdout": "", "job_stderr": "", "stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/a/c/6/dataset_ac65080c-e627-4585-bd34-3b4bfbd1514c.dat', 'table_name': 't1', 'column_names': ',FirstName,LastName,,DOB,', 'filters': [{'filter': 'regex', 'pattern': '^(#).*$', 'action': 'exclude_match'}]}, {'file_path': '/galaxy/server/database/objects/0/7/0/dataset_0704719f-85f2-4978-84bd-ab22d4cfc233.dat', 'table_name': 't2', 'column_names': '', 'filters': [{'filter': 'skip', 'count': 1}]}]}\n\nSQL: \nSELECT FirstName,LastName,sum(t2.c3) as \"TotalSales\" FROM t1 join t2 on t1.c1 = t2.c1 GROUP BY t1.c1 ORDER BY TotalSales DESC;\n \nrowcount: None\n", "stdout": "\nSELECT FirstName,LastName,sum(t2.c3) as \"TotalSales\" FROM t1 join t2 on t1.c1 = t2.c1 GROUP BY t1.c1 ORDER BY TotalSales DESC;\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": "2023-10-24 06:56:29", "plugin": "core", "name": "end_epoch", "raw_value": "1698130589.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 06:56:29", "plugin": "core", "name": "start_epoch", "raw_value": "1698130589.0000000"}, {"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": "query_tabular/3.3.0-10", "has_data": true, "data": {"tool_id": "query_tabular", "tool_version": "3.3.0", "test_index": 10, "time_seconds": 32.51338481903076, "inputs": {"tables_0|table": {"src": "hda", "id": "8e177bc4dec00c37"}, "tables_0|input_opts|linefilters_0|filter|regex_pattern": "NOT TO BE FOUND", "tables_0|input_opts|linefilters_0|filter|regex_action": "include_find", "tables_0|input_opts|linefilters_0|filter|filter_type": "regex", "tables_0|tbl_opts|table_name": "epitope", "tables_0|tbl_opts|column_names_from_first_line": false, "tables_0|tbl_opts|col_names": "pos,peptide,logscore,,,,Allele", "sqlquery": "SELECT pos,peptide,logscore,Allele FROM epitope", "query_result|header_prefix": "", "query_result|header": "yes"}, "job": {"model_class": "Job", "id": "8e26fadd3debc078", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T07:01:01.086250", "create_time": "2023-10-24T07:00:48.223273", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0", "history_id": "b8e3c9423bdc89f6", "external_id": "gxy-6gr95", "command_line": "cat '/galaxy/server/database/jobs_directory/000/140/configs/tmp49mxk32p' && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/cf34c344508d/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/140/configs/tmpu2ts7pk0' -Q '/galaxy/server/database/jobs_directory/000/140/configs/tmp49mxk32p' -o '/galaxy/server/database/objects/a/a/1/dataset_aa19a5dd-d765-4014-9169-0e369a58a3aa.dat'", "traceback": null, "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addqueries": "{\"queries\": []}", "query_result": "{\"__current_case__\": 0, \"header\": \"yes\", \"header_prefix\": \"\"}", "sqlquery": "\"SELECT pos,peptide,logscore,Allele FROM epitope\"", "save_db": "false", "modify_database": "{\"sql_stmts\": []}", "tables": "[{\"__index__\": 0, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"__current_case__\": 8, \"filter_type\": \"regex\", \"regex_action\": \"include_find\", \"regex_pattern\": \"NOT TO BE FOUND\"}}]}, \"table\": {\"values\": [{\"id\": 164, \"src\": \"hda\"}]}, \"tbl_opts\": {\"col_names\": \"pos,peptide,logscore,,,,Allele\", \"column_names_from_first_line\": false, \"indexes\": [], \"load_named_columns\": false, \"pkey_autoincr\": \"\", \"table_name\": \"epitope\"}}]", "add_to_database": "{\"withdb\": null}", "workdb": "\"workdb.sqlite\""}, "inputs": {"tables_0|table": {"id": "8e177bc4dec00c37", "src": "hda", "uuid": "2c21b82c-f67f-4799-b331-eb443dd6101d"}}, "outputs": {"output": {"id": "b9794d7281f57f72", "src": "hda", "uuid": "aa19a5dd-d765-4014-9169-0e369a58a3aa"}}, "output_collections": {}, "tool_stdout": "\nSELECT pos,peptide,logscore,Allele FROM epitope\n ", "tool_stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/2/c/2/dataset_2c21b82c-f67f-4799-b331-eb443dd6101d.dat', 'table_name': 'epitope', 'column_names': 'pos,peptide,logscore,,,,Allele', 'filters': [{'filter': 'regex', 'pattern': 'NOT TO BE FOUND', 'action': 'include_find'}]}]}\n\nSQL: \nSELECT pos,peptide,logscore,Allele FROM epitope\n \nrowcount: None\n", "job_stdout": "", "job_stderr": "", "stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/2/c/2/dataset_2c21b82c-f67f-4799-b331-eb443dd6101d.dat', 'table_name': 'epitope', 'column_names': 'pos,peptide,logscore,,,,Allele', 'filters': [{'filter': 'regex', 'pattern': 'NOT TO BE FOUND', 'action': 'include_find'}]}]}\n\nSQL: \nSELECT pos,peptide,logscore,Allele FROM epitope\n \nrowcount: None\n", "stdout": "\nSELECT pos,peptide,logscore,Allele FROM epitope\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": "2023-10-24 07:00:50", "plugin": "core", "name": "end_epoch", "raw_value": "1698130850.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 07:00:50", "plugin": "core", "name": "start_epoch", "raw_value": "1698130850.0000000"}, {"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": "query_tabular/3.3.0-11", "has_data": true, "data": {"tool_id": "query_tabular", "tool_version": "3.3.0", "test_index": 11, "time_seconds": 32.65911054611206, "inputs": {"tables_0|table": {"src": "hda", "id": "02a0a02a94ae90a1"}, "sqlquery": "SELECT c1, c2, trunc(c2), floor(c2), ceil(c2), abs(c1), fabs(c2), mod(c1,2), fmod(c2, 1.5), sqrt(c1), sqrt(c2), degrees(c1), radians(c1), log(c1), log10(c1), pow(c1,2), exp(c2), exp(c1), cos(c1), sin(c1), tan(c1), cosh(c1), sinh(c1), tanh(c1), acos(c1), asin(c1),acosh(c1), asinh(c1) FROM t1"}, "job": {"model_class": "Job", "id": "8073c888c3a180a0", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T07:01:34.421116", "create_time": "2023-10-24T07:01:20.931443", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0", "history_id": "b8e3c9423bdc89f6", "external_id": "gxy-hr25s", "command_line": "cat '/galaxy/server/database/jobs_directory/000/142/configs/tmpfu26v9t1' && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/cf34c344508d/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/142/configs/tmpz20jijqd' -Q '/galaxy/server/database/jobs_directory/000/142/configs/tmpfu26v9t1' --comment_char='#' -o '/galaxy/server/database/objects/2/d/2/dataset_2d2d134b-3f05-4259-874a-a8d0a68a6c1c.dat'", "traceback": null, "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addqueries": "{\"queries\": []}", "query_result": "{\"__current_case__\": 0, \"header\": \"yes\", \"header_prefix\": \"35\"}", "sqlquery": "\"SELECT c1, c2, trunc(c2), floor(c2), ceil(c2), abs(c1), fabs(c2), mod(c1,2), fmod(c2, 1.5), sqrt(c1), sqrt(c2), degrees(c1), radians(c1), log(c1), log10(c1), pow(c1,2), exp(c2), exp(c1), cos(c1), sin(c1), tan(c1), cosh(c1), sinh(c1), tanh(c1), acos(c1), asin(c1),acosh(c1), asinh(c1) FROM t1\"", "save_db": "false", "modify_database": "{\"sql_stmts\": []}", "tables": "[{\"__index__\": 