diff --git a/reports/anvil-edge/README.md b/reports/anvil-edge/README.md index 9cee84359..9fbbe6bfd 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 Dec 30 06:27:50 2024Mon Dec 23 06:28:04 2024
1ToolsetMon Dec 30 18:33:15 2024Mon Dec 23 18:33:14 2024
2ToolsetTue Dec 31 06:27:13 2024Tue Dec 24 06:27:21 2024
3ToolsetTue Dec 31 18:33:03 2024Tue Dec 24 18:34:20 2024
4ToolsetWed Jan 01 06:27:42 2025Wed Dec 25 06:27:49 2024
5ToolsetWed Jan 01 18:33:00 2025Wed Dec 25 18:32:38 2024
6ToolsetThu Dec 26 06:27:29 2024Thu Dec 19 06:28:20 2024
7ToolsetThu Dec 26 18:33:25 2024Thu Dec 19 18:33:25 2024
8ToolsetFri Dec 27 06:28:36 2024Fri Dec 20 06:26:59 2024
9ToolsetFri Dec 27 18:33:31 2024Fri Dec 20 18:33:41 2024
10ToolsetSat Dec 28 06:25:11 2024Sat Dec 21 06:25:50 2024
11ToolsetSat Dec 28 18:31:53 2024Sat Dec 21 18:32:26 2024
12ToolsetSun Dec 29 06:26:08 2024Sun Dec 22 06:25:30 2024
13ToolsetSun Dec 29 18:31:48 2024Sun Dec 22 18:32:07 2024
+
Chunk IDTool ListLatest reportPrevious report
0ToolsetMon Dec 30 06:27:50 2024Mon Dec 23 06:28:04 2024
1ToolsetMon Dec 30 18:33:15 2024Mon Dec 23 18:33:14 2024
2ToolsetTue Dec 31 06:27:13 2024Tue Dec 24 06:27:21 2024
3ToolsetTue Dec 31 18:33:03 2024Tue Dec 24 18:34:20 2024
4ToolsetWed Jan 01 06:27:42 2025Wed Dec 25 06:27:49 2024
5ToolsetWed Jan 01 18:33:00 2025Wed Dec 25 18:32:38 2024
6ToolsetThu Jan 02 06:27:55 2025Thu Dec 26 06:27:29 2024
7ToolsetThu Dec 26 18:33:25 2024Thu Dec 19 18:33:25 2024
8ToolsetFri Dec 27 06:28:36 2024Fri Dec 20 06:26:59 2024
9ToolsetFri Dec 27 18:33:31 2024Fri Dec 20 18:33:41 2024
10ToolsetSat Dec 28 06:25:11 2024Sat Dec 21 06:25:50 2024
11ToolsetSat Dec 28 18:31:53 2024Sat Dec 21 18:32:26 2024
12ToolsetSun Dec 29 06:26:08 2024Sun Dec 22 06:25:30 2024
13ToolsetSun Dec 29 18:31:48 2024Sun Dec 22 18:32:07 2024
diff --git a/reports/anvil-edge/tool-tests/chunks.json b/reports/anvil-edge/tool-tests/chunks.json index 29dcd6a10..f4a188f13 100644 --- a/reports/anvil-edge/tool-tests/chunks.json +++ b/reports/anvil-edge/tool-tests/chunks.json @@ -35,11 +35,11 @@ "date2": "Wed Dec 25 18:32:38 2024" }, "6": { - "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-12-26-06-12-1/results.html", - "date1": "Thu Dec 26 06:27:29 2024", - "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-12-26-06-12-1/tools.yml", - "run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-12-19-06-12-1/results.html", - "date2": "Thu Dec 19 06:28:20 2024" + "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/results.html", + "date1": "Thu Jan 02 06:27:55 2025", + "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/tools.yml", + "run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-12-26-06-12-1/results.html", + "date2": "Thu Dec 26 06:27:29 2024" }, "7": { "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-12-26-18-17-1/results.html", diff --git a/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/chunk.json b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/chunk.json new file mode 100644 index 000000000..e0ccf9504 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/chunk.json @@ -0,0 +1,7 @@ +{ + "6": { + "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/results.html", + "date1": "Thu Jan 02 06:27:55 2025", + "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/tools.yml" + } +} \ No newline at end of file diff --git a/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/chunk.txt b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/chunk.txt new file mode 100644 index 000000000..6b310ce26 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/chunk.txt @@ -0,0 +1,23 @@ +-t split_file_to_collection --tool-version 6cbe2f30c2d7 +-t deeptools_multi_bigwig_summary --tool-version 3c9f0c486cca +-t fastq_paired_end_interlacer --tool-version 2ccb8dcabddc +-t jbrowse --tool-version 4542035c1075 +-t jbrowse --tool-version a6e57ff585c0 +-t mummer_delta_filter --tool-version b3acbb3a6af0 +-t poretools_winner --tool-version 79c1ac92f31b +-t edger --tool-version 334ce9b1bac5 +-t qualimap_multi_bamqc --tool-version e38af83df163 +-t samtools_sort --tool-version e613c1ad4c4c +-t 10x_bamtofastq --tool-version f71fd828c126 +-t raceid_trajectory --tool-version 72979cac22b2 +-t raceid_trajectory --tool-version c92d0f9338c5 +-t scanpy_inspect --tool-version c5d3684f7c4c +-t scanpy_find_variable_genes --tool-version 0edb75c411a4 +-t scanpy_find_variable_genes --tool-version 5c62f39aab8f +-t concatenate_multiple_datasets --tool-version 201c568972c3 +-t snpfreqplot --tool-version e362b3143cde +-t bcftools_gtcheck --tool-version 672b6c02fbc7 +-t bcftools_reheader --tool-version 9ef52d95114b +-t bcftools_plugin_tag2tag --tool-version bdfdf5f6e950 +-t vcfgenotypes --tool-version a60ae8af21a1 +-t ivar_removereads --tool-version ee2beb764a7b diff --git a/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/039e98ef7e07fc36.json b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/039e98ef7e07fc36.json new file mode 100644 index 000000000..f1dfb52f6 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/039e98ef7e07fc36.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "039e98ef7e07fc36", + "history_id": "417947348fdacb2d", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2025-01-02T06:44:25.858843", + "update_time": "2025-01-02T06:44:39.170620", + "galaxy_version": "24.1", + "external_id": "gxy-vfs2j", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/66/registry.xml' '/galaxy/server/database/jobs_directory/000/66/upload_params.json' '111:/galaxy/server/database/objects/6/f/d/dataset_6fdb4ae0-d4b9-4455-8267-26504b1c3a4e_files:/galaxy/server/database/objects/6/f/d/dataset_6fdb4ae0-d4b9-4455-8267-26504b1c3a4e.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_oyf3asmn\"", + "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"A.gff\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_c871qbon\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"auto\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "7e10eda76b933a67", + "src": "hda", + "uuid": "6fdb4ae0-d4b9-4455-8267-26504b1c3a4e" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/24611f45b2c6f4c6.json b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/24611f45b2c6f4c6.json new file mode 100644 index 000000000..2fe08ab80 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/24611f45b2c6f4c6.json @@ -0,0 +1,55 @@ +{ + "model_class": "Job", + "id": "24611f45b2c6f4c6", + "history_id": "417947348fdacb2d", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1", + "state": "error", + "exit_code": null, + "create_time": "2025-01-02T06:43:40.627763", + "update_time": "2025-01-02T06:43:46.594588", + "galaxy_version": "24.1", + "external_id": "gxy-vgq6z", + "handler": null, + "job_runner_name": null, + "command_line": "mkdir -p /galaxy/server/database/objects/d/1/b/dataset_d1bb7e69-77ec-4295-853d-fa8a94c59224_files && cp /galaxy/server/database/jobs_directory/000/60/configs/tmprwvpsk2e /galaxy/server/database/objects/d/1/b/dataset_d1bb7e69-77ec-4295-853d-fa8a94c59224_files/galaxy.xml && export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'data' --outdir /galaxy/server/database/objects/d/1/b/dataset_d1bb7e69-77ec-4295-853d-fa8a94c59224_files /galaxy/server/database/jobs_directory/000/60/configs/tmprwvpsk2e && cp /galaxy/server/database/jobs_directory/000/60/configs/tmpghdqxa_n /galaxy/server/database/objects/d/1/b/dataset_d1bb7e69-77ec-4295-853d-fa8a94c59224.dat; cp /galaxy/server/database/jobs_directory/000/60/configs/tmprwvpsk2e /galaxy/server/database/objects/d/1/b/dataset_d1bb7e69-77ec-4295-853d-fa8a94c59224.dat", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"fasta\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "uglyTestingHack": "\"enabled\"", + "plugins": "{\"BlastView\": true, \"ComboTrackSelector\": false, \"GCContent\": false}", + "jbgen": "{\"aboutDescription\": \"\", \"defaultLocation\": \"\", \"hideGenomeOptions\": false, \"shareLink\": true, \"show_menu\": true, \"show_nav\": true, \"show_overview\": true, \"show_tracklist\": true, \"trackPadding\": \"20\"}", + "track_groups": "[]", + "action": "{\"__current_case__\": 0, \"action_select\": \"create\"}", + "gencode": "\"11\"", + "standalone": "\"data\"", + "reference_genome": "{\"__current_case__\": 1, \"genome\": {\"values\": [{\"id\": 104, \"src\": \"hda\"}]}, \"genome_type_select\": \"history\"}" + }, + "inputs": { + "reference_genome|genome": { + "id": "59e7f7bb0c0090a3", + "src": "hda", + "uuid": "f078e412-c1c9-4650-be7b-e5e1e28f0ac9" + } + }, + "outputs": { + "output": { + "id": "86e3335ea84ed5fd", + "src": "hda", + "uuid": "d1bb7e69-77ec-4295-853d-fa8a94c59224" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "WARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "WARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/2737299cf0223786.json b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/2737299cf0223786.json new file mode 100644 index 000000000..95eaa3d4c --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/2737299cf0223786.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "2737299cf0223786", + "history_id": "417947348fdacb2d", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2025-01-02T07:28:48.509281", + "update_time": "2025-01-02T07:29:00.317303", + "galaxy_version": "24.1", + "external_id": "gxy-9mg8g", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/252/registry.xml' '/galaxy/server/database/jobs_directory/000/252/upload_params.json' '330:/galaxy/server/database/objects/8/7/e/dataset_87ebc466-7379-4a64-a05c-66c208fc7c0b_files:/galaxy/server/database/objects/8/7/e/dataset_87ebc466-7379-4a64-a05c-66c208fc7c0b.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_wa0ac7yr\"", + "files_metadata": "{\"__current_case__\": 325, \"file_type\": \"tabular\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"input436.tabular\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_d496aotr\", \"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": "1bb67360a25de827", + "src": "hda", + "uuid": "87ebc466-7379-4a64-a05c-66c208fc7c0b" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/27d5e95f2f20c64a.json b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/27d5e95f2f20c64a.json new file mode 100644 index 000000000..fbc20d466 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/27d5e95f2f20c64a.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "27d5e95f2f20c64a", + "history_id": "417947348fdacb2d", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2025-01-02T07:24:22.286949", + "update_time": "2025-01-02T07:24:33.096654", + "galaxy_version": "24.1", + "external_id": "gxy-shj2j", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/228/registry.xml' '/galaxy/server/database/jobs_directory/000/228/upload_params.json' '304:/galaxy/server/database/objects/0/d/a/dataset_0da8bf9d-0629-434d-b81c-8712e4bfcc87_files:/galaxy/server/database/objects/0/d/a/dataset_0da8bf9d-0629-434d-b81c-8712e4bfcc87.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_uvmau3b2\"", + "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"krumsiek11.h5ad\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_7qyzzj7r\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"auto\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "8688d9f2b42bcb18", + "src": "hda", + "uuid": "0da8bf9d-0629-434d-b81c-8712e4bfcc87" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/313ab96f9d8f8251.json b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/313ab96f9d8f8251.json new file mode 100644 index 000000000..77817f371 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/313ab96f9d8f8251.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "313ab96f9d8f8251", + "history_id": "417947348fdacb2d", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2025-01-02T06:44:26.074855", + "update_time": "2025-01-02T06:44:39.404990", + "galaxy_version": "24.1", + "external_id": "gxy-nl8rl", + "handler": null, + "job_runner_name": null, + "command_line": "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' '112:/galaxy/server/database/objects/c/0/a/dataset_c0a39b3d-1a79-4cbc-b3aa-f58d3711a5e4_files:/galaxy/server/database/objects/c/0/a/dataset_c0a39b3d-1a79-4cbc-b3aa-f58d3711a5e4.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_9bks87yq\"", + "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"B.gff\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_d7avqvm1\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"auto\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "bb2cdd97a30e285f", + "src": "hda", + "uuid": "c0a39b3d-1a79-4cbc-b3aa-f58d3711a5e4" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/3e8cd1fa93a54128.json b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/3e8cd1fa93a54128.json new file mode 100644 index 000000000..80a5b8c99 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/3e8cd1fa93a54128.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "3e8cd1fa93a54128", + "history_id": "417947348fdacb2d", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2025-01-02T06:44:26.989906", + "update_time": "2025-01-02T06:44:55.079112", + "galaxy_version": "24.1", + "external_id": "gxy-2jvcs", + "handler": null, + "job_runner_name": null, + "command_line": "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' '116:/galaxy/server/database/objects/d/6/0/dataset_d604e90e-77f3-472a-9043-73f2ce850a5c_files:/galaxy/server/database/objects/d/6/0/dataset_d604e90e-77f3-472a-9043-73f2ce850a5c.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_nk3htj2u\"", + "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"interpro.gff\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_7xtcn_br\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"auto\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "4963a0f517e742b4", + "src": "hda", + "uuid": "d604e90e-77f3-472a-9043-73f2ce850a5c" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/52803ce717ec40bb.json b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/52803ce717ec40bb.json new file mode 100644 index 000000000..7580239af --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/52803ce717ec40bb.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "52803ce717ec40bb", + "history_id": "417947348fdacb2d", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2025-01-02T06:37:44.318341", + "update_time": "2025-01-02T06:37:54.371100", + "galaxy_version": "24.1", + "external_id": "gxy-cj5vn", + "handler": null, + "job_runner_name": null, + "command_line": "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' '72:/galaxy/server/database/objects/8/c/0/dataset_8c031b9d-2c7d-4fc8-b8ea-f13f7170c690_files:/galaxy/server/database/objects/8/c/0/dataset_8c031b9d-2c7d-4fc8-b8ea-f13f7170c690.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_qddtf6b0\"", + "files_metadata": "{\"__current_case__\": 542, \"file_type\": \"sdf\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"3_molecules.sdf\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_i8a5i9k0\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"sdf\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "808d25e5c3af11a1", + "src": "hda", + "uuid": "8c031b9d-2c7d-4fc8-b8ea-f13f7170c690" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/55cbbbefccf62e5d.json b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/55cbbbefccf62e5d.json new file mode 100644 index 000000000..28cbafd10 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/55cbbbefccf62e5d.json @@ -0,0 +1,65 @@ +{ + "model_class": "Job", + "id": "55cbbbefccf62e5d", + "history_id": "417947348fdacb2d", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1", + "state": "error", + "exit_code": null, + "create_time": "2025-01-02T06:52:25.269427", + "update_time": "2025-01-02T06:52:30.510140", + "galaxy_version": "24.1", + "external_id": "gxy-7xdf9", + "handler": null, + "job_runner_name": null, + "command_line": "mkdir -p /galaxy/server/database/objects/2/2/7/dataset_2274b1b4-c97d-4e21-afd9-5753a52565c3_files && cp /galaxy/server/database/jobs_directory/000/110/configs/tmpwhxq0acu /galaxy/server/database/objects/2/2/7/dataset_2274b1b4-c97d-4e21-afd9-5753a52565c3_files/galaxy.xml && export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'data' --outdir /galaxy/server/database/objects/2/2/7/dataset_2274b1b4-c97d-4e21-afd9-5753a52565c3_files /galaxy/server/database/jobs_directory/000/110/configs/tmpwhxq0acu && cp /galaxy/server/database/jobs_directory/000/110/configs/tmp_jc7em4p /galaxy/server/database/objects/2/2/7/dataset_2274b1b4-c97d-4e21-afd9-5753a52565c3.dat; cp /galaxy/server/database/jobs_directory/000/110/configs/tmpwhxq0acu /galaxy/server/database/objects/2/2/7/dataset_2274b1b4-c97d-4e21-afd9-5753a52565c3.dat", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"fasta\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "uglyTestingHack": "\"enabled\"", + "plugins": "{\"BlastView\": true, \"ComboTrackSelector\": false, \"GCContent\": false}", + "jbgen": "{\"aboutDescription\": \"\", \"defaultLocation\": \"\", \"hideGenomeOptions\": false, \"shareLink\": true, \"show_menu\": true, \"show_nav\": true, \"show_overview\": true, \"show_tracklist\": true, \"trackPadding\": \"20\"}", + "track_groups": "[{\"__index__\": 0, \"category\": \"With canvas config\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"__current_case__\": 2, \"annotation\": {\"values\": [{\"id\": 154, \"src\": \"hda\"}]}, \"data_format_select\": \"gene_calls\", \"index\": false, \"jb_custom_config\": {\"option\": []}, \"jbcolor_scale\": {\"color_score\": {\"__current_case__\": 0, \"color\": {\"__current_case__\": 0, \"color_select\": \"automatic\"}, \"color_score_select\": \"none\"}}, \"jbmenu\": {\"track_menu\": []}, \"jbstyle\": {\"max_height\": \"600\", \"style_classname\": \"feature\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"style_label\": \"product,name,id\"}, \"match_part\": {\"__current_case__\": 1, \"match_part_select\": false}, \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"track_config\": {\"__current_case__\": 0, \"canvas_options\": {\"impliedUTRs\": true, \"subParts\": \"exon\", \"transcriptType\": \"transcript\"}, \"track_class\": \"JBrowse/View/Track/CanvasFeatures\"}, \"track_visibility\": \"default_off\"}}]}]", + "action": "{\"__current_case__\": 0, \"action_select\": \"create\"}", + "gencode": "\"11\"", + "standalone": "\"data\"", + "reference_genome": "{\"__current_case__\": 1, \"genome\": {\"values\": [{\"id\": 153, \"src\": \"hda\"}]}, \"genome_type_select\": \"history\"}" + }, + "inputs": { + "reference_genome|genome": { + "id": "bbe5504370b59d77", + "src": "hda", + "uuid": "3ae56a62-a01f-4787-b723-06dd2d0cc18b" + }, + "track_groups_0|data_tracks_0|data_format|annotation": { + "id": "af6c4fd171b336e0", + "src": "hda", + "uuid": "d214596b-e006-4110-866d-f4557616e26f" + }, + "track_groups_0|data_tracks_0|data_format|annotation1": { + "id": "af6c4fd171b336e0", + "src": "hda", + "uuid": "d214596b-e006-4110-866d-f4557616e26f" + } + }, + "outputs": { + "output": { + "id": "6ac8f9c789c25e5a", + "src": "hda", + "uuid": "2274b1b4-c97d-4e21-afd9-5753a52565c3" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "INFO:jbrowse:Processing With canvas config / 1.gff\nWARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "INFO:jbrowse:Processing With canvas config / 1.gff\nWARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/6e386b278832dd3b.json b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/6e386b278832dd3b.json new file mode 100644 index 000000000..998190c11 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/6e386b278832dd3b.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "6e386b278832dd3b", + "history_id": "417947348fdacb2d", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2025-01-02T07:03:19.753384", + "update_time": "2025-01-02T07:04:16.575307", + "galaxy_version": "24.1", + "external_id": "gxy-t4qtj", + "handler": null, + "job_runner_name": null, + "command_line": "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' '214:/galaxy/server/database/objects/3/7/7/dataset_377ccfe7-3a38-414f-af77-1c2ce2208c7e_files:/galaxy/server/database/objects/3/7/7/dataset_377ccfe7-3a38-414f-af77-1c2ce2208c7e.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_7umkv9zu\"", + "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"Mut3.counts\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_qlld1ajk\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"auto\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "0be8a66f99e4f300", + "src": "hda", + "uuid": "377ccfe7-3a38-414f-af77-1c2ce2208c7e" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/7e902eabb9a394c6.json b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/7e902eabb9a394c6.json new file mode 100644 index 000000000..daf260a1f --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/7e902eabb9a394c6.json @@ -0,0 +1,75 @@ +{ + "model_class": "Job", + "id": "7e902eabb9a394c6", + "history_id": "417947348fdacb2d", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1", + "state": "error", + "exit_code": null, + "create_time": "2025-01-02T06:51:57.581066", + "update_time": "2025-01-02T06:52:04.717107", + "galaxy_version": "24.1", + "external_id": "gxy-j9hk4", + "handler": null, + "job_runner_name": null, + "command_line": "mkdir -p /galaxy/server/database/objects/6/a/d/dataset_6ad5f93f-7e06-49fb-9ce4-e26ca54cfa65_files && cp /galaxy/server/database/jobs_directory/000/107/configs/tmp3dvoatg_ /galaxy/server/database/objects/6/a/d/dataset_6ad5f93f-7e06-49fb-9ce4-e26ca54cfa65_files/galaxy.xml && export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'data' --outdir /galaxy/server/database/objects/6/a/d/dataset_6ad5f93f-7e06-49fb-9ce4-e26ca54cfa65_files /galaxy/server/database/jobs_directory/000/107/configs/tmp3dvoatg_ && cp /galaxy/server/database/jobs_directory/000/107/configs/tmpjyjqcxe6 /galaxy/server/database/objects/6/a/d/dataset_6ad5f93f-7e06-49fb-9ce4-e26ca54cfa65.dat; cp /galaxy/server/database/jobs_directory/000/107/configs/tmp3dvoatg_ /galaxy/server/database/objects/6/a/d/dataset_6ad5f93f-7e06-49fb-9ce4-e26ca54cfa65.dat", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"fasta\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "uglyTestingHack": "\"enabled\"", + "plugins": "{\"BlastView\": true, \"ComboTrackSelector\": false, \"GCContent\": false}", + "jbgen": "{\"aboutDescription\": \"\", \"defaultLocation\": \"\", \"hideGenomeOptions\": false, \"shareLink\": true, \"show_menu\": true, \"show_nav\": true, \"show_overview\": true, \"show_tracklist\": true, \"trackPadding\": \"20\"}", + "track_groups": "[{\"__index__\": 0, \"category\": \"With menu or index\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"__current_case__\": 2, \"annotation\": {\"values\": [{\"id\": 151, \"src\": \"hda\"}]}, \"data_format_select\": \"gene_calls\", \"index\": false, \"jb_custom_config\": {\"option\": []}, \"jbcolor_scale\": {\"color_score\": {\"__current_case__\": 0, \"color\": {\"__current_case__\": 0, \"color_select\": \"automatic\"}, \"color_score_select\": \"none\"}}, \"jbmenu\": {\"track_menu\": [{\"__index__\": 0, \"menu_action\": \"iframeDialog\", \"menu_icon\": \"dijitIconNewTask\", \"menu_label\": \"Some menu item\", \"menu_title\": \"Frame title\", \"menu_url\": \"https://example.com/#!/?id={name}&q={type}&z=\\\"{end}\\\"\"}, {\"__index__\": 1, \"menu_action\": \"newWindow\", \"menu_icon\": \"dijitIconBookmark\", \"menu_label\": \"Another menu item\", \"menu_title\": \"Frame title 2\", \"menu_url\": \"https://example.com/#!/?id={name}&q={type}&z=\\\"{end}\\\"\"}]}, \"jbstyle\": {\"max_height\": \"600\", \"style_classname\": \"feature\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"style_label\": \"product,name,id\"}, \"match_part\": {\"__current_case__\": 1, \"match_part_select\": false}, \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"track_config\": {\"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": null}, \"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\"}, \"track_visibility\": \"default_off\"}}, {\"__index__\": 1, \"data_format\": {\"__current_case__\": 2, \"annotation\": {\"values\": [{\"id\": 151, \"src\": \"hda\"}]}, \"data_format_select\": \"gene_calls\", \"index\": true, \"jb_custom_config\": {\"option\": []}, \"jbcolor_scale\": {\"color_score\": {\"__current_case__\": 0, \"color\": {\"__current_case__\": 0, \"color_select\": \"automatic\"}, \"color_score_select\": \"none\"}}, \"jbmenu\": {\"track_menu\": []}, \"jbstyle\": {\"max_height\": \"600\", \"style_classname\": \"feature\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"style_label\": \"product,name,id\"}, \"match_part\": {\"__current_case__\": 1, \"match_part_select\": false}, \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"track_config\": {\"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": null}, \"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\"}, \"track_visibility\": \"default_off\"}}]}]", + "action": "{\"__current_case__\": 0, \"action_select\": \"create\"}", + "gencode": "\"11\"", + "standalone": "\"data\"", + "reference_genome": "{\"__current_case__\": 1, \"genome\": {\"values\": [{\"id\": 150, \"src\": \"hda\"}]}, \"genome_type_select\": \"history\"}" + }, + "inputs": { + "reference_genome|genome": { + "id": "bfa7fc5290d195fc", + "src": "hda", + "uuid": "0feac21b-17ad-418a-8aaa-b9dfbda2c9f5" + }, + "track_groups_0|data_tracks_0|data_format|annotation": { + "id": "54d4553682370391", + "src": "hda", + "uuid": "6bd31719-2a2c-491b-a446-d403a8d406eb" + }, + "track_groups_0|data_tracks_0|data_format|annotation1": { + "id": "54d4553682370391", + "src": "hda", + "uuid": "6bd31719-2a2c-491b-a446-d403a8d406eb" + }, + "track_groups_0|data_tracks_1|data_format|annotation": { + "id": "54d4553682370391", + "src": "hda", + "uuid": "6bd31719-2a2c-491b-a446-d403a8d406eb" + }, + "track_groups_0|data_tracks_1|data_format|annotation1": { + "id": "54d4553682370391", + "src": "hda", + "uuid": "6bd31719-2a2c-491b-a446-d403a8d406eb" + } + }, + "outputs": { + "output": { + "id": "25e804484ced14fc", + "src": "hda", + "uuid": "6ad5f93f-7e06-49fb-9ce4-e26ca54cfa65" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "INFO:jbrowse:Processing With menu or index / 1.gff\nINFO:jbrowse:Processing With menu or index / 1.gff\n", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "INFO:jbrowse:Processing With menu or index / 1.gff\nINFO:jbrowse:Processing With menu or index / 1.gff\n", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/7fd375b8233b3119.json b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/7fd375b8233b3119.json new file mode 100644 index 000000000..0ed2c481b --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/7fd375b8233b3119.json @@ -0,0 +1,48 @@ +{ + "model_class": "Job", + "id": "7fd375b8233b3119", + "history_id": "417947348fdacb2d", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/poretools_winner/poretools_winner/0.6.1a1.0", + "state": "error", + "exit_code": null, + "create_time": "2025-01-02T06:55:55.397511", + "update_time": "2025-01-02T06:56:23.316711", + "galaxy_version": "24.1", + "external_id": "gxy-4hk54", + "handler": null, + "job_runner_name": null, + "command_line": "poretools winner --type fwd '/galaxy/server/database/objects/9/8/d/dataset_98d9e8e7-f47b-4f38-8b87-7dc9706b6c30.dat' > '/galaxy/server/database/objects/1/1/8/dataset_11823e5b-61db-4d8b-9dc0-7660c973cd70.