0, \"input_opts\": {\"linefilters\": []}, \"table\": {\"values\": [{\"id\": 166, \"src\": \"hda\"}]}, \"tbl_opts\": {\"col_names\": \"\", \"column_names_from_first_line\": false, \"indexes\": [], \"load_named_columns\": false, \"pkey_autoincr\": \"\", \"table_name\": \"\"}}]", "add_to_database": "{\"withdb\": null}", "workdb": "\"workdb.sqlite\""}, "inputs": {"tables_0|table": {"id": "02a0a02a94ae90a1", "src": "hda", "uuid": "40da69dc-21a9-419c-a984-99e342d70f3c"}}, "outputs": {"output": {"id": "e62095c09f1c2171", "src": "hda", "uuid": "2d2d134b-3f05-4259-874a-a8d0a68a6c1c"}}, "output_collections": {}, "tool_stdout": "\nSELECT c1, c2, trunc(c2), floor(c2), ceil(c2), abs(c1), fabs(c2), mod(c1,2), fmod(c2, 1.5), sqrt(c1), sqrt(c2), degrees(c1), radians(c1), log(c1), log10(c1), pow(c1,2), exp(c2), exp(c1), cos(c1), sin(c1), tan(c1), cosh(c1), sinh(c1), tanh(c1), acos(c1), asin(c1),acosh(c1), asinh(c1) FROM t1\n ", "tool_stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/4/0/d/dataset_40da69dc-21a9-419c-a984-99e342d70f3c.dat', 'table_name': 't1', 'column_names': ''}]}\nsqrt(-2): math domain error\nsqrt(-2.222): math domain error\nlog(-2): math domain error\nlog10(-2): math domain error\nacos(-2): math domain error\nasin(-2): math domain error\nacosh(-2): math domain error\nsqrt(-1): math domain error\nsqrt(-1.999): math domain error\nlog(-1): math domain error\nlog10(-1): math domain error\nacosh(-1): math domain error\nlog(0): math domain error\nlog10(0): math domain error\nacosh(0): math domain error\nacos(2): math domain error\nasin(2): math domain error\nacos(3): math domain error\nasin(3): math domain error\nacos(4): math domain error\nasin(4): math domain error\nacos(5): math domain error\nasin(5): math domain error\n\nSQL: \nSELECT c1, c2, trunc(c2), floor(c2), ceil(c2), abs(c1), fabs(c2), mod(c1,2), fmod(c2, 1.5), sqrt(c1), sqrt(c2), degrees(c1), radians(c1), log(c1), log10(c1), pow(c1,2), exp(c2), exp(c1), cos(c1), sin(c1), tan(c1), cosh(c1), sinh(c1), tanh(c1), acos(c1), asin(c1),acosh(c1), asinh(c1) FROM t1\n \nrowcount: None\n", "job_stdout": "", "job_stderr": "", "stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/4/0/d/dataset_40da69dc-21a9-419c-a984-99e342d70f3c.dat', 'table_name': 't1', 'column_names': ''}]}\nsqrt(-2): math domain error\nsqrt(-2.222): math domain error\nlog(-2): math domain error\nlog10(-2): math domain error\nacos(-2): math domain error\nasin(-2): math domain error\nacosh(-2): math domain error\nsqrt(-1): math domain error\nsqrt(-1.999): math domain error\nlog(-1): math domain error\nlog10(-1): math domain error\nacosh(-1): math domain error\nlog(0): math domain error\nlog10(0): math domain error\nacosh(0): math domain error\nacos(2): math domain error\nasin(2): math domain error\nacos(3): math domain error\nasin(3): math domain error\nacos(4): math domain error\nasin(4): math domain error\nacos(5): math domain error\nasin(5): math domain error\n\nSQL: \nSELECT c1, c2, trunc(c2), floor(c2), ceil(c2), abs(c1), fabs(c2), mod(c1,2), fmod(c2, 1.5), sqrt(c1), sqrt(c2), degrees(c1), radians(c1), log(c1), log10(c1), pow(c1,2), exp(c2), exp(c1), cos(c1), sin(c1), tan(c1), cosh(c1), sinh(c1), tanh(c1), acos(c1), asin(c1),acosh(c1), asinh(c1) FROM t1\n \nrowcount: None\n", "stdout": "\nSELECT c1, c2, trunc(c2), floor(c2), ceil(c2), abs(c1), fabs(c2), mod(c1,2), fmod(c2, 1.5), sqrt(c1), sqrt(c2), degrees(c1), radians(c1), log(c1), log10(c1), pow(c1,2), exp(c2), exp(c1), cos(c1), sin(c1), tan(c1), cosh(c1), sinh(c1), tanh(c1), acos(c1), asin(c1),acosh(c1), asinh(c1) FROM t1\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": "2023-10-24 07:01:23", "plugin": "core", "name": "end_epoch", "raw_value": "1698130883.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 07:01:23", "plugin": "core", "name": "start_epoch", "raw_value": "1698130883.0000000"}, {"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": "query_tabular/3.3.0-2", "has_data": true, "data": {"tool_id": "query_tabular", "tool_version": "3.3.0", "test_index": 2, "time_seconds": 31.51359987258911, "inputs": {"tables_0|table": {"src": "hda", "id": "e2c00607622263d9"}, "tables_0|input_opts|linefilters_0|filter|skip_lines": "1", "tables_0|input_opts|linefilters_0|filter|filter_type": "skip", "tables_0|tbl_opts|col_names": ",FirstName,LastName,,BirthDate,", "sqlquery": "select FirstName,LastName,re_sub('^\\d{2}(\\d{2})-(\\d\\d)-(\\d\\d)','\\3/\\2/\\1',BirthDate) as \"DOB\" from t1 WHERE re_search('[hp]er',c4)"}, "job": {"model_class": "Job", "id": "2508872f2388dfce", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T06:57:11.435078", "create_time": "2023-10-24T06:56:59.787256", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0", "history_id": "b8e3c9423bdc89f6", "external_id": "gxy-f9784", "command_line": "cat '/galaxy/server/database/jobs_directory/000/123/configs/tmp4it7886o' && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/cf34c344508d/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/123/configs/tmpnzi0reyf' -Q '/galaxy/server/database/jobs_directory/000/123/configs/tmp4it7886o' --comment_char='#' -o '/galaxy/server/database/objects/2/4/3/dataset_243ecf36-dd3a-4d88-83bd-2ae44308991b.dat'", "traceback": null, "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addqueries": "{\"queries\": []}", "query_result": "{\"__current_case__\": 0, \"header\": \"yes\", \"header_prefix\": \"35\"}", "sqlquery": "\"select FirstName,LastName,re_sub('^\\\\d{2}(\\\\d{2})-(\\\\d\\\\d)-(\\\\d\\\\d)','\\\\3/\\\\2/\\\\1',BirthDate) as \\\"DOB\\\" from t1 WHERE re_search('[hp]er',c4)\"", "save_db": "false", "modify_database": "{\"sql_stmts\": []}", "tables": "[{\"__index__\": 0, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"__current_case__\": 0, \"filter_type\": \"skip\", \"skip_lines\": \"1\"}}]}, \"table\": {\"values\": [{\"id\": 146, \"src\": \"hda\"}]}, \"tbl_opts\": {\"col_names\": \",FirstName,LastName,,BirthDate,\", \"column_names_from_first_line\": false, \"indexes\": [], \"load_named_columns\": false, \"pkey_autoincr\": \"\", \"table_name\": \"\"}}]", "add_to_database": "{\"withdb\": null}", "workdb": "\"workdb.sqlite\""}, "inputs": {"tables_0|table": {"id": "e2c00607622263d9", "src": "hda", "uuid": "f64d601c-6819-4f97-a6e6-31460789f26a"}}, "outputs": {"output": {"id": "69510454f39def74", "src": "hda", "uuid": "243ecf36-dd3a-4d88-83bd-2ae44308991b"}}, "output_collections": {}, "tool_stdout": "\nselect FirstName,LastName,re_sub('^\\d{2}(\\d{2})-(\\d\\d)-(\\d\\d)','\\3/\\2/\\1',BirthDate) as \"DOB\" from t1 WHERE re_search('[hp]er',c4)\n ", "tool_stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/f/6/4/dataset_f64d601c-6819-4f97-a6e6-31460789f26a.dat', 'table_name': 't1', 'column_names': ',FirstName,LastName,,BirthDate,', 'filters': [{'filter': 'skip', 'count': 1}]}]}\n\nSQL: \nselect FirstName,LastName,re_sub('^\\d{2}(\\d{2})-(\\d\\d)-(\\d\\d)','\\3/\\2/\\1',BirthDate) as \"DOB\" from t1 WHERE re_search('[hp]er',c4)\n \nrowcount: None\n", "job_stdout": "", "job_stderr": "", "stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/f/6/4/dataset_f64d601c-6819-4f97-a6e6-31460789f26a.dat', 'table_name': 't1', 'column_names': ',FirstName,LastName,,BirthDate,', 'filters': [{'filter': 'skip', 'count': 1}]}]}\n\nSQL: \nselect FirstName,LastName,re_sub('^\\d{2}(\\d{2})-(\\d\\d)-(\\d\\d)','\\3/\\2/\\1',BirthDate) as \"DOB\" from t1 WHERE re_search('[hp]er',c4)\n \nrowcount: None\n", "stdout": "\nselect FirstName,LastName,re_sub('^\\d{2}(\\d{2})-(\\d\\d)-(\\d\\d)','\\3/\\2/\\1',BirthDate) as \"DOB\" from t1 WHERE re_search('[hp]er',c4)\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": "2023-10-24 06:57:01", "plugin": "core", "name": "end_epoch", "raw_value": "1698130621.