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"input\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "type": "\"fwd\"" + }, + "inputs": { + "input": { + "id": "3bc6697b14d2f281", + "src": "hda", + "uuid": "98d9e8e7-f47b-4f38-8b87-7dc9706b6c30" + } + }, + "outputs": { + "output": { + "id": "c2ebd14675ce2289", + "src": "hda", + "uuid": "11823e5b-61db-4d8b-9dc0-7660c973cd70" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/804dcea5bbe17c90.json b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/804dcea5bbe17c90.json new file mode 100644 index 000000000..7c1569739 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/804dcea5bbe17c90.json @@ -0,0 +1,47 @@ +{ + "model_class": "Job", + "id": "804dcea5bbe17c90", + "history_id": "417947348fdacb2d", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2", + "state": "error", + "exit_code": null, + "create_time": "2025-01-02T06:28:56.100572", + "update_time": "2025-01-02T06:29:30.542699", + "galaxy_version": "24.1", + "external_id": "gxy-kd8fq", + "handler": null, + "job_runner_name": null, + "command_line": "mkdir ./out && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/2dae863c8f42/split_file_to_collection/split_file_to_collection.py' --out ./out --in '/galaxy/server/database/objects/7/7/3/dataset_7731d777-7741-4f81-a845-f70e1b18e559.dat' --ftype 'tabular' --top '2' --by 'col' --id_column '1' --match '(.*)__backslash__.mgf' --sub '__backslash__1.tab'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"tabular\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "split_parms": "{\"__current_case__\": 0, \"input\": {\"values\": [{\"id\": 1, \"src\": \"hda\"}]}, \"select_ftype\": \"tabular\", \"split_by\": {\"__current_case__\": 0, \"id_col\": \"1\", \"match_regex\": \"(.*)\\\\.mgf\", \"select_split_by\": \"col\", \"sub_regex\": \"\\\\1.tab\"}, \"top\": \"2\"}" + }, + "inputs": { + "split_parms|input": { + "id": "417947348fdacb2d", + "src": "hda", + "uuid": "7731d777-7741-4f81-a845-f70e1b18e559" + } + }, + "outputs": {}, + "copied_from_job_id": null, + "output_collections": { + "list_output_tab": { + "src": "hdca", + "id": "417947348fdacb2d" + } + }, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/8790449e336e97fc.json b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/8790449e336e97fc.json new file mode 100644 index 000000000..f6457527a --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/8790449e336e97fc.json @@ -0,0 +1,49 @@ +{ + "model_class": "Job", + "id": "8790449e336e97fc", + "history_id": "417947348fdacb2d", + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.5", + "state": "error", + "exit_code": null, + "create_time": "2025-01-02T07:09:37.825692", + "update_time": "2025-01-02T07:09:42.291682", + "galaxy_version": "24.1", + "external_id": "gxy-64245", + "handler": null, + "job_runner_name": null, + "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && samtools sort -@ $addthreads -m $addmemory\"M\" -n -O bam -T \"${TMPDIR:-.}\" '/galaxy/server/database/objects/e/9/2/dataset_e925a5ba-b4c0-4ac4-9833-342c18d74f20.dat' > '/galaxy/server/database/objects/8/b/c/dataset_8bcfd7ad-3933-4add-95c7-72fa872e5e20.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"input\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "minhash": "false", + "prim_key_cond": "{\"__current_case__\": 1, \"prim_key_select\": \"-n\"}" + }, + "inputs": { + "input1": { + "id": "312f3442d7fe35ff", + "src": "hda", + "uuid": "e925a5ba-b4c0-4ac4-9833-342c18d74f20" + } + }, + "outputs": { + "output1": { + "id": "bab3afaea06cd231", + "src": "hda", + "uuid": "8bcfd7ad-3933-4add-95c7-72fa872e5e20" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/8f31f5360e3ac469.json b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/8f31f5360e3ac469.json new file mode 100644 index 000000000..755ba40b7 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/8f31f5360e3ac469.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "8f31f5360e3ac469", + "history_id": "417947348fdacb2d", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2025-01-02T07:22:48.439061", + "update_time": "2025-01-02T07:22:58.723113", + "galaxy_version": "24.1", + "external_id": "gxy-p5h8l", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/222/registry.xml' '/galaxy/server/database/jobs_directory/000/222/upload_params.json' '296:/galaxy/server/database/objects/1/b/b/dataset_1bba2375-a8cf-4e68-8298-172fe303c64c_files:/galaxy/server/database/objects/1/b/b/dataset_1bba2375-a8cf-4e68-8298-172fe303c64c.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_smdtsmc5\"", + "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"pbmc68k_reduced.h5ad\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_myvfwl8j\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"auto\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "a6e0df31d81c6cb1", + "src": "hda", + "uuid": "1bba2375-a8cf-4e68-8298-172fe303c64c" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/918acd168a1154d0.json b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/918acd168a1154d0.json new file mode 100644 index 000000000..5e031ab38 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/918acd168a1154d0.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "918acd168a1154d0", + "history_id": "417947348fdacb2d", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2025-01-02T07:11:20.323509", + "update_time": "2025-01-02T07:11:31.668756", + "galaxy_version": "24.1", + "external_id": "gxy-8djjr", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/190/registry.xml' '/galaxy/server/database/jobs_directory/000/190/upload_params.json' '252:/galaxy/server/database/objects/0/a/b/dataset_0ab7f786-c953-4846-80d0-1e59214e895d_files:/galaxy/server/database/objects/0/a/b/dataset_0ab7f786-c953-4846-80d0-1e59214e895d.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_zj27pauk\"", + "files_metadata": "{\"__current_case__\": 36, \"file_type\": \"bam\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"test_input_1_a.bam\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_n1uvl8h6\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"bam\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "2737299cf0223786", + "src": "hda", + "uuid": "0ab7f786-c953-4846-80d0-1e59214e895d" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/985cff68b895fef7.json b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/985cff68b895fef7.json new file mode 100644 index 000000000..e4f29a73b --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/985cff68b895fef7.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "985cff68b895fef7", + "history_id": "417947348fdacb2d", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2025-01-02T07:35:43.141032", + "update_time": "2025-01-02T07:35:54.168569", + "galaxy_version": "24.1", + "external_id": "gxy-6bhfn", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/288/registry.xml' '/galaxy/server/database/jobs_directory/000/288/upload_params.json' '366:/galaxy/server/database/objects/4/9/3/dataset_49357917-e873-4cd2-82b5-50f905a08d99_files:/galaxy/server/database/objects/4/9/3/dataset_49357917-e873-4cd2-82b5-50f905a08d99.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_4l06ehhc\"", + "files_metadata": "{\"__current_case__\": 325, \"file_type\": \"tabular\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"reheader.samples\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_w9so0j_4\", \"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": "bff4ccdb6d9873a5", + "src": "hda", + "uuid": "49357917-e873-4cd2-82b5-50f905a08d99" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/9cbe38f6b92875dd.json b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/9cbe38f6b92875dd.json new file mode 100644 index 000000000..306c6f08f --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/9cbe38f6b92875dd.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "9cbe38f6b92875dd", + "history_id": "417947348fdacb2d", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2025-01-02T06:40:47.249667", + "update_time": "2025-01-02T06:40:57.006688", + "galaxy_version": "24.1", + "external_id": "gxy-5zpb4", + "handler": null, + "job_runner_name": null, + "command_line": "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' '88:/galaxy/server/database/objects/7/f/6/dataset_7f65b562-4f49-485f-981b-f89809ebb25d_files:/galaxy/server/database/objects/7/f/6/dataset_7f65b562-4f49-485f-981b-f89809ebb25d.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_dq8mi_c9\"", + "files_metadata": "{\"__current_case__\": 81, \"file_type\": \"fastqsanger\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"paired_end_1_errors.fastqsanger\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_j2lud6im\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"fastqsanger\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "464fc29f22a0c501", + "src": "hda", + "uuid": "7f65b562-4f49-485f-981b-f89809ebb25d" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/a7333bc2f91bf09b.json b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/a7333bc2f91bf09b.json new file mode 100644 index 000000000..9e5580bf0 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/a7333bc2f91bf09b.json @@ -0,0 +1,63 @@ +{ + "model_class": "Job", + "id": "a7333bc2f91bf09b", + "history_id": "417947348fdacb2d", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/3.5.4+galaxy0", + "state": "error", + "exit_code": null, + "create_time": "2025-01-02T06:39:11.413423", + "update_time": "2025-01-02T06:39:33.582364", + "galaxy_version": "24.1", + "external_id": "gxy-dt29r", + "handler": null, + "job_runner_name": null, + "command_line": "ln -f -s '/galaxy/server/database/objects/2/0/f/dataset_20f1ad7c-6aed-4845-b64b-82326c2eea8b.dat' 'test.bw_0.bw' && ln -f -s '/galaxy/server/database/objects/2/0/f/dataset_20f1ad7c-6aed-4845-b64b-82326c2eea8b.dat' 'test.bw_1.bw' && multiBigwigSummary bins --numberOfProcessors \"${GALAXY_SLOTS:-4}\" --outFileName /galaxy/server/database/objects/3/a/6/dataset_3a6c971e-0db2-49c0-b2c8-da42f9a73c82.dat --bwfiles 'test.bw_0.bw' 'test.bw_1.bw' --binSize '10' --distanceBetweenBins '0'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"input\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "advancedOpt": "{\"__current_case__\": 0, \"showAdvancedOpt\": \"no\"}", + "outRawCounts": "false", + "region": "\"\"", + "mode": "{\"__current_case__\": 0, \"binSize\": \"10\", \"distanceBetweenBins\": \"0\", \"modeOpt\": \"bins\"}", + "custom_sample_labels_conditional": "{\"__current_case__\": 0, \"custom_labels_select\": \"No\"}", + "multibigwig_conditional": "{\"__current_case__\": 0, \"bigwigfiles\": {\"values\": [{\"id\": 79, \"src\": \"hda\"}, {\"id\": 79, \"src\": \"hda\"}]}, \"orderMatters\": \"No\"}" + }, + "inputs": { + "multibigwig_conditional|bigwigfiles": { + "id": "fad171ff350126b1", + "src": "hda", + "uuid": "20f1ad7c-6aed-4845-b64b-82326c2eea8b" + }, + "multibigwig_conditional|bigwigfiles1": { + "id": "fad171ff350126b1", + "src": "hda", + "uuid": "20f1ad7c-6aed-4845-b64b-82326c2eea8b" + }, + "multibigwig_conditional|bigwigfiles2": { + "id": "fad171ff350126b1", + "src": "hda", + "uuid": "20f1ad7c-6aed-4845-b64b-82326c2eea8b" + } + }, + "outputs": { + "outFile": { + "id": "5dd4a8bb8b279535", + "src": "hda", + "uuid": "3a6c971e-0db2-49c0-b2c8-da42f9a73c82" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "Number of bins found: 120\n", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "Number of bins found: 120\n", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/af900f0a581f1633.json b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/af900f0a581f1633.json new file mode 100644 index 000000000..b8efd408b --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/af900f0a581f1633.json @@ -0,0 +1,50 @@ +{ + "model_class": "Job", + "id": "af900f0a581f1633", + "history_id": "417947348fdacb2d", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.15.1+galaxy4", + "state": "error", + "exit_code": null, + "create_time": "2025-01-02T07:36:56.584802", + "update_time": "2025-01-02T07:37:01.532206", + "galaxy_version": "24.1", + "external_id": "gxy-lh2qn", + "handler": null, + "job_runner_name": null, + "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/3/8/f/dataset_38fa3f46-f58d-4658-b9c4-ecdc2d88d0d5.