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 06:57:01", "plugin": "core", "name": "start_epoch", "raw_value": "1698130621.0000000"}, {"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": "query_tabular/3.3.0-3", "has_data": true, "data": {"tool_id": "query_tabular", "tool_version": "3.3.0", "test_index": 3, "time_seconds": 32.150394916534424, "inputs": {"tables_0|table": {"src": "hda", "id": "7b8a8352110e45b6"}, "tables_0|input_opts|linefilters_0|filter|comment_char": "35", "tables_0|input_opts|linefilters_0|filter|filter_type": "comment", "tables_0|tbl_opts|table_name": "iedb", "tables_0|tbl_opts|col_names": "ID,allele,seq_num,start,end,length,peptide,method,percentile_rank,ann_ic50,ann_rank,smm_ic50,smm_rank,comblib_sidney2008_score,comblib_sidney2008_rank,netmhcpan_ic50,netmhcpan_rank", "tables_1|table": {"src": "hda", "id": "c41381f06c649741"}, "tables_1|input_opts|linefilters_0|filter|skip_lines": "1", "tables_1|input_opts|linefilters_0|filter|filter_type": "skip", "tables_1|tbl_opts|table_name": "mhc_summary", "tables_1|tbl_opts|col_names": "pos,peptide,logscore,affinity,Bind_Level,Protein,Allele", "sqlquery": "select iedb.ID,iedb.peptide,iedb.start,iedb.end,iedb.percentile_rank,mhc_summary.logscore,mhc_summary.affinity,mhc_summary.Bind_Level from iedb left outer join mhc_summary on iedb.peptide = mhc_summary.peptide order by affinity,Bind_Level,percentile_rank"}, "job": {"model_class": "Job", "id": "0b46f4832cf85eda", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T06:57:43.944849", "create_time": "2023-10-24T06:57:31.666685", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0", "history_id": "b8e3c9423bdc89f6", "external_id": "gxy-cdbds", "command_line": "cat '/galaxy/server/database/jobs_directory/000/126/configs/tmpzt7nusp0' && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/cf34c344508d/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/126/configs/tmpj2td2193' -Q '/galaxy/server/database/jobs_directory/000/126/configs/tmpzt7nusp0' --comment_char='#' -o '/galaxy/server/database/objects/9/5/0/dataset_950f612a-2fba-4fe0-8620-483ff86dcaf0.dat'", "traceback": null, "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addqueries": "{\"queries\": []}", "query_result": "{\"__current_case__\": 0, \"header\": \"yes\", \"header_prefix\": \"35\"}", "sqlquery": "\"select iedb.ID,iedb.peptide,iedb.start,iedb.end,iedb.percentile_rank,mhc_summary.logscore,mhc_summary.affinity,mhc_summary.Bind_Level from iedb left outer join mhc_summary on iedb.peptide = mhc_summary.peptide order by affinity,Bind_Level,percentile_rank\"", "save_db": "false", "modify_database": "{\"sql_stmts\": []}", "tables": "[{\"__index__\": 0, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"__current_case__\": 1, \"comment_char\": \"35\", \"filter_type\": \"comment\"}}]}, \"table\": {\"values\": [{\"id\": 148, \"src\": \"hda\"}]}, \"tbl_opts\": {\"col_names\": \"ID,allele,seq_num,start,end,length,peptide,method,percentile_rank,ann_ic50,ann_rank,smm_ic50,smm_rank,comblib_sidney2008_score,comblib_sidney2008_rank,netmhcpan_ic50,netmhcpan_rank\", \"column_names_from_first_line\": false, \"indexes\": [], \"load_named_columns\": false, \"pkey_autoincr\": \"\", \"table_name\": \"iedb\"}}, {\"__index__\": 1, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"__current_case__\": 0, \"filter_type\": \"skip\", \"skip_lines\": \"1\"}}]}, \"table\": {\"values\": [{\"id\": 149, \"src\": \"hda\"}]}, \"tbl_opts\": {\"col_names\": \"pos,peptide,logscore,affinity,Bind_Level,Protein,Allele\", \"column_names_from_first_line\": false, \"indexes\": [], \"load_named_columns\": false, \"pkey_autoincr\": \"\", \"table_name\": \"mhc_summary\"}}]", "add_to_database": "{\"withdb\": null}", "workdb": "\"workdb.sqlite\""}, "inputs": {"tables_0|table": {"id": "7b8a8352110e45b6", "src": "hda", "uuid": "1757fefb-3436-4e88-af51-9b7c72829efe"}, "tables_1|table": {"id": "c41381f06c649741", "src": "hda", "uuid": "809854ab-c155-4ad7-a2eb-b800365d78fc"}}, "outputs": {"output": {"id": "4dafd9736a46b5aa", "src": "hda", "uuid": "950f612a-2fba-4fe0-8620-483ff86dcaf0"}}, "output_collections": {}, "tool_stdout": "\nselect iedb.ID,iedb.peptide,iedb.start,iedb.end,iedb.percentile_rank,mhc_summary.logscore,mhc_summary.affinity,mhc_summary.Bind_Level from iedb left outer join mhc_summary on iedb.peptide = mhc_summary.peptide order by affinity,Bind_Level,percentile_rank\n ", "tool_stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/1/7/5/dataset_1757fefb-3436-4e88-af51-9b7c72829efe.dat', 'table_name': 'iedb', 'column_names': 'ID,allele,seq_num,start,end,length,peptide,method,percentile_rank,ann_ic50,ann_rank,smm_ic50,smm_rank,comblib_sidney2008_score,comblib_sidney2008_rank,netmhcpan_ic50,netmhcpan_rank', 'filters': [{'filter': 'regex', 'pattern': '^(#).*$', 'action': 'exclude_match'}]}, {'file_path': '/galaxy/server/database/objects/8/0/9/dataset_809854ab-c155-4ad7-a2eb-b800365d78fc.dat', 'table_name': 'mhc_summary', 'column_names': 'pos,peptide,logscore,affinity,Bind_Level,Protein,Allele', 'filters': [{'filter': 'skip', 'count': 1}]}]}\n\nSQL: \nselect iedb.ID,iedb.peptide,iedb.start,iedb.end,iedb.percentile_rank,mhc_summary.logscore,mhc_summary.affinity,mhc_summary.Bind_Level from iedb left outer join mhc_summary on iedb.peptide = mhc_summary.peptide order by affinity,Bind_Level,percentile_rank\n \nrowcount: None\n", "job_stdout": "", "job_stderr": "", "stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/1/7/5/dataset_1757fefb-3436-4e88-af51-9b7c72829efe.dat', 'table_name': 'iedb', 'column_names': 'ID,allele,seq_num,start,end,length,peptide,method,percentile_rank,ann_ic50,ann_rank,smm_ic50,smm_rank,comblib_sidney2008_score,comblib_sidney2008_rank,netmhcpan_ic50,netmhcpan_rank', 'filters': [{'filter': 'regex', 'pattern': '^(#).*$', 'action': 'exclude_match'}]}, {'file_path': '/galaxy/server/database/objects/8/0/9/dataset_809854ab-c155-4ad7-a2eb-b800365d78fc.dat', 'table_name': 'mhc_summary', 'column_names': 'pos,peptide,logscore,affinity,Bind_Level,Protein,Allele', 'filters': [{'filter': 'skip', 'count': 1}]}]}\n\nSQL: \nselect iedb.ID,iedb.peptide,iedb.start,iedb.end,iedb.percentile_rank,mhc_summary.logscore,mhc_summary.affinity,mhc_summary.Bind_Level from iedb left outer join mhc_summary on iedb.peptide = mhc_summary.peptide order by affinity,Bind_Level,percentile_rank\n \nrowcount: None\n", "stdout": "\nselect iedb.ID,iedb.peptide,iedb.start,iedb.end,iedb.percentile_rank,mhc_summary.logscore,mhc_summary.affinity,mhc_summary.Bind_Level from iedb left outer join mhc_summary on iedb.peptide = mhc_summary.peptide order by affinity,Bind_Level,percentile_rank\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": "2023-10-24 06:57:34", "plugin": "core", "name": "end_epoch", "raw_value": "1698130654.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 06:57:34", "plugin": "core", "name": "start_epoch", "raw_value": "1698130654.0000000"}, {"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": "query_tabular/3.3.0-4", "has_data": true, "data": {"tool_id": "query_tabular", "tool_version": "3.3.0", "test_index": 4, "time_seconds": 34.66865086555481, "inputs": {"add_to_database|withdb": {"src": "hda", "id": "db8b8af119989393"}, "tables_0|table": {"src": "hda", "id": "70d4db306a0fab2b"}, "tables_0|input_opts|linefilters_0|filter|regex_pattern": "^\\d+", "tables_0|input_opts|linefilters_0|filter|regex_action": "include_find", "tables_0|input_opts|linefilters_0|filter|filter_type": "regex", "tables_0|input_opts|linefilters_1|filter|comment_char": "35", "tables_0|input_opts|linefilters_1|filter|filter_type": "comment", "tables_0|input_opts|linefilters_2|filter|filter_type": "append_line_num", "tables_0|input_opts|linefilters_3|filter|columns": "7,2,3,4,1", "tables_0|input_opts|linefilters_3|filter|filter_type": "select_columns", "tables_0|input_opts|linefilters_4|filter|column": "c4", "tables_0|input_opts|linefilters_4|filter|regex_pattern": "(\\d+)/(\\d+)/(\\d+)", "tables_0|input_opts|linefilters_4|filter|regex_replace": "19\\3-\\2-\\1", "tables_0|input_opts|linefilters_4|filter|filter_type": "replace", "tables_0|tbl_opts|table_name": "people", "tables_0|tbl_opts|col_names": "id,first,last,dob,pets", "sqlquery": "SELECT people.id,first,last,pets,quote FROM people JOIN contacts ON people.first = contacts.first_name"}, "job": {"model_class": "Job", "id": "1fba13c59ee144a3", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T06:58:18.537324", "create_time": "2023-10-24T06:58:05.239469", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0", "history_id": "b8e3c9423bdc89f6", "external_id": "gxy-rfx54", "command_line": "cat '/galaxy/server/database/jobs_directory/000/129/configs/tmpwnxe09ke' && cp '/galaxy/server/database/objects/c/4/4/dataset_c44b2bea-960c-498d-8197-035dc99cfd00.dat' 'workdb.sqlite' && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/cf34c344508d/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/129/configs/tmp9m01rjnp' -Q '/galaxy/server/database/jobs_directory/000/129/configs/tmpwnxe09ke' --comment_char='#' -o '/galaxy/server/database/objects/e/e/1/dataset_ee13ebf3-8a7a-4ac9-a645-c3565f72e525.dat'", "traceback": null, "params": {"__input_ext": "\"sqlite\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addqueries": "{\"queries\": []}", "query_result": "{\"__current_case__\": 0, \"header\": \"yes\", \"header_prefix\": \"35\"}", "sqlquery": "\"SELECT people.id,first,last,pets,quote FROM people JOIN contacts ON people.first = contacts.first_name\"", "save_db": "false", "modify_database": "{\"sql_stmts\": []}", "tables": "[{\"__index__\": 0, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"__current_case__\": 8, \"filter_type\": \"regex\", \"regex_action\": \"include_find\", \"regex_pattern\": \"^\\\\d+\"}}, {\"__index__\": 1, \"filter\": {\"__current_case__\": 1, \"comment_char\": \"35\", \"filter_type\": \"comment\"}}, {\"__index__\": 2, \"filter\": {\"__current_case__\": 3, \"filter_type\": \"append_line_num\"}}, {\"__index__\": 3, \"filter\": {\"__current_case__\": 9, \"columns\": \"7,2,3,4,1\", \"filter_type\": \"select_columns\"}}, {\"__index__\": 4, \"filter\": {\"__current_case__\": 11, \"add\": null, \"column\": \"c4\", \"filter_type\": \"replace\", \"regex_pattern\": \"(\\\\d+)/(\\\\d+)/(\\\\d+)\", \"regex_replace\": \"19\\\\3-\\\\2-\\\\1\"}}]}, \"table\": {\"values\": [{\"id\": 152, \"src\": \"hda\"}]}, \"tbl_opts\": {\"col_names\": \"id,first,last,dob,pets\", \"column_names_from_first_line\": false, \"indexes\": [], \"load_named_columns\": false, \"pkey_autoincr\": \"\", \"table_name\": \"people\"}}]", "add_to_database": "{\"withdb\": {\"values\": [{\"id\": 151, \"src\": \"hda\"}]}}", "workdb": "\"workdb.sqlite\""}, "inputs": {"add_to_database|withdb": {"id": "db8b8af119989393", "src": "hda", "uuid": "c44b2bea-960c-498d-8197-035dc99cfd00"}, "tables_0|table": {"id": "70d4db306a0fab2b", "src": "hda", "uuid": "adf80f14-c180-4217-b554-155534825961"}}, "outputs": {"output": {"id": "f6f155cd30b2fe54", "src": "hda", "uuid": "ee13ebf3-8a7a-4ac9-a645-c3565f72e525"}}, "output_collections": {}, "tool_stdout": "\nSELECT people.id,first,last,pets,quote FROM people JOIN contacts ON people.first = contacts.first_name\n ", "tool_stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/a/d/f/dataset_adf80f14-c180-4217-b554-155534825961.dat', 'table_name': 'people', 'column_names': 'id,first,last,dob,pets', 'filters': [{'filter': 'regex', 'pattern': '^\\\\d+', 'action': 'include_find'}, {'filter': 'regex', 'pattern': '^(#).*$', 'action': 'exclude_match'}, {'filter': 'append_line_num'}, {'filter': 'select_columns', 'columns': [7, 2, 3, 4, 1]}, {'filter': 'replace', 'column': 4, 'pattern': '(\\\\d+)/(\\\\d+)/(\\\\d+)', 'replace': '19\\\\3-\\\\2-\\\\1'}]}]}\n\nSQL: \nSELECT people.id,first,last,pets,quote FROM people JOIN contacts ON people.first = contacts.first_name\n \nrowcount: None\n", "job_stdout": "", "job_stderr": "", "stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/a/d/f/dataset_adf80f14-c180-4217-b554-155534825961.dat', 'table_name': 'people', 'column_names': 'id,first,last,dob,pets', 'filters': [{'filter': 'regex', 'pattern': '^\\\\d+', 'action': 'include_find'}, {'filter': 'regex', 'pattern': '^(#).