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools plugin tag2tag --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz -- --gl-to-pl --replace > '/galaxy/server/database/objects/d/d/4/dataset_dd4603ec-46f1-4d20-aa02-0f67aa7536ca.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"input\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "output_type": "\"v\"", + "sec_plugin": "{\"conversion\": \"--gl-to-pl\", \"replace\": true, \"threshold\": \"0.1\"}", + "sec_restrict": "{\"exclude\": null, \"include\": null, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}" + }, + "inputs": { + "input_file": { + "id": "eeb2e6fc769b3746", + "src": "hda", + "uuid": "38fa3f46-f58d-4658-b9c4-ecdc2d88d0d5" + } + }, + "outputs": { + "output_file": { + "id": "7309f62fab20a5ce", + "src": "hda", + "uuid": "dd4603ec-46f1-4d20-aa02-0f67aa7536ca" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/b4c1b98d6bb1ff17.json b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/b4c1b98d6bb1ff17.json new file mode 100644 index 000000000..f93a7c0b5 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/b4c1b98d6bb1ff17.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "b4c1b98d6bb1ff17", + "history_id": "417947348fdacb2d", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2025-01-02T07:13:11.788992", + "update_time": "2025-01-02T07:13:23.306559", + "galaxy_version": "24.1", + "external_id": "gxy-qcrm6", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/197/registry.xml' '/galaxy/server/database/jobs_directory/000/197/upload_params.json' '259:/galaxy/server/database/objects/2/7/2/dataset_272e02d4-6270-4bf0-a942-be8f0c3bbc54_files:/galaxy/server/database/objects/2/7/2/dataset_272e02d4-6270-4bf0-a942-be8f0c3bbc54.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_80a2tupb\"", + "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"A10.sub.bam\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_z1z0scl0\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"auto\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "4264759ecc8e87f8", + "src": "hda", + "uuid": "272e02d4-6270-4bf0-a942-be8f0c3bbc54" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/b5109b578da9c816.json b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/b5109b578da9c816.json new file mode 100644 index 000000000..72e2d99bf --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/b5109b578da9c816.json @@ -0,0 +1,47 @@ +{ + "model_class": "Job", + "id": "b5109b578da9c816", + "history_id": "417947348fdacb2d", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2", + "state": "error", + "exit_code": null, + "create_time": "2025-01-02T06:38:12.846820", + "update_time": "2025-01-02T06:38:17.646409", + "galaxy_version": "24.1", + "external_id": "gxy-5v5rx", + "handler": null, + "job_runner_name": null, + "command_line": "mkdir ./out && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/2dae863c8f42/split_file_to_collection/split_file_to_collection.py' --out ./out --in '/galaxy/server/database/objects/e/6/9/dataset_e690dc82-0c4d-4dc8-a731-0bc5ef17a552.dat' --ftype 'generic' --generic_re '^[^>].*' --split_after --numnew '2' --rand --seed '1010' --file_names 'rand' --file_ext 'fasta'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"fasta\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "split_parms": "{\"__current_case__\": 6, \"input\": {\"values\": [{\"id\": 73, \"src\": \"hda\"}]}, \"newfilenames\": \"rand\", \"select_allocate\": {\"__current_case__\": 0, \"allocate\": \"random\", \"seed\": \"1010\"}, \"select_ftype\": \"generic\", \"select_mode\": {\"__current_case__\": 1, \"mode\": \"numnew\", \"numnew\": \"2\"}, \"split_method\": {\"__current_case__\": 0, \"generic_regex\": \"^[^>].*\", \"select_split_method\": \"regex\", \"split_after\": \"true\"}}" + }, + "inputs": { + "split_parms|input": { + "id": "0e916bfa231d1662", + "src": "hda", + "uuid": "e690dc82-0c4d-4dc8-a731-0bc5ef17a552" + } + }, + "outputs": {}, + "copied_from_job_id": null, + "output_collections": { + "list_output_generic": { + "src": "hdca", + "id": "81ab1de02ece1727" + } + }, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/b5b5b391681960d4.json b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/b5b5b391681960d4.json new file mode 100644 index 000000000..258423ed8 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/b5b5b391681960d4.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "b5b5b391681960d4", + "history_id": "417947348fdacb2d", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2025-01-02T07:26:04.458165", + "update_time": "2025-01-02T07:26:33.135838", + "galaxy_version": "24.1", + "external_id": "gxy-sm5wp", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/240/registry.xml' '/galaxy/server/database/jobs_directory/000/240/upload_params.json' '318:/galaxy/server/database/objects/7/9/f/dataset_79ff0023-a953-4fd1-9055-e745e7d2feb7_files:/galaxy/server/database/objects/7/9/f/dataset_79ff0023-a953-4fd1-9055-e745e7d2feb7.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_2gz2socc\"", + "files_metadata": "{\"__current_case__\": 325, \"file_type\": \"tabular\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"input443.tabular\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data__lhlr9t5\", \"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": "c6e444ee690a210f", + "src": "hda", + "uuid": "79ff0023-a953-4fd1-9055-e745e7d2feb7" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/b903ee4231e92e43.json b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/b903ee4231e92e43.json new file mode 100644 index 000000000..c09569838 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/b903ee4231e92e43.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "b903ee4231e92e43", + "history_id": "417947348fdacb2d", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2025-01-02T07:22:59.722956", + "update_time": "2025-01-02T07:23:09.076209", + "galaxy_version": "24.1", + "external_id": "gxy-t8dcf", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/223/registry.xml' '/galaxy/server/database/jobs_directory/000/223/upload_params.json' '297:/galaxy/server/database/objects/a/3/1/dataset_a3142ef5-bee3-4449-a8dd-e8dbb147c221_files:/galaxy/server/database/objects/a/3/1/dataset_a3142ef5-bee3-4449-a8dd-e8dbb147c221.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_tyy5i2_h\"", + "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"pbmc68k_reduced.h5ad\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_rlvuazz8\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"auto\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "5e8b21a67f00293c", + "src": "hda", + "uuid": "a3142ef5-bee3-4449-a8dd-e8dbb147c221" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/c2c9997c29a1ad4a.json b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/c2c9997c29a1ad4a.json new file mode 100644 index 000000000..237fc505c --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/c2c9997c29a1ad4a.json @@ -0,0 +1,47 @@ +{ + "model_class": "Job", + "id": "c2c9997c29a1ad4a", + "history_id": "417947348fdacb2d", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2", + "state": "error", + "exit_code": null, + "create_time": "2025-01-02T06:36:35.497964", + "update_time": "2025-01-02T06:36:40.253026", + "galaxy_version": "24.1", + "external_id": "gxy-6w8zt", + "handler": null, + "job_runner_name": null, + "command_line": "mkdir ./out && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/2dae863c8f42/split_file_to_collection/split_file_to_collection.py' --out ./out --in '/galaxy/server/database/objects/3/d/9/dataset_3d9ff423-ec48-4de4-9fa7-62c7d3e1213f.dat' --ftype 'generic' --generic_re '^.*' --numnew '2' --file_names 'test' --file_ext 'txt'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"txt\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "split_parms": "{\"__current_case__\": 6, \"input\": {\"values\": [{\"id\": 64, \"src\": \"hda\"}]}, \"newfilenames\": \"test\", \"select_allocate\": {\"__current_case__\": 2, \"allocate\": \"byrow\"}, \"select_ftype\": \"generic\", \"select_mode\": {\"__current_case__\": 1, \"mode\": \"numnew\", \"numnew\": \"2\"}, \"split_method\": {\"__current_case__\": 0, \"generic_regex\": \"^.*\", \"select_split_method\": \"regex\", \"split_after\": \"false\"}}" + }, + "inputs": { + "split_parms|input": { + "id": "2862c9a90cb5fc49", + "src": "hda", + "uuid": "3d9ff423-ec48-4de4-9fa7-62c7d3e1213f" + } + }, + "outputs": {}, + "copied_from_job_id": null, + "output_collections": { + "list_output_generic": { + "src": "hdca", + "id": "b6825f59da9f7281" + } + }, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/c4520508ec6517a8.json b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/c4520508ec6517a8.json new file mode 100644 index 000000000..65f0d14b5 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/c4520508ec6517a8.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "c4520508ec6517a8", + "history_id": "417947348fdacb2d", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2025-01-02T06:33:57.472413", + "update_time": "2025-01-02T06:34:08.231344", + "galaxy_version": "24.1", + "external_id": "gxy-bk5f4", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/19/registry.xml' '/galaxy/server/database/jobs_directory/000/19/upload_params.json' '51:/galaxy/server/database/objects/c/c/8/dataset_cc8997a1-6b07-4934-8041-59ed8fa73a8e_files:/galaxy/server/database/objects/c/c/8/dataset_cc8997a1-6b07-4934-8041-59ed8fa73a8e.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_x6kot1zv\"", + "files_metadata": "{\"__current_case__\": 78, \"file_type\": \"fastq\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"test.fastq\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_xunp7ql2\", \"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": "9a4a3fd8012dabf4", + "src": "hda", + "uuid": "cc8997a1-6b07-4934-8041-59ed8fa73a8e" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/c5a244451d0c5bca.json b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/c5a244451d0c5bca.json new file mode 100644 index 000000000..34fc27939 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/c5a244451d0c5bca.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "c5a244451d0c5bca", + "history_id": "417947348fdacb2d", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2025-01-02T06:53:09.412978", + "update_time": "2025-01-02T06:53:19.635199", + "galaxy_version": "24.1", + "external_id": "gxy-8hwt8", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/114/registry.xml' '/galaxy/server/database/jobs_directory/000/114/upload_params.json' '159:/galaxy/server/database/objects/a/b/e/dataset_abec78d5-79e8-4d09-9375-467c33cbe882_files:/galaxy/server/database/objects/a/b/e/dataset_abec78d5-79e8-4d09-9375-467c33cbe882.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_i7cdxagk\"", + "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"merlin.fa\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_hwc5gura\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"auto\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "c1de528a8c238fa0", + "src": "hda", + "uuid": "abec78d5-79e8-4d09-9375-467c33cbe882" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/d3a6b95897339494.json b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/d3a6b95897339494.json new file mode 100644 index 000000000..f892b7a74 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/d3a6b95897339494.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "d3a6b95897339494", + "history_id": "417947348fdacb2d", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2025-01-02T07:30:42.102350", + "update_time": "2025-01-02T07:30:54.127789", + "galaxy_version": "24.1", + "external_id": "gxy-ftdgf", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/264/registry.xml' '/galaxy/server/database/jobs_directory/000/264/upload_params.json' '342:/galaxy/server/database/objects/6/9/5/dataset_695f2b86-dc75-496d-b97c-bae2e5542ea9_files:/galaxy/server/database/objects/6/9/5/dataset_695f2b86-dc75-496d-b97c-bae2e5542ea9.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_4vnchwyi\"", + "files_metadata": "{\"__current_case__\": 325, \"file_type\": \"tabular\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"input438.tabular\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_4s7dbbjv\", \"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": "8900ff43a3cd8f0c", + "src": "hda", + "uuid": "695f2b86-dc75-496d-b97c-bae2e5542ea9" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/f23509e5c74c32af.json b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/f23509e5c74c32af.json new file mode 100644 index 000000000..a8b4907ea --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/f23509e5c74c32af.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "f23509e5c74c32af", + "history_id": "417947348fdacb2d", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2025-01-02T07:26:04.249252", + "update_time": "2025-01-02T07:26:17.433082", + "galaxy_version": "24.1", + "external_id": "gxy-4tqnk", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/239/registry.xml' '/galaxy/server/database/jobs_directory/000/239/upload_params.json' '317:/galaxy/server/database/objects/f/c/1/dataset_fc1efc00-6593-4599-a21d-67139234067a_files:/galaxy/server/database/objects/f/c/1/dataset_fc1efc00-6593-4599-a21d-67139234067a.