*$', 'action': 'exclude_match'}, {'filter': 'append_line_num'}, {'filter': 'select_columns', 'columns': [7, 2, 3, 4, 1]}, {'filter': 'replace', 'column': 4, 'pattern': '(\\\\d+)/(\\\\d+)/(\\\\d+)', 'replace': '19\\\\3-\\\\2-\\\\1'}]}]}\n\nSQL: \nSELECT people.id,first,last,pets,quote FROM people JOIN contacts ON people.first = contacts.first_name\n \nrowcount: None\n", "stdout": "\nSELECT 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"copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0", "history_id": "b8e3c9423bdc89f6", "external_id": "gxy-hwbvw", "command_line": "cat '/galaxy/server/database/jobs_directory/000/132/configs/tmpbda3x3ay' && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/cf34c344508d/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/132/configs/tmp_68kvdhw' -Q '/galaxy/server/database/jobs_directory/000/132/configs/tmpbda3x3ay' -o '/galaxy/server/database/objects/4/0/b/dataset_40bbc802-7da5-42cd-a02f-7ec164644760.dat'", "traceback": null, "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addqueries": "{\"queries\": []}", "query_result": "{\"__current_case__\": 0, \"header\": \"yes\", \"header_prefix\": \"\"}", "sqlquery": "\"SELECT * from PSMs\"", "save_db": "false", "modify_database": "{\"sql_stmts\": []}", "tables": "[{\"__index__\": 0, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"__current_case__\": 9, \"columns\": \"1,3,2,6,14,19\", \"filter_type\": \"select_columns\"}}]}, \"table\": {\"values\": [{\"id\": 155, \"src\": \"hda\"}]}, \"tbl_opts\": {\"col_names\": \"Scan\", \"column_names_from_first_line\": true, \"indexes\": [], \"load_named_columns\": false, \"pkey_autoincr\": \"\", \"table_name\": \"PSMs\"}}]", "add_to_database": "{\"withdb\": null}", "workdb": "\"workdb.sqlite\""}, "inputs": {"tables_0|table": {"id": "fb8a865dfbb79992", "src": "hda", "uuid": "d3cc82fb-bf61-4111-bc29-51ccee707c82"}}, "outputs": {"output": {"id": "081fda218d170895", "src": "hda", "uuid": "40bbc802-7da5-42cd-a02f-7ec164644760"}}, "output_collections": {}, "tool_stdout": "\nSELECT * from PSMs\n ", "tool_stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/d/3/c/dataset_d3cc82fb-bf61-4111-bc29-51ccee707c82.dat', 'table_name': 'PSMs', 'firstlinenames': True, 'column_names': 'Scan', 'filters': [{'filter': 'select_columns', 'columns': [1, 3, 2, 6, 14, 19]}]}]}\n\nSQL: \nSELECT * from PSMs\n \nrowcount: None\n", "job_stdout": "", "job_stderr": "", "stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/d/3/c/dataset_d3cc82fb-bf61-4111-bc29-51ccee707c82.dat', 'table_name': 'PSMs', 'firstlinenames': True, 'column_names': 'Scan', 'filters': [{'filter': 'select_columns', 'columns': [1, 3, 2, 6, 14, 19]}]}]}\n\nSQL: \nSELECT * from PSMs\n \nrowcount: None\n", "stdout": "\nSELECT * from PSMs\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": "2023-10-24 06:58:49", "plugin": "core", "name": "end_epoch", "raw_value": "1698130729.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 06:58:49", "plugin": "core", "name": "start_epoch", "raw_value": "1698130729.0000000"}, {"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": "query_tabular/3.3.0-7", "has_data": true, "data": {"tool_id": "query_tabular", "tool_version": "3.3.0", "test_index": 7, "time_seconds": 30.679646253585815, "inputs": {"tables_0|table": {"src": "hda", "id": "c7d9fee5801aa918"}, "tables_0|input_opts|linefilters_0|filter|columns": "1,3,2,6,14,19", "tables_0|input_opts|linefilters_0|filter|filter_type": "select_columns", "tables_0|tbl_opts|table_name": "PSMs", "tables_0|tbl_opts|column_names_from_first_line": true, "tables_0|tbl_opts|col_names": "Scan", "sqlquery": "SELECT Scan,\"m/z\", \"Precursor m/z Error [ppm]\", Sequence, \"Protein(s)\" FROM PSMs WHERE NOT re_search(', ',\"Protein(s)\")", "query_result|header_prefix": "", "query_result|header": "yes"}, "job": {"model_class": "Job", "id": "85f23abbadb9fa4e", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T06:59:31.683521", "create_time": "2023-10-24T06:59:20.091091", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0", "history_id": "b8e3c9423bdc89f6", "external_id": "gxy-rltz6", "command_line": "cat '/galaxy/server/database/jobs_directory/000/134/configs/tmpsh9bqowl' && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/cf34c344508d/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/134/configs/tmp59xo480q' -Q '/galaxy/server/database/jobs_directory/000/134/configs/tmpsh9bqowl' -o '/galaxy/server/database/objects/1/6/0/dataset_160a5ce3-5645-4742-9ce0-0de933b13228.dat'", "traceback": null, "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addqueries": "{\"queries\": []}", "query_result": "{\"__current_case__\": 0, \"header\": \"yes\", \"header_prefix\": \"\"}", "sqlquery": "\"SELECT Scan,\\\"m/z\\\", \\\"Precursor m/z Error [ppm]\\\", Sequence, \\\"Protein(s)\\\" FROM PSMs WHERE NOT re_search(', ',\\\"Protein(s)\\\")\"", "save_db": "false", "modify_database": "{\"sql_stmts\": []}", "tables": "[{\"__index__\": 0, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"__current_case__\": 9, \"columns\": \"1,3,2,6,14,19\", \"filter_type\": \"select_columns\"}}]}, \"table\": {\"values\": [{\"id\": 157, \"src\": \"hda\"}]}, \"tbl_opts\": {\"col_names\": \"Scan\", \"column_names_from_first_line\": true, \"indexes\": [], \"load_named_columns\": false, \"pkey_autoincr\": \"\", \"table_name\": \"PSMs\"}}]", "add_to_database": "{\"withdb\": null}", "workdb": "\"workdb.sqlite\""}, "inputs": {"tables_0|table": {"id": "c7d9fee5801aa918", "src": "hda", "uuid": "dbd79a2c-6a46-4d9f-9e11-9d629c82d7de"}}, "outputs": {"output": {"id": "cc021280a2ddec1b", "src": "hda", "uuid": "160a5ce3-5645-4742-9ce0-0de933b13228"}}, "output_collections": {}, "tool_stdout": "\nSELECT Scan,\"m/z\", \"Precursor m/z Error [ppm]\", Sequence, \"Protein(s)\" FROM PSMs WHERE NOT re_search(', ',\"Protein(s)\")\n ", "tool_stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/d/b/d/dataset_dbd79a2c-6a46-4d9f-9e11-9d629c82d7de.dat', 'table_name': 'PSMs', 'firstlinenames': True, 'column_names': 'Scan', 'filters': [{'filter': 'select_columns', 'columns': [1, 3, 2, 6, 14, 19]}]}]}\n\nSQL: \nSELECT Scan,\"m/z\", \"Precursor m/z Error [ppm]\", Sequence, \"Protein(s)\" FROM PSMs WHERE NOT re_search(', ',\"Protein(s)\")\n \nrowcount: None\n", "job_stdout": "", "job_stderr": "", "stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/d/b/d/dataset_dbd79a2c-6a46-4d9f-9e11-9d629c82d7de.dat', 'table_name': 'PSMs', 'firstlinenames': True, 'column_names': 'Scan', 'filters': [{'filter': 'select_columns', 'columns': [1, 3, 2, 6, 14, 19]}]}]}\n\nSQL: \nSELECT Scan,\"m/z\", \"Precursor m/z Error [ppm]\", Sequence, \"Protein(s)\" FROM PSMs WHERE NOT re_search(', ',\"Protein(s)\")\n \nrowcount: None\n", "stdout": "\nSELECT Scan,\"m/z\", \"Precursor m/z Error [ppm]\", Sequence, \"Protein(s)\" FROM PSMs WHERE NOT re_search(', ',\"Protein(s)\")\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": "2023-10-24 06:59:21", "plugin": "core", "name": "end_epoch", "raw_value": "1698130761.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 06:59:21", "plugin": "core", "name": "start_epoch", 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'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/136/configs/tmp_mvqe1xq' -Q '/galaxy/server/database/jobs_directory/000/136/configs/tmpkgl6zl5q' --comment_char='#' -o '/galaxy/server/database/objects/9/d/9/dataset_9d97200a-860c-4cbf-b5d0-f148971d13cc.dat'", "traceback": null, "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addqueries": "{\"queries\": [{\"__index__\": 0, \"query_result\": {\"__current_case__\": 0, \"header\": \"yes\", \"header_prefix\": \"\"}, \"sqlquery\": \"SELECT * FROM psms WHERE confidence > 97.0\"}]}", "query_result": "{\"__current_case__\": 0, \"header\": \"yes\", \"header_prefix\": \"35\"}", "sqlquery": "\"SELECT scan,\\\"m/z\\\", \\\"Precursor m/z Error [ppm]\\\", Sequence, \\\"Protein(s)\\\", confidence FROM PSMs WHERE NOT re_search(', ',\\\"Protein(s)\\\")\"", "save_db": "false", "modify_database": "{\"sql_stmts\": [{\"__index__\": 0, \"sqlstmt\": \"UPDATE psms SET confidence = 99.999 WHERE confidence = 100.0\"}]}", "tables": "[{\"__index__\": 0, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"__current_case__\": 9, \"columns\": \"1,3,2,6,14,19,23\", \"filter_type\": \"select_columns\"}}]}, \"table\": {\"values\": [{\"id\": 159, \"src\": \"hda\"}]}, \"tbl_opts\": {\"col_names\": \"scan,,,,,,confidence\", \"column_names_from_first_line\": true, \"indexes\": [], \"load_named_columns\": false, \"pkey_autoincr\": \"\", \"table_name\": \"PSMs\"}}]", "add_to_database": "{\"withdb\": null}", "workdb": "\"workdb.sqlite\""}, "inputs": {"tables_0|table": {"id": "11fb2a0834893de8", "src": "hda", "uuid": "4205196f-f5fe-4d09-a48d-0ad19b421c6d"}}, "outputs": {"output": {"id": "544076db5bd97db8", "src": "hda", "uuid": "9d97200a-860c-4cbf-b5d0-f148971d13cc"}, "output1": {"id": "61be5cba484a304d", "src": "hda", "uuid": "8f744d3d-98e2-4a61-ba4a-0a4d07b57705"}}, "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/iuc/query_tabular/query_tabular/3.3.0, exit_code: None, stderr: .", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0, exit_code: None, stderr: .", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0, exit_code: None, stderr: ."], "status": "failure"}}, {"id": "query_tabular/3.3.0-9", "has_data": true, "data": {"tool_id": "query_tabular", "tool_version": "3.3.0", "test_index": 9, "time_seconds": 31.273890733718872, "inputs": {"tables_0|table": {"src": "hda", "id": "3614a7eaafacffac"}, "tables_0|input_opts|linefilters_0|filter|regex_pattern": "peptide", "tables_0|input_opts|linefilters_0|filter|regex_action": "include_find", "tables_0|input_opts|linefilters_0|filter|filter_type": "regex", "tables_0|tbl_opts|table_name": "epitope", "tables_0|tbl_opts|column_names_from_first_line": true, "sqlquery": "SELECT * FROM epitope", "query_result|header_prefix": "", "query_result|header": "yes"}, "job": {"model_class": "Job", "id": "5902f11b4b6256af", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T07:00:28.749869", "create_time": "2023-10-24T07:00:15.997892", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0", "history_id": "b8e3c9423bdc89f6", "external_id": "gxy-mt275", "command_line": "cat '/galaxy/server/database/jobs_directory/000/138/configs/tmpef0c3bi0' && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/cf34c344508d/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/138/configs/tmpzpc6a817' -Q '/galaxy/server/database/jobs_directory/000/138/configs/tmpef0c3bi0' -o '/galaxy/server/database/objects/7/0/b/dataset_70b7a446-b831-422a-9599-13df75423eef.dat'", "traceback": null, "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addqueries": "{\"queries\": []}", "query_result": "{\"__current_case__\": 0, \"header\": \"yes\", \"header_prefix\": \"\"}", "sqlquery": "\"SELECT * FROM epitope\"", "save_db": "false", "modify_database": "{\"sql_stmts\": []}", "tables": "[{\"__index__\": 0, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"__current_case__\": 8, \"filter_type\": \"regex\", \"regex_action\": \"include_find\", \"regex_pattern\": \"peptide\"}}]}, \"table\": {\"values\": [{\"id\": 162, \"src\": \"hda\"}]}, \"tbl_opts\": {\"col_names\": \"\", \"column_names_from_first_line\": true, \"indexes\": [], \"load_named_columns\": false, \"pkey_autoincr\": \"\", \"table_name\": \"epitope\"}}]", "add_to_database": "{\"withdb\": null}", "workdb": "\"workdb.sqlite\""}, "inputs": {"tables_0|table": {"id": "3614a7eaafacffac", "src": "hda", "uuid": "2f9b7b40-979d-40cf-bbdf-eaa3499504a6"}}, "outputs": {"output": {"id": "e562c8cc639a1899", "src": "hda", "uuid": "70b7a446-b831-422a-9599-13df75423eef"}}, "output_collections": {}, "tool_stdout": "\nSELECT * FROM epitope\n ", "tool_stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/2/f/9/dataset_2f9b7b40-979d-40cf-bbdf-eaa3499504a6.dat', 'table_name': 'epitope', 'firstlinenames': True, 'column_names': '', 'filters': [{'filter': 'regex', 'pattern': 'peptide', 'action': 'include_find'}]}]}\n\nSQL: \nSELECT * FROM epitope\n \nrowcount: None\n", "job_stdout": "", "job_stderr": "", "stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/2/f/9/dataset_2f9b7b40-979d-40cf-bbdf-eaa3499504a6.dat', 'table_name': 'epitope', 'firstlinenames': True, 'column_names': '', 'filters': [{'filter': 'regex', 'pattern': 'peptide', 'action': 'include_find'}]}]}\n\nSQL: \nSELECT * FROM epitope\n \nrowcount: None\n", "stdout": "\nSELECT * FROM epitope\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": "2023-10-24 07:00:18", "plugin": "core", "name": "end_epoch", "raw_value": "1698130818.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 07:00:18", "plugin": "core", "name": "start_epoch", "raw_value": "1698130818.0000000"}, {"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": "sam_pileup/1.1.3-0", "has_data": true, "data": {"tool_id": "sam_pileup", "tool_version": "1.1.3", "test_index": 0, "time_seconds": 34.58007192611694, "inputs": {"refOrHistory|input1": {"src": "hda", "id": "0b46f4832cf85eda"}, "refOrHistory|ownFile": {"src": "hda", "id": "606f27db86776ff6"}, "refOrHistory|reference": "history", "lastCol": "no", "indels": "no", "mapCap": "60", "c|consensus": "no"}, "job": {"model_class": "Job", "id": "1b14fde99d7533f4", "state": "error", "exit_code": 127, "update_time": "2023-10-24T06:52:19.846117", "create_time": "2023-10-24T06:52:05.518898", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.3", "history_id": "b8e3c9423bdc89f6", "external_id": "gxy-97tz8", "command_line": "ln -s '/galaxy/server/database/objects/1/5/b/dataset_15b2290e-dd2b-41d0-b5e4-3af2f3bae9b2.dat' input1.bam && ln -s '/galaxy/server/database/objects/_metadata_files/2/f/f/metadata_2ffd98a9-7424-4f3c-bcd0-a652ef3aa4f1.dat' 'input1.bam.bai' && ln -s '/galaxy/server/database/objects/1/8/5/dataset_18585bf8-66ce-43d3-a8e5-643d1a838a77.dat' reference.fasta && samtools faidx reference.fasta && samtools pileup -M 60 -f reference.fasta input1.bam > '/galaxy/server/database/objects/8/1/1/dataset_811d3f5c-0004-45af-a361-17b8d7e6c31e.dat'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"equCab2\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/equCab2.len\"", "c": "{\"__current_case__\": 0, \"consensus\": \"no\"}", "mapCap": "\"60\"", "indels": "\"no\"", "lastCol": "\"no\"", "refOrHistory": "{\"__current_case__\": 1, \"input1\": {\"values\": [{\"id\": 126, \"src\": \"hda\"}]}, \"ownFile\": {\"values\": [{\"id\": 127, \"src\": \"hda\"}]}, \"reference\": \"history\"}"}, "inputs": {"refOrHistory|input1": {"id": "0b46f4832cf85eda", "src": "hda", "uuid": "15b2290e-dd2b-41d0-b5e4-3af2f3bae9b2"}, "refOrHistory|ownFile": {"id": "606f27db86776ff6", "src": "hda", "uuid": 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{"title": "Job Start Time", "value": "2023-10-24 06:52:09", "plugin": "core", "name": "start_epoch", "raw_value": "1698130329.0000000"}, {"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": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.3, exit_code: 127, stderr: samtools: error while loading shared libraries: libncurses.so.5: cannot open shared object file: No such file or directory\n.", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.3, exit_code: 127, stderr: samtools: error while loading shared libraries: libncurses.so.5: cannot open shared object file: No such file or directory\n."], "status": "failure"}}, {"id": "samtools_calmd/2.0.2-0", "has_data": true, "data": {"tool_id": 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calmd -b -@ $addthreads '/galaxy/server/database/objects/7/0/7/dataset_70747206-b018-47c5-9d35-7fac0f117944.dat' 'ref.fa' > '/galaxy/server/database/objects/3/e/e/dataset_3ee6d011-23c7-4981-a7d4-799b97817b80.dat'", "traceback": null, "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "option_set": "{\"__current_case__\": 0, \"option_sets\": \"default\"}", "baq_settings": "{\"__current_case__\": 0, \"extended_baq\": \"\", \"modify_quality\": \"\", \"use_baq\": \"\"}", "reference_source": "{\"__current_case__\": 1, \"ref_fasta\": {\"values\": [{\"id\": 130, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}"}, "inputs": {"input_bam": {"id": "1fba13c59ee144a3", "src": "hda", "uuid": "70747206-b018-47c5-9d35-7fac0f117944"}, "reference_source|ref_fasta": {"id": "911c99275447de60", "src": "hda", "uuid": "72f6c4f1-7bec-4058-bee1-4eb5d892f439"}}, "outputs": {"calmd_output": {"id": "478fd91263330e3d", 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$(echo '1, 5, 10' | sed 's/,/ /g'); do echo $param > outputs/'perplexity'_$param\\.txt; done", "traceback": null, "params": {"__input_ext": "\"data\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "input_type": "{\"__current_case__\": 0, \"input_values\": \"1, 5, 10\", \"parameter_values\": \"list_comma_separated_values\"}", "parameter_name": "\"perplexity\""}, "inputs": {}, "outputs": {"__new_primary_file_parameter_iteration|perplexity_1__": {"id": "7b20b7ac3e79d9df", "src": "hda", "uuid": "b061c68e-f113-4e21-963c-334b48b8e55c"}, "__new_primary_file_parameter_iteration|perplexity_10__": {"id": "5902f11b4b6256af", "src": "hda", "uuid": "60e02e49-7cdd-4da0-a616-f9ddc54816aa"}, "__new_primary_file_parameter_iteration|perplexity_5__": {"id": "04deda8802bf0a5f", "src": "hda", "uuid": "3b82bc71-7a83-41d3-801f-97ba42481965"}}, "output_collections": {"parameter_iteration": {"id": "7ba13d1e0fea166b", "src": "hdca"}}, "tool_stdout": "", 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If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "scater_plot_exprs_freq/1.12.2-0", "has_data": true, "data": {"tool_id": "scater_plot_exprs_freq", "tool_version": "1.12.2", "test_index": 0, "time_seconds": 65.9176139831543, "inputs": {"input_loom": {"src": "hda", "id": "b24ef8d5e9b69a46"}}, "job": {"model_class": "Job", "id": "eed4de4bbc4a1574", "state": "error", "exit_code": null, "update_time": "2023-10-24T06:54:44.082001", "create_time": "2023-10-24T06:53:56.736521", "galaxy_version": "23.1", "command_version": null, "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_exprs_freq/scater_plot_exprs_freq/1.12.2", "history_id": "b8e3c9423bdc89f6", "external_id": "gxy-v7k2l", "command_line": "Rscript '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_exprs_freq/058b40656107/scater_plot_exprs_freq/scater-plot-exprs-freq.R' -i '/galaxy/server/database/objects/8/9/8/dataset_8982029b-6ea0-4ec3-83b7-136b88db722a.dat' -o '/galaxy/server/database/objects/c/6/c/dataset_c6cb4916-bb05-44f2-9348-644ac95c379b.dat'", "traceback": null, "params": {"__input_ext": "\"loom\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\""}, "inputs": {"input_loom": {"id": "b24ef8d5e9b69a46", "src": "hda", "uuid": "8982029b-6ea0-4ec3-83b7-136b88db722a"}}, "outputs": {"output_plot": {"id": "9c5885c0875e8135", "src": "hda", "uuid": "c6cb4916-bb05-44f2-9348-644ac95c379b"}}, "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/iuc/scater_plot_exprs_freq/scater_plot_exprs_freq/1.12.2, exit_code: None, stderr: .", "Job in error state.. tool_id: 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'/galaxy/server/database/objects/0/6/b/dataset_06b34c7c-23aa-415c-9b08-96d727af3151.dat' > '/galaxy/server/database/objects/d/0/7/dataset_d07a5a35-5d5d-4cea-a039-7793d457962f.dat'", "traceback": null, "params": {"__input_ext": "\"vcf\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\""}, "inputs": {"input1": {"id": "ed6e5bfdf15fec77", "src": "hda", "uuid": "c33d11d1-7a53-432f-b42c-6dd60e09e9ae"}, "input2": {"id": "eb456316e03ca9bb", "src": "hda", "uuid": "06b34c7c-23aa-415c-9b08-96d727af3151"}}, "outputs": {"out_file1": {"id": "278a304499cdb25a", "src": "hda", "uuid": "d07a5a35-5d5d-4cea-a039-7793d457962f"}}, "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"}, 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b/reports/anvil-edge/tool-tests/edge-23-10-24-06-08-1/results.xunit @@ -0,0 +1,872 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Step 1: reading read mappings <===[M::ma_hit_read::0.197*1.00] read 100000 hits; stored 187742 hits and 12067 sequences (111354001 bp)[M::main] ===> Step 2: 1-pass (crude) read selection <===[M::ma_hit_sub::0.221*1.00] 9155 query sequences remain after sub[M::ma_hit_cut::0.224*1.00] 161122 hits remain after cut[M::ma_hit_flt::0.227*1.00] 156936 hits remain after filtering; crude coverage after filtering: 11.85[M::main] ===> Step 3: 2-pass (fine) read selection <===[M::ma_hit_sub::0.238*1.00] 9023 query sequences remain after sub[M::ma_hit_cut::0.241*1.00] 152071 hits remain after cut[M::ma_hit_contained::0.246*1.00] 1536 sequences and 8359 hits remain after containment removal[M::main] ===> Step 4: graph cleaning <===[M::ma_sg_gen] read 8236 arcs[M::main] ===> Step 4.1: transitive reduction <===[M::asg_arc_del_trans] transitively reduced 4182 