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_w_wajvpy\"", + "files_metadata": "{\"__current_case__\": 325, \"file_type\": \"tabular\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"input442.tabular\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_a61xpr_n\", \"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": "5e7ab2c16f52d817", + "src": "hda", + "uuid": "fc1efc00-6593-4599-a21d-67139234067a" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/f31ba40a134f0e3c.json b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/f31ba40a134f0e3c.json new file mode 100644 index 000000000..6d55d3bec --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/f31ba40a134f0e3c.json @@ -0,0 +1,58 @@ +{ + "model_class": "Job", + "id": "f31ba40a134f0e3c", + "history_id": "417947348fdacb2d", + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0", + "state": "error", + "exit_code": null, + "create_time": "2025-01-02T06:41:48.980207", + "update_time": "2025-01-02T06:41:53.676215", + "galaxy_version": "24.1", + "external_id": "gxy-49lj5", + "handler": null, + "job_runner_name": null, + "command_line": "gx-fastq-paired-end-interlacer '/galaxy/server/database/objects/1/1/0/dataset_110891a7-a7ef-4b89-91b1-909c075c5782.dat' sanger.bz2 '/galaxy/server/database/objects/0/8/8/dataset_08870eeb-ec0d-4772-8630-6c7f61fb4045.dat' sanger.bz2 '/galaxy/server/database/objects/e/4/7/dataset_e4708117-4478-4970-be04-d482d790800e.dat' '/galaxy/server/database/objects/4/e/b/dataset_4ebaf2aa-c616-42e3-861e-5c0ca1956377.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"fastqsanger.bz2\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "reads": "{\"__current_case__\": 0, \"input1_file\": {\"values\": [{\"id\": 94, \"src\": \"hda\"}]}, \"input2_file\": {\"values\": [{\"id\": 95, \"src\": \"hda\"}]}, \"reads_selector\": \"paired\"}" + }, + "inputs": { + "reads|input1_file": { + "id": "b1c9669bde4c754f", + "src": "hda", + "uuid": "110891a7-a7ef-4b89-91b1-909c075c5782" + }, + "reads|input2_file": { + "id": "4efedd6493da126f", + "src": "hda", + "uuid": "08870eeb-ec0d-4772-8630-6c7f61fb4045" + } + }, + "outputs": { + "outfile_singles": { + "id": "cea9f5165af2a27f", + "src": "hda", + "uuid": "4ebaf2aa-c616-42e3-861e-5c0ca1956377" + }, + "outfile_pairs": { + "id": "6bd4476c315259fd", + "src": "hda", + "uuid": "e4708117-4478-4970-be04-d482d790800e" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "There were 4 single reads.\nInterlaced 3 pairs of sequences.\n", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "There were 4 single reads.\nInterlaced 3 pairs of sequences.\n", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/fc56de97fc753237.json b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/fc56de97fc753237.json new file mode 100644 index 000000000..2ea51f387 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/fc56de97fc753237.json @@ -0,0 +1,55 @@ +{ + "model_class": "Job", + "id": "fc56de97fc753237", + "history_id": "417947348fdacb2d", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1", + "state": "error", + "exit_code": null, + "create_time": "2025-01-02T06:49:17.448574", + "update_time": "2025-01-02T06:49:23.287877", + "galaxy_version": "24.1", + "external_id": "gxy-6wbkl", + "handler": null, + "job_runner_name": null, + "command_line": "mkdir -p /galaxy/server/database/objects/1/e/4/dataset_1e47a883-be24-495d-9a82-6d19c876453c_files && cp /galaxy/server/database/jobs_directory/000/89/configs/tmpdaik8q5d /galaxy/server/database/objects/1/e/4/dataset_1e47a883-be24-495d-9a82-6d19c876453c_files/galaxy.xml && export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'data' --outdir /galaxy/server/database/objects/1/e/4/dataset_1e47a883-be24-495d-9a82-6d19c876453c_files /galaxy/server/database/jobs_directory/000/89/configs/tmpdaik8q5d && cp /galaxy/server/database/jobs_directory/000/89/configs/tmplxq90css /galaxy/server/database/objects/1/e/4/dataset_1e47a883-be24-495d-9a82-6d19c876453c.dat; cp /galaxy/server/database/jobs_directory/000/89/configs/tmpdaik8q5d /galaxy/server/database/objects/1/e/4/dataset_1e47a883-be24-495d-9a82-6d19c876453c.dat", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"fasta\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "uglyTestingHack": "\"enabled\"", + "plugins": "{\"BlastView\": true, \"ComboTrackSelector\": false, \"GCContent\": false}", + "jbgen": "{\"aboutDescription\": \"\", \"defaultLocation\": \"\", \"hideGenomeOptions\": false, \"shareLink\": true, \"show_menu\": true, \"show_nav\": true, \"show_overview\": true, \"show_tracklist\": true, \"trackPadding\": \"20\"}", + "track_groups": "[]", + "action": "{\"__current_case__\": 0, \"action_select\": \"create\"}", + "gencode": "\"1\"", + "standalone": "\"data\"", + "reference_genome": "{\"__current_case__\": 1, \"genome\": {\"values\": [{\"id\": 133, \"src\": \"hda\"}]}, \"genome_type_select\": \"history\"}" + }, + "inputs": { + "reference_genome|genome": { + "id": "27c7c932589d02a8", + "src": "hda", + "uuid": "4a0d2ccb-6139-457a-b293-0f27bbdfdebe" + } + }, + "outputs": { + "output": { + "id": "040f59f1ef394007", + "src": "hda", + "uuid": "1e47a883-be24-495d-9a82-6d19c876453c" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "WARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "WARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/job-metrics.csv b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/job-metrics.csv new file mode 100644 index 000000000..19336a67d --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/job-metrics.csv @@ -0,0 +1,305 @@ 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2025-01-02T07:29:40.758707 upload1 +4264759ecc8e87f8 ok 2025-01-02T07:29:37.122799 upload1 +f0ebfcddbd4eac17 ok 2025-01-02T07:29:35.866474 upload1 +d4ba988d8114743a ok 2025-01-02T07:29:30.243728 upload1 +8512113d23d65e82 ok 2025-01-02T07:29:30.174100 upload1 +fef920eed3b2bb9a ok 2025-01-02T07:29:22.635695 upload1 +b8487305a64c8e88 ok 2025-01-02T07:29:20.267957 upload1 +411641dc4e3905fa ok 2025-01-02T07:29:12.348548 upload1 +2737299cf0223786 error 2025-01-02T07:29:00.317303 upload1 +4a67f711d60438e3 ok 2025-01-02T07:28:47.536163 toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3 +5b4f286a8f2107ba ok 2025-01-02T07:27:51.039335 upload1 +9302f661c8bc4d07 ok 2025-01-02T07:27:43.528842 upload1 +2497ce2dffb7179d ok 2025-01-02T07:27:43.377349 upload1 +1037fbc5d5569fca ok 2025-01-02T07:27:43.333322 upload1 +d21e0c5e25017839 ok 2025-01-02T07:27:42.323660 upload1 +312f3442d7fe35ff ok 2025-01-02T07:27:25.837779 upload1 +bab3afaea06cd231 ok 2025-01-02T07:27:25.794166 upload1 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ok 2025-01-02T07:12:56.174339 upload1 +d51774b0f26d2f15 ok 2025-01-02T07:12:36.922675 toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.5 +e249f90a4f6999d3 ok 2025-01-02T07:12:23.773880 upload1 +a8ccef55ff307cde ok 2025-01-02T07:12:03.463961 toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.5 +dfe0cc2d300a8419 ok 2025-01-02T07:11:50.196557 upload1 +918acd168a1154d0 error 2025-01-02T07:11:31.668756 upload1 +708d8819903e2249 ok 2025-01-02T07:11:19.526871 toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.5 +d7341bbf89d9344e ok 2025-01-02T07:11:05.680374 upload1 +801ece6004fff63a ok 2025-01-02T07:10:46.240106 toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.5 +472d2049f13ec082 ok 2025-01-02T07:10:33.199587 upload1 +0961a381074d40d9 ok 2025-01-02T07:10:13.926298 toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.5 +a37c4acb3fc4721a ok 2025-01-02T07:10:00.795901 upload1 +8790449e336e97fc error 2025-01-02T07:09:42.291682 toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.5 +508dfd3b89fa496c ok 2025-01-02T07:09:37.603049 upload1 +5fa1c21cd11de4ce ok 2025-01-02T07:09:18.104808 toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.5 +9e86c34dc85fc9c3 ok 2025-01-02T07:08:58.757930 upload1 +004fc63303625c27 ok 2025-01-02T07:08:38.797956 toolshed.g2.bx.psu.edu/repos/iuc/qualimap_multi_bamqc/qualimap_multi_bamqc/2.3+galaxy0 +fef993a7ccf659a3 ok 2025-01-02T07:07:43.173244 upload1 +70c182b97ebd328c ok 2025-01-02T07:07:42.232868 upload1 +769fa26b9dcf2036 ok 2025-01-02T07:07:36.254134 upload1 +246bbf24761f3fdf ok 2025-01-02T07:07:36.030216 upload1 +fab6cb90ff6a0960 ok 2025-01-02T07:07:34.434815 upload1 +948b64f23b92f540 ok 2025-01-02T07:07:32.622204 upload1 +0ea2c2968d5e50e0 ok 2025-01-02T07:07:20.433920 upload1 +96722cfa8e7f5f50 ok 2025-01-02T07:07:20.057577 upload1 +784d8067765821e3 ok 2025-01-02T07:07:18.528984 upload1 +8b5665ece2d98723 ok 2025-01-02T07:07:16.546680 upload1 +42067da38216ecab ok 2025-01-02T07:06:48.874479 toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.36.0+galaxy5 +3bc6697b14d2f281 ok 2025-01-02T07:06:29.374967 upload1 +c2ebd14675ce2289 ok 2025-01-02T07:06:29.363780 upload1 +a9062a17810006ff ok 2025-01-02T07:06:09.083363 toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.36.0+galaxy5 +667e5431a134908a ok 2025-01-02T07:05:50.612405 upload1 +6337d112ca25c320 ok 2025-01-02T07:05:31.440963 toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.36.0+galaxy5 +c33db1863748b37d ok 2025-01-02T07:05:14.239132 upload1 +8f3aaede24ad8be6 ok 2025-01-02T07:04:55.127441 toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.36.0+galaxy5 +98baee9b2768ca42 ok 2025-01-02T07:04:36.933151 upload1 +ddc070378ca3ecf8 ok 2025-01-02T07:04:17.937024 upload1 +f209d4249397848c ok 2025-01-02T07:04:17.896931 upload1 +6ac8f9c789c25e5a ok 2025-01-02T07:04:17.688953 upload1 +6e386b278832dd3b error 2025-01-02T07:04:16.575307 upload1 +c1de528a8c238fa0 ok 2025-01-02T07:04:15.824211 upload1 +af6c4fd171b336e0 ok 2025-01-02T07:04:02.919669 upload1 +bbe5504370b59d77 ok 2025-01-02T07:04:02.887866 upload1 +25e804484ced14fc ok 2025-01-02T07:04:02.668625 upload1 +f2efca6f659a474b ok 2025-01-02T07:03:59.854130 upload1 +bfa7fc5290d195fc ok 2025-01-02T07:03:46.813226 upload1 +54d4553682370391 ok 2025-01-02T07:03:46.795712 upload1 +d42319a28dee733d ok 2025-01-02T07:03:46.670995 upload1 +45b5f63126351244 ok 2025-01-02T07:03:44.534994 upload1 +63595e06f91e4c77 ok 2025-01-02T07:03:16.504907 toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.36.0+galaxy5 +9c7ffa381ed047d5 ok 2025-01-02T07:02:59.198668 upload1 +f30b2a399ca810d7 ok 2025-01-02T07:02:40.021069 toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.36.0+galaxy5 +1f3136644b950c4e ok 2025-01-02T07:02:22.870331 upload1 +ee896aa35de40137 ok 2025-01-02T07:02:04.620271 toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.36.0+galaxy5 +43b711b8ef0c5e46 ok 2025-01-02T07:01:46.752880 upload1 +a5284223a1f64a54 ok 2025-01-02T07:01:46.724579 upload1 +fdca54d393a7a551 ok 2025-01-02T07:01:26.815229 toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.36.0+galaxy5 +9dfb9ab628f00936 ok 2025-01-02T07:01:09.401730 upload1 +fad5685674975133 ok 2025-01-02T07:00:50.179274 toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.36.0+galaxy5 +1aa6b9331aa13111 ok 2025-01-02T07:00:33.099467 upload1 +dbe845cfdafc6fb2 ok 2025-01-02T07:00:14.201804 toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.36.0+galaxy5 +040f59f1ef394007 ok 2025-01-02T06:59:56.128845 upload1 +27c7c932589d02a8 ok 2025-01-02T06:59:56.062067 upload1 +babaa99004e96057 ok 2025-01-02T06:59:35.367746 toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.36.0+galaxy5 +0bbec1c4b4ec8188 ok 2025-01-02T06:59:18.757016 upload1 +2ba188dd08e677d1 ok 2025-01-02T06:58:59.649317 toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.36.0+galaxy5 +ad7cdefb17e24f31 ok 2025-01-02T06:58:26.763090 upload1 +5711a2960ca45e3c ok 2025-01-02T06:58:00.737534 toolshed.g2.bx.psu.edu/repos/iuc/poretools_winner/poretools_winner/0.6.1a1.0 +f90b805bacc4c138 ok 2025-01-02T06:57:46.548844 upload1 +9fa5638ea7c7019e ok 2025-01-02T06:57:27.188569 toolshed.g2.bx.psu.edu/repos/iuc/poretools_winner/poretools_winner/0.6.1a1.0 +f17becfa74bb10c7 ok 2025-01-02T06:57:14.258547 upload1 +e76cff200bf710f5 ok 2025-01-02T06:56:56.010850 toolshed.g2.bx.psu.edu/repos/iuc/poretools_winner/poretools_winner/0.6.1a1.0 +62a8ef6bb482441a ok 2025-01-02T06:56:41.777779 upload1 +7fd375b8233b3119 error 2025-01-02T06:56:23.316711 toolshed.g2.bx.psu.edu/repos/iuc/poretools_winner/poretools_winner/0.6.1a1.0 +b0e95d401bc1ff67 ok 2025-01-02T06:55:55.157171 upload1 +ced3cbd85f71829a ok 2025-01-02T06:55:35.831746 toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0rc1+galaxy3 +fc72c3209ee3fe87 ok 2025-01-02T06:55:17.572951 upload1 +1e77095bebc3b3c7 ok 2025-01-02T06:54:57.540638 toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1 +83f61fccece2af58 ok 2025-01-02T06:54:43.191076 upload1 +4963a0f517e742b4 ok 2025-01-02T06:54:24.879678 toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1 +1e88791af14104f4 ok 2025-01-02T06:53:30.255168 upload1 +c5a244451d0c5bca error 2025-01-02T06:53:19.635199 upload1 +27e96da2ddad3da3 ok 2025-01-02T06:53:03.378073 toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1 +bb2cdd97a30e285f ok 2025-01-02T06:52:49.535708 upload1 +7e10eda76b933a67 ok 2025-01-02T06:52:49.371190 upload1 +55cbbbefccf62e5d error 2025-01-02T06:52:30.510140 toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1 +ff8c65f5f2aaf055 ok 2025-01-02T06:52:24.994375 upload1 +abb7871dbf6325f9 ok 2025-01-02T06:52:24.860723 upload1 +7e902eabb9a394c6 error 2025-01-02T06:52:04.717107 toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1 +e25c262d60016a05 ok 2025-01-02T06:51:57.176027 upload1 +86e3335ea84ed5fd ok 2025-01-02T06:51:57.138836 upload1 +59e7f7bb0c0090a3 ok 2025-01-02T06:51:38.398318 toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1 +127b7060f892c121 ok 2025-01-02T06:51:22.043865 upload1 +c067909e5f63b4bf ok 2025-01-02T06:51:21.936552 upload1 +047c29d7543a0b6d ok 2025-01-02T06:51:21.644258 upload1 +beff140338e13f0a ok 2025-01-02T06:51:21.638815 upload1 +1cd18935d5504101 ok 2025-01-02T06:51:05.990115 upload1 +d0b4ada06108d401 ok 2025-01-02T06:51:05.909749 upload1 +6bd4476c315259fd ok 2025-01-02T06:51:05.747738 upload1 +cea9f5165af2a27f ok 2025-01-02T06:51:05.728344 upload1 +4efedd6493da126f ok 2025-01-02T06:50:35.040970 toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1 +0d0c9db3722fb76f ok 2025-01-02T06:50:20.510168 upload1 +b1c9669bde4c754f ok 2025-01-02T06:50:20.479235 upload1 +55263d1cb66db542 ok 2025-01-02T06:50:19.346945 upload1 +d8e297280a597dec ok 2025-01-02T06:49:55.927591 toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1 +5bfca613015f3d4d ok 2025-01-02T06:49:41.591049 upload1 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toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1 +7d590e2aab35997b ok 2025-01-02T06:45:48.794438 upload1 +4ae9ef01a8862b59 ok 2025-01-02T06:45:48.767655 upload1 +3765a9dbf6de90a8 ok 2025-01-02T06:45:28.831540 toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1 +0e916bfa231d1662 ok 2025-01-02T06:45:14.138299 upload1 +e520b254cad009c5 ok 2025-01-02T06:45:14.126627 upload1 +808d25e5c3af11a1 ok 2025-01-02T06:44:58.801468 upload1 +3e8cd1fa93a54128 error 2025-01-02T06:44:55.079112 upload1 +23099d778d2eb38a ok 2025-01-02T06:44:55.053025 upload1 +1adfc04efc82c30c ok 2025-01-02T06:44:54.861337 upload1 +109483ea678a2726 ok 2025-01-02T06:44:54.538751 upload1 +87de444ed74458c4 ok 2025-01-02T06:44:47.534435 upload1 +313ab96f9d8f8251 error 2025-01-02T06:44:39.404990 upload1 +039e98ef7e07fc36 error 2025-01-02T06:44:39.170620 upload1 +2862c9a90cb5fc49 ok 2025-01-02T06:44:24.679039 toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1 +2c6dddfa20f05e64 ok 2025-01-02T06:44:10.517954 upload1 +12be6bb5ce7b2302 ok 2025-01-02T06:44:09.712238 upload1 +928abf10b09916b8 ok 2025-01-02T06:44:08.651106 upload1 +24611f45b2c6f4c6 error 2025-01-02T06:43:46.594588 toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1 +6e2017aab688e208 ok 2025-01-02T06:43:40.533128 upload1 +1e96e1d58f839ce0 ok 2025-01-02T06:43:21.190962 toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1 +f1e7ec6971c91b6c ok 2025-01-02T06:42:47.747515 upload1 +b20a6f5b6dfc46b8 ok 2025-01-02T06:42:27.649081 toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0 +9b787033c9052aa6 ok 2025-01-02T06:42:13.527926 upload1 +055bd6bd17ad1036 ok 2025-01-02T06:42:13.520602 upload1 +f31ba40a134f0e3c error 2025-01-02T06:41:53.676215 toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0 +33b124f4a0e08d37 ok 2025-01-02T06:41:48.883932 upload1 +9a4a3fd8012dabf4 ok 2025-01-02T06:41:48.814211 upload1 +294c47ae7ea33e75 ok 2025-01-02T06:41:29.978417 toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0 +d612dfbfd1130b42 ok 2025-01-02T06:41:16.167363 upload1 +c096ce05add57702 ok 2025-01-02T06:41:16.132635 upload1 +da152380dd2f9bf1 ok 2025-01-02T06:41:05.455751 upload1 +9cbe38f6b92875dd error 2025-01-02T06:40:57.006688 upload1 +c68db52f6074a879 ok 2025-01-02T06:40:45.878962 toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0 +e7ac640723d4ad6f ok 2025-01-02T06:40:27.023633 upload1 +bb15c2d946ad8a9e ok 2025-01-02T06:40:26.911905 upload1 +be431f3fd6e35768 ok 2025-01-02T06:40:06.379125 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/3.5.4+galaxy0 +81359fa1d48d9bab ok 2025-01-02T06:39:52.112551 upload1 +a7333bc2f91bf09b error 2025-01-02T06:39:33.582364 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/3.5.4+galaxy0 +d90ec30be9b29d47 ok 2025-01-02T06:39:11.307372 upload1 +8414badffa71b2a6 ok 2025-01-02T06:38:50.235035 toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2 +2e865966e3c3766e ok 2025-01-02T06:38:36.286419 upload1 +b5109b578da9c816 error 2025-01-02T06:38:17.646409 toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2 +391e5b1591bc17af ok 2025-01-02T06:38:12.681045 upload1 +52803ce717ec40bb error 2025-01-02T06:37:54.371100 upload1 +14b55797034a16ee ok 2025-01-02T06:37:43.086472 toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2 +b05369fb76ed1035 ok 2025-01-02T06:37:29.883365 upload1 +00fed3ded302320f ok 2025-01-02T06:37:10.730574 toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2 +3225cbe6af27668b ok 2025-01-02T06:36:57.824788 upload1 +c2c9997c29a1ad4a error 2025-01-02T06:36:40.253026 toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2 +5c3d35f5b5f60693 ok 2025-01-02T06:36:35.237425 upload1 +8c6a9a635ccb6b1c ok 2025-01-02T06:36:17.280552 toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2 +5a07dcc0f79b3c50 ok 2025-01-02T06:36:03.794319 upload1 +2dca843539d91a0d ok 2025-01-02T06:35:44.637548 toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2 +deecf5987acb48d2 ok 2025-01-02T06:35:31.554633 upload1 +1b77217c2414c23e ok 2025-01-02T06:35:13.132434 toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2 +1b86423d2d9923d4 ok 2025-01-02T06:34:59.037269 upload1 +b691c7254e38a402 ok 2025-01-02T06:34:39.709222 toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2 +f479df8956fff6f2 ok 2025-01-02T06:34:26.674990 upload1 +c4520508ec6517a8 error 2025-01-02T06:34:08.231344 upload1 +4f527a71b6c9dd50 ok 2025-01-02T06:33:56.608111 toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2 +81ab1de02ece1727 ok 2025-01-02T06:33:43.242818 upload1 +dcbf6c083c690e6e ok 2025-01-02T06:33:24.168426 toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2 +307e56616f72abf0 ok 2025-01-02T06:33:10.949803 upload1 +b6825f59da9f7281 ok 2025-01-02T06:32:51.836152 toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2 +9de504bc018e2949 ok 2025-01-02T06:32:39.044256 upload1 +ecd04b30e568d759 ok 2025-01-02T06:32:19.558931 toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2 +345f6aa96f8fc5bc ok 2025-01-02T06:32:05.445633 upload1 +2da80dd8d646d9cd ok 2025-01-02T06:31:42.526064 toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2 +4bb5a07230ffcb62 ok 2025-01-02T06:31:29.018830 upload1 +816fa2444522560a ok 2025-01-02T06:31:09.792795 toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2 +86525e5b18646427 ok 2025-01-02T06:30:55.688085 upload1 +eb32687926f00cfa ok 2025-01-02T06:30:35.890365 toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2 +af6ecdbda415fbdd ok 2025-01-02T06:30:21.949519 upload1 +7ffebc1e07d84419 ok 2025-01-02T06:30:02.379337 toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2 +fa19a58c7eaf71b5 ok 2025-01-02T06:29:50.041728 upload1 +804dcea5bbe17c90 error 2025-01-02T06:29:30.542699 toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2 +417947348fdacb2d ok 2025-01-02T06:28:55.816396 upload1 diff --git a/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/results.html b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/results.html new file mode 100644 index 000000000..afc2b3c79 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/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-25-01-02-06-11-1/results.json b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/results.json new file mode 100644 index 000000000..08fe0c986 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/results.json @@ -0,0 +1 @@ +{"version": "0.1", "suitename": "Galaxy Tool Tests", "results": {"total": 117, "errors": 21, "failures": 22, "skips": 0}, "tests": [{"id": "10x_bamtofastq/1.4.1-0", "has_data": true, "data": {"tool_id": "10x_bamtofastq", "tool_version": "1.4.1", "test_index": 0, "time_seconds": 11.950011730194092, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "bcftools_gtcheck/1.15.1+galaxy4-0", "has_data": true, "data": {"tool_id": "bcftools_gtcheck", "tool_version": "1.15.1+galaxy4", "test_index": 0, "time_seconds": 39.37142634391785, "inputs": {"input_file": {"src": "hda", "id": "6a2df3a6533eb30c"}}, "job": {"model_class": "Job", "id": "444b3d9caa993193", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.15.1+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2025-01-02T07:34:47.932286", "update_time": "2025-01-02T07:35:06.652561", "galaxy_version": "24.1", "external_id": "gxy-zv8c5", "handler": null, "job_runner_name": null, "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/0/e/4/dataset_0e4433d6-9fc4-44a2-ba63-87977dc276c7.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools gtcheck input.vcf.gz > '/galaxy/server/database/objects/a/0/1/dataset_a01da257-88fe-46aa-83f1-5711dec969c1.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.15.1 (using htslib 1.15.1)", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "sec_default": "{\"all_sites\": false, \"genotypes\": null, \"homs_only\": false, \"plot\": null, \"query_sample\": null, \"target_sample\": null}", "sec_restrict": "{\"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}"}, "inputs": {"input_file": {"id": "6a2df3a6533eb30c", "src": "hda", "uuid": "0e4433d6-9fc4-44a2-ba63-87977dc276c7"}}, "outputs": {"output_file": {"id": "6b7ac7576c67f747", "src": "hda", "uuid": "a01da257-88fe-46aa-83f1-5711dec969c1"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "INFO: skipping 11:2343543, monoallelic site. (This is printed only once.)\nINFO:\tTime required to process one record .. 0.000005 seconds\nINFO: skipping 20:271225, not a biallelic site, run `bcftools norm -m -` first. (This is printed only once.)\nINFO: skipping Y:8657215, only diploid FORMAT/PL fields supported. (This is printed only once.)\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "INFO: skipping 11:2343543, monoallelic site. (This is printed only once.)\nINFO:\tTime required to process one record .. 0.000005 seconds\nINFO: skipping 20:271225, not a biallelic site, run `bcftools norm -m -` first. (This is printed only once.)\nINFO: skipping Y:8657215, only diploid FORMAT/PL fields supported. (This is printed only once.)\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2025-01-02 07:34:53", "plugin": "core", "name": "end_epoch", "raw_value": "1735803293.0000000"}, {"title": "Job Start Time", "value": "2025-01-02 07:34:53", "plugin": "core", "name": "start_epoch", "raw_value": "1735803293.0000000"}, {"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_tag2tag/1.15.1+galaxy4-0", "has_data": true, "data": {"tool_id": "bcftools_plugin_tag2tag", "tool_version": "1.15.1+galaxy4", "test_index": 0, "time_seconds": 24.7186861038208, "inputs": {"input_file": {"src": "hda", "id": "eeb2e6fc769b3746"}, "sec_plugin|conversion": "--gl-to-pl", "sec_plugin|replace": true, "output_type": "v"}, "job": {"model_class": "Job", "id": "af900f0a581f1633", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.15.1+galaxy4", "state": "error", "exit_code": null, "create_time": "2025-01-02T07:36:56.584802", "update_time": "2025-01-02T07:37:01.532206", "galaxy_version": "24.1", "external_id": "gxy-lh2qn", "handler": null, "job_runner_name": null, "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/3/8/f/dataset_38fa3f46-f58d-4658-b9c4-ecdc2d88d0d5.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools plugin tag2tag --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz -- --gl-to-pl --replace > '/galaxy/server/database/objects/d/d/4/dataset_dd4603ec-46f1-4d20-aa02-0f67aa7536ca.dat'", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "sec_plugin": "{\"conversion\": \"--gl-to-pl\", \"replace\": true, \"threshold\": \"0.1\"}", "sec_restrict": "{\"exclude\": null, \"include\": null, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}"}, "inputs": {"input_file": {"id": "eeb2e6fc769b3746", "src": "hda", "uuid": "38fa3f46-f58d-4658-b9c4-ecdc2d88d0d5"}}, "outputs": {"output_file": {"id": "7309f62fab20a5ce", "src": "hda", "uuid": "dd4603ec-46f1-4d20-aa02-0f67aa7536ca"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": null, "job_stderr": null, "stdout": "", "stderr": "", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.15.1+galaxy4, exit_code: None, stderr: .", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.15.1+galaxy4, exit_code: None, stderr: ."], "status": "failure"}}, {"id": "bcftools_reheader/1.15.1+galaxy4-0", "has_data": true, "data": {"tool_id": "bcftools_reheader", "tool_version": "1.15.1+galaxy4", "test_index": 0, "time_seconds": 34.58607721328735, "inputs": {"input_file": {"src": "hda", "id": "326977419fd47766"}, "sec_default|header": {"src": "hda", "id": "1e7ea79d481f232c"}, "output_type": "v"}, "job": {"model_class": "Job", "id": "cee70782e38f3ef6", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.15.1+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2025-01-02T07:35:28.584105", "update_time": "2025-01-02T07:35:42.165367", "galaxy_version": "24.1", "external_id": "gxy-zgdsp", "handler": null, "job_runner_name": null, "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/3/0/9/dataset_309a7042-cf1b-45f1-955d-20295161af52.