arcs[M::asg_arc_del_multi] removed 0 multi-arcs[M::asg_arc_del_asymm] removed 362 asymmetric arcs[M::main] ===> Step 4.2: initial tip cutting and bubble popping <===[M::asg_cut_tip] cut 260 tips[M::asg_pop_bubble] popped 105 bubbles and trimmed 4 tips[M::main] ===> Step 4.3: cutting short overlaps (3 rounds in total) <===[M::asg_arc_del_multi] removed 0 multi-arcs[M::asg_arc_del_asymm] removed 29 asymmetric arcs[M::asg_arc_del_short] removed 37 short overlaps[M::asg_cut_tip] cut 104 tips[M::asg_pop_bubble] popped 1 bubbles and trimmed 0 tips[M::asg_arc_del_multi] removed 0 multi-arcs[M::asg_arc_del_asymm] removed 1 asymmetric arcs[M::asg_arc_del_short] removed 1 short overlaps[M::asg_cut_tip] cut 3 tips[M::asg_pop_bubble] popped 0 bubbles and trimmed 0 tips[M::asg_arc_del_short] removed 0 short overlaps[M::main] ===> Step 4.4: removing short internal sequences and bi-loops <===[M::asg_cut_internal] cut 0 internal sequences[M::asg_cut_biloop] cut 0 small bi-loops[M::asg_cut_tip] cut 0 tips[M::asg_pop_bubble] popped 0 bubbles and trimmed 0 tips[M::main] ===> Step 4.5: aggressively cutting short overlaps <===[M::asg_arc_del_short] removed 0 short overlaps[M::main] ===> Step 5: generating unitigs <===[M::main] Version: 0.3-r179[M::main] CMD: miniasm -f /galaxy/server/database/objects/9/6/b/dataset_96bf6207-9ec4-46ab-91b3-c5d3b12b4a5a.dat -m 100 -i 0.05 -s 1000 -c 3 -o 1000 -h 1000 -I 0.08 -g 1000 -d 50000 -e 4 -n 3 -F 0.8 /galaxy/server/database/objects/d/a/8/dataset_da87cc5f-3019-40ec-b718-dad37a80f901.dat[M::main] Real time: 0.257 sec; CPU: 0.254 sec + ]]> + + + + + + + + Step 1: reading read mappings <===[M::ma_hit_read::0.201*1.00] read 100000 hits; stored 187766 hits and 12068 sequences (111355211 bp)[M::main] ===> Step 2: 1-pass (crude) read selection <===[M::ma_hit_sub::0.225*1.00] 10122 query sequences remain after sub[M::ma_hit_cut::0.228*1.00] 171862 hits remain after cut[M::ma_hit_flt::0.232*1.00] 165533 hits remain after filtering; crude coverage after filtering: 11.51[M::main] ===> Step 3: 2-pass (fine) read selection <===[M::ma_hit_sub::0.244*1.00] 9994 query sequences remain after sub[M::ma_hit_cut::0.247*1.00] 163595 hits remain after cut[M::ma_hit_contained::0.253*1.00] 1772 sequences and 10061 hits remain after containment removal[M::main] ===> Step 4: graph cleaning <===[M::ma_sg_gen] read 9758 arcs[M::main] ===> Step 4.1: transitive reduction <===[M::asg_arc_del_trans] transitively reduced 4694 arcs[M::asg_arc_del_multi] removed 0 multi-arcs[M::asg_arc_del_asymm] removed 484 asymmetric arcs[M::main] ===> Step 4.2: initial tip cutting and bubble popping <===[M::asg_cut_tip] cut 282 tips[M::asg_pop_bubble] popped 173 bubbles and trimmed 6 tips[M::main] ===> Step 4.3: cutting short overlaps (2 rounds in total) <===[M::asg_arc_del_multi] removed 0 multi-arcs[M::asg_arc_del_asymm] removed 26 asymmetric arcs[M::asg_arc_del_short] removed 38 short overlaps[M::asg_cut_tip] cut 53 tips[M::asg_pop_bubble] popped 8 bubbles and trimmed 0 tips[M::asg_arc_del_multi] removed 0 multi-arcs[M::asg_arc_del_asymm] removed 2 asymmetric arcs[M::asg_arc_del_short] removed 2 short overlaps[M::asg_cut_tip] cut 2 tips[M::asg_pop_bubble] popped 0 bubbles and trimmed 0 tips[M::main] ===> Step 4.4: removing short internal sequences and bi-loops <===[M::asg_cut_internal] cut 0 internal sequences[M::asg_cut_biloop] cut 0 small bi-loops[M::asg_cut_tip] cut 0 tips[M::asg_pop_bubble] popped 0 bubbles and trimmed 0 tips[M::main] ===> Step 4.5: aggressively cutting short overlaps <===[M::asg_arc_del_short] removed 0 short overlaps[M::main] ===> Step 5: generating unitigs <===[M::main] Version: 0.3-r179[M::main] CMD: miniasm -f /galaxy/server/database/objects/1/9/c/dataset_19c452e5-5cbf-4d01-9715-7a67e96dc63f.dat -m 99 -i 0.04 -s 999 -c 2 -o 999 -h 999 -I 0.7 -g 999 -d 45000 -e 3 -n 2 -F 0.7 /galaxy/server/database/objects/4/3/9/dataset_439051bb-ee13-4445-ba66-22f93ba24532.dat[M::main] Real time: 0.266 sec; CPU: 0.264 sec + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/reports/anvil-edge/tool-tests/edge-23-10-24-06-08-1/tools.yml b/reports/anvil-edge/tool-tests/edge-23-10-24-06-08-1/tools.yml new file mode 100644 index 000000000..08a6e2b7b --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-23-10-24-06-08-1/tools.yml @@ -0,0 +1,122 @@ +chunk: 2 +tools: +- name: miniasm + owner: iuc + revisions: + - 8dee0218ac7d + tool_panel_section_id: assembly + tool_panel_section_label: Assembly +- name: deeptools_bigwig_compare + owner: bgruening + revisions: + - 26e7304d6737 + tool_panel_section_id: deeptools + tool_panel_section_label: deepTools +- name: fastq_groomer + owner: devteam + revisions: + - 47e5dbc3e790 + tool_panel_section_id: fasta_fastq + tool_panel_section_label: FASTA/FASTQ +- name: sra_tools + owner: iuc + revisions: + - 83c7d564b128 + tool_panel_section_id: get_data + tool_panel_section_label: Get Data +- name: mummer_mummerplot + owner: iuc + revisions: + - ebe3b0f84de9 + tool_panel_section_id: multiple_alignments + tool_panel_section_label: Multiple Alignments +- name: poretools_qualpos + owner: iuc + revisions: + - 4fe6b96aff72 + tool_panel_section_id: nanopore + tool_panel_section_label: Nanopore +- name: kallisto_pseudo + owner: iuc + revisions: + - 5ae5c312d718 + tool_panel_section_id: rna_seq + tool_panel_section_label: RNA-seq +- name: sam_pileup + owner: devteam + revisions: + - a3b4ad6858ff + tool_panel_section_id: sam_bam + tool_panel_section_label: SAM/BAM +- name: samtools_calmd + owner: devteam + revisions: + - 06dc50b7b711 + tool_panel_section_id: sam_bam + tool_panel_section_label: SAM/BAM +- name: music_manipulate_eset + owner: bgruening + revisions: + - 22232092be53 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: droplet_barcode_plot + owner: ebi-gxa + revisions: + - 8f605643ccfd + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: scater_plot_exprs_freq + owner: iuc + revisions: + - 058b40656107 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: scanpy_parameter_iterator + owner: ebi-gxa + revisions: + - 0387a2179f88 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: query_tabular + owner: iuc + revisions: + - cf34c344508d + tool_panel_section_id: text_manipulation + tool_panel_section_label: Text Manipulation +- name: column_remove_by_header + owner: iuc + revisions: + - 372967836e98 + tool_panel_section_id: text_manipulation + tool_panel_section_label: Text Manipulation +- name: snpsift + owner: iuc + revisions: + - 2e497a770bca + tool_panel_section_id: variant_calling + tool_panel_section_label: Variant Calling +- name: bcftools_plugin_mendelian + owner: iuc + revisions: + - bf235558f2cf + tool_panel_section_id: vcf_bcf + tool_panel_section_label: VCF/BCF +- name: bcftools_csq + owner: iuc + 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