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools reheader --header \"/galaxy/server/database/objects/1/4/0/dataset_1403d132-036f-4959-860c-471b5fa5c83a.dat\" input.vcf.gz | bcftools view --output-type 'v' > '/galaxy/server/database/objects/6/c/2/dataset_6c2e7a1d-9783-4666-95c7-639e88187e52.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.15.1 (using htslib 1.15.1)", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "sec_default": "{\"header\": {\"values\": [{\"id\": 363, \"src\": \"hda\"}]}, \"rename_samples\": {\"__current_case__\": 0, \"samples_src\": \"none\"}}"}, "inputs": {"input_file": {"id": "326977419fd47766", "src": "hda", "uuid": "309a7042-cf1b-45f1-955d-20295161af52"}, "sec_default|header": {"id": "1e7ea79d481f232c", "src": "hda", "uuid": "1403d132-036f-4959-860c-471b5fa5c83a"}}, "outputs": {"output_file": {"id": "e3faf5b994b09f0b", "src": "hda", "uuid": "6c2e7a1d-9783-4666-95c7-639e88187e52"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2025-01-02 07:35:30", "plugin": "core", "name": "end_epoch", "raw_value": "1735803330.0000000"}, {"title": "Job Start Time", "value": "2025-01-02 07:35:29", "plugin": "core", "name": "start_epoch", "raw_value": "1735803329.0000000"}, {"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_reheader/1.15.1+galaxy4-1", "has_data": true, "data": {"tool_id": "bcftools_reheader", "tool_version": "1.15.1+galaxy4", "test_index": 1, "time_seconds": 19.090662240982056, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "bcftools_reheader/1.15.1+galaxy4-2", "has_data": true, "data": {"tool_id": "bcftools_reheader", "tool_version": "1.15.1+galaxy4", "test_index": 2, "time_seconds": 34.53036451339722, "inputs": {"input_file": {"src": "hda", "id": "a38790d3ce30e7bc"}, "sec_default|rename_samples|sample_file": {"src": "hda", "id": "e951a784c8173e42"}, "sec_default|rename_samples|samples_src": "history", "output_type": "v"}, "job": {"model_class": "Job", "id": "414408a001dd2431", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.15.1+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2025-01-02T07:36:21.621560", "update_time": "2025-01-02T07:36:35.884268", "galaxy_version": "24.1", "external_id": "gxy-rtp4x", "handler": null, "job_runner_name": null, "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/1/c/3/dataset_1c327843-057a-411b-931f-931b53f5cd9c.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools reheader --samples \"/galaxy/server/database/objects/d/b/2/dataset_db242966-7eda-4c8e-98ce-2b8d35375c6d.dat\" input.vcf.gz | bcftools view --output-type 'v' > '/galaxy/server/database/objects/b/4/7/dataset_b471319f-0f27-4f8c-9138-60c09755db62.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.15.1 (using htslib 1.15.1)", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "sec_default": "{\"header\": null, \"rename_samples\": {\"__current_case__\": 1, \"sample_file\": {\"values\": [{\"id\": 368, \"src\": \"hda\"}]}, \"samples_src\": \"history\"}}"}, "inputs": {"input_file": {"id": "a38790d3ce30e7bc", "src": "hda", "uuid": "1c327843-057a-411b-931f-931b53f5cd9c"}, "sec_default|rename_samples|sample_file": {"id": "e951a784c8173e42", "src": "hda", "uuid": "db242966-7eda-4c8e-98ce-2b8d35375c6d"}}, "outputs": {"output_file": {"id": "c3ec81528627a6d8", "src": "hda", "uuid": "b471319f-0f27-4f8c-9138-60c09755db62"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2025-01-02 07:36:24", "plugin": "core", "name": "end_epoch", "raw_value": "1735803384.0000000"}, {"title": "Job Start Time", "value": "2025-01-02 07:36:23", "plugin": "core", "name": "start_epoch", "raw_value": "1735803383.0000000"}, {"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_multi_bigwig_summary/3.5.4+galaxy0-0", "has_data": true, "data": {"tool_id": "deeptools_multi_bigwig_summary", "tool_version": "3.5.4+galaxy0", "test_index": 0, "time_seconds": 41.83625507354736, "inputs": {"multibigwig_conditional|bigwigfiles": [{"src": "hda", "id": "fad171ff350126b1"}, {"src": "hda", "id": "fad171ff350126b1"}], "mode|binSize": "10", "mode|modeOpt": "bins"}, "job": {"model_class": "Job", "id": "a7333bc2f91bf09b", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/3.5.4+galaxy0", "state": "error", "exit_code": null, "create_time": "2025-01-02T06:39:11.413423", "update_time": "2025-01-02T06:39:33.582364", "galaxy_version": "24.1", "external_id": "gxy-dt29r", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/2/0/f/dataset_20f1ad7c-6aed-4845-b64b-82326c2eea8b.dat' 'test.bw_0.bw' && ln -f -s '/galaxy/server/database/objects/2/0/f/dataset_20f1ad7c-6aed-4845-b64b-82326c2eea8b.dat' 'test.bw_1.bw' && multiBigwigSummary bins --numberOfProcessors \"${GALAXY_SLOTS:-4}\" --outFileName /galaxy/server/database/objects/3/a/6/dataset_3a6c971e-0db2-49c0-b2c8-da42f9a73c82.dat --bwfiles 'test.bw_0.bw' 'test.bw_1.bw' --binSize '10' --distanceBetweenBins '0'", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advancedOpt": "{\"__current_case__\": 0, \"showAdvancedOpt\": \"no\"}", "outRawCounts": "false", "region": "\"\"", "mode": "{\"__current_case__\": 0, \"binSize\": \"10\", \"distanceBetweenBins\": \"0\", \"modeOpt\": \"bins\"}", "custom_sample_labels_conditional": "{\"__current_case__\": 0, \"custom_labels_select\": \"No\"}", "multibigwig_conditional": "{\"__current_case__\": 0, \"bigwigfiles\": {\"values\": [{\"id\": 79, \"src\": \"hda\"}, {\"id\": 79, \"src\": \"hda\"}]}, \"orderMatters\": \"No\"}"}, "inputs": {"multibigwig_conditional|bigwigfiles": {"id": "fad171ff350126b1", "src": "hda", "uuid": "20f1ad7c-6aed-4845-b64b-82326c2eea8b"}, "multibigwig_conditional|bigwigfiles1": {"id": "fad171ff350126b1", "src": "hda", "uuid": "20f1ad7c-6aed-4845-b64b-82326c2eea8b"}, "multibigwig_conditional|bigwigfiles2": {"id": "fad171ff350126b1", "src": "hda", "uuid": "20f1ad7c-6aed-4845-b64b-82326c2eea8b"}}, "outputs": {"outFile": {"id": "5dd4a8bb8b279535", "src": "hda", "uuid": "3a6c971e-0db2-49c0-b2c8-da42f9a73c82"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Number of bins found: 120\n", "job_stdout": null, "job_stderr": null, "stdout": "", "stderr": "Number of bins found: 120\n", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/3.5.4+galaxy0, exit_code: None, stderr: Number of bins found: 120\n.", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/3.5.4+galaxy0, exit_code: None, stderr: Number of bins found: 120\n."], "status": "failure"}}, {"id": "deeptools_multi_bigwig_summary/3.5.4+galaxy0-1", "has_data": true, "data": {"tool_id": "deeptools_multi_bigwig_summary", "tool_version": "3.5.4+galaxy0", "test_index": 1, "time_seconds": 32.98186373710632, "inputs": {"multibigwig_conditional|bigwigfiles": [{"src": "hda", "id": "1ee8d5aaf8a35324"}, {"src": "hda", "id": "1ee8d5aaf8a35324"}], "custom_sample_labels_conditional|labels": "sample1 sample2", "custom_sample_labels_conditional|custom_labels_select": "Yes", "mode|binSize": "10", "mode|modeOpt": "bins", "outRawCounts": true}, "job": {"model_class": "Job", "id": "be431f3fd6e35768", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/3.5.4+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2025-01-02T06:39:52.314356", "update_time": "2025-01-02T06:40:06.379125", "galaxy_version": "24.1", "external_id": "gxy-rwvwz", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/9/e/4/dataset_9e4b46b3-1f83-49d4-a5c2-93d8a769cd53.dat' 'test.bw_0.bw' && ln -f -s '/galaxy/server/database/objects/9/e/4/dataset_9e4b46b3-1f83-49d4-a5c2-93d8a769cd53.dat' 'test.bw_1.bw' && multiBigwigSummary bins --numberOfProcessors \"${GALAXY_SLOTS:-4}\" --outFileName /galaxy/server/database/objects/3/2/5/dataset_3258b57b-614f-4165-bcf7-b59722d393c5.dat --bwfiles 'test.bw_0.bw' 'test.bw_1.bw' --labels sample1 sample2 --outRawCounts '/galaxy/server/database/objects/c/b/3/dataset_cb31ae82-f9de-4e0f-86eb-d0626a800aba.dat' --binSize '10' --distanceBetweenBins '0'", "user_email": "tests@fake.org", "command_version": "multiBigwigSummary 3.5.4", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advancedOpt": "{\"__current_case__\": 0, \"showAdvancedOpt\": \"no\"}", "outRawCounts": "true", "region": "\"\"", "mode": "{\"__current_case__\": 0, \"binSize\": \"10\", \"distanceBetweenBins\": \"0\", \"modeOpt\": \"bins\"}", "custom_sample_labels_conditional": "{\"__current_case__\": 1, \"custom_labels_select\": \"Yes\", \"labels\": \"sample1 sample2\"}", "multibigwig_conditional": "{\"__current_case__\": 0, \"bigwigfiles\": {\"values\": [{\"id\": 81, \"src\": \"hda\"}, {\"id\": 81, \"src\": \"hda\"}]}, \"orderMatters\": \"No\"}"}, "inputs": {"multibigwig_conditional|bigwigfiles": {"id": "1ee8d5aaf8a35324", "src": "hda", "uuid": "9e4b46b3-1f83-49d4-a5c2-93d8a769cd53"}, "multibigwig_conditional|bigwigfiles1": {"id": "1ee8d5aaf8a35324", "src": "hda", "uuid": "9e4b46b3-1f83-49d4-a5c2-93d8a769cd53"}, "multibigwig_conditional|bigwigfiles2": {"id": "1ee8d5aaf8a35324", "src": "hda", "uuid": "9e4b46b3-1f83-49d4-a5c2-93d8a769cd53"}}, "outputs": {"outFile": {"id": "4c71a771ab6a849f", "src": "hda", "uuid": "3258b57b-614f-4165-bcf7-b59722d393c5"}, "outFileRawCounts": {"id": "a0f8054d02b4c2b6", "src": "hda", "uuid": "cb31ae82-f9de-4e0f-86eb-d0626a800aba"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Number of bins found: 120\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Number of bins found: 120\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}, {"title": "Memory Allocated (MB)", "value": "42949", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "42949.0000000"}, {"title": "Job Start Time", "value": "2025-01-02 06:39:54", "plugin": "core", "name": "start_epoch", "raw_value": "1735799994.0000000"}, {"title": "Job End Time", "value": "2025-01-02 06:39:55", "plugin": "core", "name": "end_epoch", "raw_value": "1735799995.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}]}, "output_problems": ["Output outFileRawCounts: different than expected, difference (using diff):\n( /tmp/tmpjvwljfqemultiBigwigSummary_result2.tabular v. /tmp/tmpo7rvcx2mmultiBigwigSummary_result2.tabular )\n--- local_file\n+++ history_data\n@@ -39,6 +39,46 @@\n ch1\t370\t380\t0.0\t0.0\n ch1\t380\t390\t0.0\t0.0\n ch1\t390\t400\t0.0\t0.0\n+ch3\t0\t10\t0.0\t0.0\n+ch3\t10\t20\t0.0\t0.0\n+ch3\t20\t30\t0.0\t0.0\n+ch3\t30\t40\t0.0\t0.0\n+ch3\t40\t50\t0.0\t0.0\n+ch3\t50\t60\t3.0\t3.0\n+ch3\t60\t70\t3.0\t3.0\n+ch3\t70\t80\t1.5\t1.5\n+ch3\t80\t90\t0.0\t0.0\n+ch3\t90\t100\t0.0\t0.0\n+ch3\t100\t110\t0.0\t0.0\n+ch3\t110\t120\t0.0\t0.0\n+ch3\t120\t130\t0.0\t0.0\n+ch3\t130\t140\t0.0\t0.0\n+ch3\t140\t150\t0.0\t0.0\n+ch3\t150\t160\t1.0\t1.0\n+ch3\t160\t170\t1.0\t1.0\n+ch3\t170\t180\t0.5\t0.5\n+ch3\t180\t190\t0.0\t0.0\n********\n*SNIP *\n********\n-ch3\t150\t160\t1.0\t1.0\n-ch3\t160\t170\t1.0\t1.0\n-ch3\t170\t180\t0.5\t0.5\n-ch3\t180\t190\t0.0\t0.0\n-ch3\t190\t200\t0.0\t0.0\n-ch3\t200\t210\t0.0\t0.0\n-ch3\t210\t220\t0.0\t0.0\n-ch3\t220\t230\t0.0\t0.0\n-ch3\t230\t240\t0.0\t0.0\n-ch3\t240\t250\t0.0\t0.0\n-ch3\t250\t260\t0.0\t0.0\n-ch3\t260\t270\t0.0\t0.0\n-ch3\t270\t280\t0.0\t0.0\n-ch3\t280\t290\t0.0\t0.0\n-ch3\t290\t300\t0.0\t0.0\n-ch3\t300\t310\t0.0\t0.0\n-ch3\t310\t320\t0.0\t0.0\n-ch3\t320\t330\t0.0\t0.0\n-ch3\t330\t340\t0.0\t0.0\n-ch3\t340\t350\t0.0\t0.0\n-ch3\t350\t360\t0.0\t0.0\n-ch3\t360\t370\t0.0\t0.0\n-ch3\t370\t380\t0.0\t0.0\n-ch3\t380\t390\t0.0\t0.0\n-ch3\t390\t400\t0.0\t0.0\n"], "status": "failure"}}, {"id": "edger/3.36.0+galaxy5-0", "has_data": true, "data": {"tool_id": "edger", "tool_version": "3.36.0+galaxy5", "test_index": 0, "time_seconds": 52.67897176742554, "inputs": {"input|counts": {"src": "hda", "id": "948b64f23b92f540"}, "input|fact|rep_factor_0|factorName": "Genotype", "input|fact|rep_factor_0|groupNames": "Mut,Mut,Mut,WT,WT,WT", "input|format": "matrix", "contrasts|rep_contrast_0|contrast": "Mut-WT", "contrasts|rep_contrast_1|contrast": "WT-Mut", "contrasts|contrastOpt": "manual", "adv|normalisationOption": "TMM"}, "job": {"model_class": "Job", "id": "2ba188dd08e677d1", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.36.0+galaxy5", "state": "ok", "exit_code": 0, "create_time": "2025-01-02T06:58:26.925566", "update_time": "2025-01-02T06:58:59.649317", "galaxy_version": "24.1", "external_id": "gxy-9vt2g", "handler": null, "job_runner_name": null, "command_line": "Rscript '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/edger/ae2aad0a6d50/edger/edger.R' -R '/galaxy/server/database/objects/9/1/e/dataset_91ee1b28-94d1-471f-9fcc-34c061c010fd.dat' -o '/galaxy/server/database/objects/9/1/e/dataset_91ee1b28-94d1-471f-9fcc-34c061c010fd_files' -m '/galaxy/server/database/objects/0/f/d/dataset_0fd542fc-5d20-4a27-8042-280954a16f32.dat' -i 'Genotype::Mut,Mut,Mut,WT,WT,WT' -C 'Mut-WT,WT-Mut' -l '0.0' -p '0.05' -d 'BH' -n 'TMM' -b && mkdir ./output_dir && cp '/galaxy/server/database/objects/9/1/e/dataset_91ee1b28-94d1-471f-9fcc-34c061c010fd_files'/*.tsv output_dir/", "user_email": "tests@fake.org", "command_version": "R version 4.1.2 (2021-11-01) -- \"Bird Hippie\", edgeR version 3.36.0, limma version 3.50.0, scales version 1.1.1, rjson version 0.2.20, getopt version 1.20.3", "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"lfc\": \"0.0\", \"lrtOption\": false, \"normalisationOption\": \"TMM\", \"pAdjust\": \"BH\", \"pVal\": \"0.05\", \"robOption\": true}", "out": "{\"normCounts\": false, \"rdaOption\": false, \"rscript\": false}", "f": "{\"filt\": {\"__current_case__\": 1, \"filt_select\": \"no\"}}", "contrasts": "{\"__current_case__\": 0, \"contrastOpt\": \"manual\", \"rep_contrast\": [{\"__index__\": 0, \"contrast\": \"Mut-WT\"}, {\"__index__\": 1, \"contrast\": \"WT-Mut\"}]}", "formula": null, "anno": "{\"__current_case__\": 1, \"annoOpt\": \"no\"}", "input": "{\"__current_case__\": 1, \"counts\": {\"values\": [{\"id\": 174, \"src\": \"hda\"}]}, \"fact\": {\"__current_case__\": 1, \"ffile\": \"no\", \"rep_factor\": [{\"__index__\": 0, \"factorName\": \"Genotype\", \"groupNames\": \"Mut,Mut,Mut,WT,WT,WT\"}]}, \"format\": \"matrix\"}"}, "inputs": {"input|counts": {"id": "948b64f23b92f540", "src": "hda", "uuid": "0fd542fc-5d20-4a27-8042-280954a16f32"}}, "outputs": {"outReport": {"id": "246bbf24761f3fdf", "src": "hda", "uuid": "91ee1b28-94d1-471f-9fcc-34c061c010fd"}, "__new_primary_file_outTables|edgeR_Mut-WT__": {"id": "769fa26b9dcf2036", "src": "hda", "uuid": "b9d9c7b8-193d-4a29-952e-82efa30fee3c"}, "__new_primary_file_outTables|edgeR_WT-Mut__": {"id": "70c182b97ebd328c", "src": "hda", "uuid": "fcefc78b-2f30-4ef4-83e8-3ed13a569631"}}, "copied_from_job_id": null, "output_collections": {"outTables": {"src": "hdca", "id": "f479df8956fff6f2"}}, "tool_stdout": "", "tool_stderr": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\nWarning message:\nIn plot.xy(xy, type, ...) : NAs introduced by coercion\nWarning message:\nIn plot.xy(xy, type, ...) : NAs introduced by coercion\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\nWarning message:\nIn plot.xy(xy, type, ...) : NAs introduced by coercion\nWarning message:\nIn plot.xy(xy, type, ...) : NAs introduced by coercion\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "4 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "4.0000000"}, {"title": "Job End Time", "value": "2025-01-02 06:58:43", "plugin": "core", "name": "end_epoch", "raw_value": "1735801123.0000000"}, {"title": "Job Start Time", "value": "2025-01-02 06:58:39", "plugin": "core", "name": "start_epoch", "raw_value": "1735801119.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "edger/3.36.0+galaxy5-1", "has_data": true, "data": {"tool_id": "edger", "tool_version": "3.36.0+galaxy5", "test_index": 1, "time_seconds": 35.704073667526245, "inputs": {"input|counts": {"src": "hda", "id": "fef993a7ccf659a3"}, "input|fact|rep_factor_0|factorName": "Genotype", "input|fact|rep_factor_0|groupNames": "MutA,MutA,MutA,MutB,MutB,MutB,WTA,WTA,WTA,WTB,WTB,WTB", "input|format": "matrix", "contrasts|rep_contrast_0|contrast": "(MutA-MutB)-(WTA-WTB)", "contrasts|contrastOpt": "manual", "adv|normalisationOption": "TMM"}, "job": {"model_class": "Job", "id": "babaa99004e96057", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.36.0+galaxy5", "state": "ok", "exit_code": 0, "create_time": "2025-01-02T06:59:18.966051", "update_time": "2025-01-02T06:59:35.367746", "galaxy_version": "24.1", "external_id": "gxy-bb4pn", "handler": null, "job_runner_name": null, "command_line": "Rscript '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/edger/ae2aad0a6d50/edger/edger.R' -R '/galaxy/server/database/objects/8/1/f/dataset_81f66761-8307-448c-b09a-5f3bb5c98e87.dat' -o '/galaxy/server/database/objects/8/1/f/dataset_81f66761-8307-448c-b09a-5f3bb5c98e87_files' -m '/galaxy/server/database/objects/0/c/b/dataset_0cb26e2f-e9a8-445e-8408-897b3197249a.dat' -i 'Genotype::MutA,MutA,MutA,MutB,MutB,MutB,WTA,WTA,WTA,WTB,WTB,WTB' -C '(MutA-MutB)-(WTA-WTB)' -l '0.0' -p '0.05' -d 'BH' -n 'TMM' -b && mkdir ./output_dir && cp '/galaxy/server/database/objects/8/1/f/dataset_81f66761-8307-448c-b09a-5f3bb5c98e87_files'/*.tsv output_dir/", "user_email": "tests@fake.org", "command_version": "R version 4.1.2 (2021-11-01) -- \"Bird Hippie\", edgeR version 3.36.0, limma version 3.50.0, scales version 1.1.1, rjson version 0.2.20, getopt version 1.20.3", "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"lfc\": \"0.0\", \"lrtOption\": false, \"normalisationOption\": \"TMM\", \"pAdjust\": \"BH\", \"pVal\": \"0.05\", \"robOption\": true}", "out": "{\"normCounts\": false, \"rdaOption\": false, \"rscript\": false}", "f": "{\"filt\": {\"__current_case__\": 1, \"filt_select\": \"no\"}}", "contrasts": "{\"__current_case__\": 0, \"contrastOpt\": \"manual\", \"rep_contrast\": [{\"__index__\": 0, \"contrast\": \"(MutA-MutB)-(WTA-WTB)\"}]}", "formula": null, "anno": "{\"__current_case__\": 1, \"annoOpt\": \"no\"}", "input": "{\"__current_case__\": 1, \"counts\": {\"values\": [{\"id\": 178, \"src\": \"hda\"}]}, \"fact\": {\"__current_case__\": 1, \"ffile\": \"no\", \"rep_factor\": [{\"__index__\": 0, \"factorName\": \"Genotype\", \"groupNames\": \"MutA,MutA,MutA,MutB,MutB,MutB,WTA,WTA,WTA,WTB,WTB,WTB\"}]}, \"format\": \"matrix\"}"}, "inputs": {"input|counts": {"id": "fef993a7ccf659a3", "src": "hda", "uuid": "0cb26e2f-e9a8-445e-8408-897b3197249a"}}, "outputs": {"outReport": {"id": "004fc63303625c27", "src": "hda", "uuid": "81f66761-8307-448c-b09a-5f3bb5c98e87"}, "__new_primary_file_outTables|edgeR_(MutA-MutB)-(WTA-WTB)__": {"id": "9e86c34dc85fc9c3", "src": "hda", "uuid": "cd3410cf-525a-4408-ab5f-e61663dfd622"}}, "copied_from_job_id": null, "output_collections": {"outTables": {"src": "hdca", "id": "b691c7254e38a402"}}, "tool_stdout": "", "tool_stderr": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\nWarning message:\nIn plot.xy(xy, type, ...) : NAs introduced by coercion\nWarning message:\nIn plot.xy(xy, type, ...) : NAs introduced by coercion\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\nWarning message:\nIn plot.xy(xy, type, ...) : NAs introduced by coercion\nWarning message:\nIn plot.xy(xy, type, ...) : NAs introduced by coercion\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "4 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "4.0000000"}, {"title": "Job End Time", "value": "2025-01-02 06:59:24", "plugin": "core", "name": "end_epoch", "raw_value": "1735801164.0000000"}, {"title": "Job Start Time", "value": "2025-01-02 06:59:20", "plugin": "core", "name": "start_epoch", 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{"model_class": "Job", "id": "6337d112ca25c320", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.36.0+galaxy5", "state": "ok", "exit_code": 0, "create_time": "2025-01-02T07:05:14.398737", "update_time": "2025-01-02T07:05:31.440963", "galaxy_version": "24.1", "external_id": "gxy-m7wln", "handler": null, "job_runner_name": null, "command_line": "Rscript '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/edger/ae2aad0a6d50/edger/edger.R' -R '/galaxy/server/database/objects/d/b/2/dataset_db2aa293-d517-4dcb-987c-3333cbaae3b5.dat' -o '/galaxy/server/database/objects/d/b/2/dataset_db2aa293-d517-4dcb-987c-3333cbaae3b5_files' -m '/galaxy/server/database/objects/8/f/a/dataset_8faf333b-52e1-4072-8f99-89fc08bf414b.dat' -i 'Genotype::Mut,Mut,Mut,WT,WT,WT' -C 'Mut-WT' -z '10' -s '3' -l '0.0' -p '0.05' -d 'BH' -n 'TMM' -b && mkdir ./output_dir && cp 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"fastq_paired_end_interlacer/1.2.0.1+galaxy0-2", "has_data": true, "data": {"tool_id": "fastq_paired_end_interlacer", "tool_version": "1.2.0.1+galaxy0", "test_index": 2, "time_seconds": 33.6605966091156, "inputs": {"reads|input1_file": {"src": "hda", "id": "5bfca613015f3d4d"}, "reads|input2_file": {"src": "hda", "id": "d8e297280a597dec"}, "reads|reads_selector": "paired"}, "job": {"model_class": "Job", "id": "294c47ae7ea33e75", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2025-01-02T06:41:16.567054", "update_time": "2025-01-02T06:41:29.978417", "galaxy_version": "24.1", "external_id": "gxy-b4k67", "handler": null, "job_runner_name": null, "command_line": "gx-fastq-paired-end-interlacer '/galaxy/server/database/objects/f/3/8/dataset_f383f466-ef65-4b66-9f71-3847e09085e3.dat' sanger.gz '/galaxy/server/database/objects/3/b/4/dataset_3b45ad3a-6967-45de-a3b1-514079d511ce.dat' sanger.gz '/galaxy/server/database/objects/a/c/5/dataset_ac5a2899-4050-49b7-9f7c-29375059338a.dat' '/galaxy/server/database/objects/9/6/6/dataset_96668be9-490a-43ac-886d-7efcfc60b975.dat'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"fastqsanger.gz\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "reads": "{\"__current_case__\": 0, \"input1_file\": {\"values\": [{\"id\": 90, \"src\": \"hda\"}]}, \"input2_file\": {\"values\": [{\"id\": 91, \"src\": \"hda\"}]}, \"reads_selector\": \"paired\"}"}, "inputs": {"reads|input1_file": {"id": "5bfca613015f3d4d", "src": "hda", "uuid": "f383f466-ef65-4b66-9f71-3847e09085e3"}, "reads|input2_file": {"id": "d8e297280a597dec", "src": "hda", "uuid": "3b45ad3a-6967-45de-a3b1-514079d511ce"}}, "outputs": {"outfile_pairs": {"id": "55263d1cb66db542", "src": "hda", "uuid": "ac5a2899-4050-49b7-9f7c-29375059338a"}, "outfile_singles": {"id": "0d0c9db3722fb76f", "src": "hda", "uuid": "96668be9-490a-43ac-886d-7efcfc60b975"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "There were 4 single reads.\nInterlaced 3 pairs of sequences.\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "There were 4 single reads.\nInterlaced 3 pairs of sequences.\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2025-01-02 06:41:18", "plugin": "core", "name": "end_epoch", "raw_value": "1735800078.0000000"}, {"title": "Job Start Time", "value": "2025-01-02 06:41:18", "plugin": "core", "name": "start_epoch", "raw_value": "1735800078.0000000"}, {"title": "Memory Allocated (MB)", "value": "32641", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "32641.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "fastq_paired_end_interlacer/1.2.0.1+galaxy0-3", "has_data": true, "data": {"tool_id": "fastq_paired_end_interlacer", "tool_version": "1.2.0.1+galaxy0", "test_index": 3, "time_seconds": 23.337684869766235, "inputs": {"reads|input1_file": {"src": "hda", "id": "b1c9669bde4c754f"}, "reads|input2_file": {"src": "hda", "id": "4efedd6493da126f"}, "reads|reads_selector": "paired"}, "job": {"model_class": "Job", "id": "f31ba40a134f0e3c", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0", "state": "error", "exit_code": null, "create_time": "2025-01-02T06:41:48.980207", "update_time": "2025-01-02T06:41:53.676215", "galaxy_version": "24.1", "external_id": "gxy-49lj5", "handler": null, "job_runner_name": null, "command_line": "gx-fastq-paired-end-interlacer '/galaxy/server/database/objects/1/1/0/dataset_110891a7-a7ef-4b89-91b1-909c075c5782.dat' sanger.bz2 '/galaxy/server/database/objects/0/8/8/dataset_08870eeb-ec0d-4772-8630-6c7f61fb4045.dat' sanger.bz2 '/galaxy/server/database/objects/e/4/7/dataset_e4708117-4478-4970-be04-d482d790800e.dat' '/galaxy/server/database/objects/4/e/b/dataset_4ebaf2aa-c616-42e3-861e-5c0ca1956377.dat'", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"fastqsanger.bz2\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "reads": "{\"__current_case__\": 0, \"input1_file\": {\"values\": [{\"id\": 94, \"src\": \"hda\"}]}, \"input2_file\": {\"values\": [{\"id\": 95, \"src\": \"hda\"}]}, \"reads_selector\": \"paired\"}"}, "inputs": {"reads|input1_file": {"id": "b1c9669bde4c754f", "src": "hda", "uuid": "110891a7-a7ef-4b89-91b1-909c075c5782"}, "reads|input2_file": {"id": "4efedd6493da126f", "src": "hda", "uuid": "08870eeb-ec0d-4772-8630-6c7f61fb4045"}}, "outputs": {"outfile_pairs": {"id": "6bd4476c315259fd", "src": "hda", "uuid": "e4708117-4478-4970-be04-d482d790800e"}, "outfile_singles": {"id": "cea9f5165af2a27f", "src": "hda", "uuid": "4ebaf2aa-c616-42e3-861e-5c0ca1956377"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "There were 4 single reads.\nInterlaced 3 pairs of sequences.\n", "tool_stderr": "", "job_stdout": null, "job_stderr": null, "stdout": "There were 4 single reads.\nInterlaced 3 pairs of sequences.\n", "stderr": "", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0, exit_code: None, stderr: .", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0, exit_code: None, stderr: .", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0, exit_code: None, stderr: ."], "status": "failure"}}, {"id": "fastq_paired_end_interlacer/1.2.0.1+galaxy0-4", "has_data": true, "data": {"tool_id": "fastq_paired_end_interlacer", "tool_version": "1.2.0.1+galaxy0", "test_index": 4, "time_seconds": 34.21478867530823, "inputs": {"reads|reads_coll": {"src": "hdca", "id": "c4520508ec6517a8"}, "reads|reads_selector": "paired_collection"}, "job": {"model_class": "Job", "id": "b20a6f5b6dfc46b8", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2025-01-02T06:42:13.882133", "update_time": "2025-01-02T06:42:27.649081", "galaxy_version": "24.1", "external_id": "gxy-v2d86", "handler": null, "job_runner_name": null, "command_line": "gx-fastq-paired-end-interlacer '/galaxy/server/database/objects/0/3/f/dataset_03f1354f-a0bd-47d7-bd54-042738012571.dat' sanger '/galaxy/server/database/objects/1/8/4/dataset_184da7e2-9b73-48d9-974e-b3de24d52431.dat' sanger '/galaxy/server/database/objects/a/a/5/dataset_aa59c7ce-f1cd-4cb2-9f70-0dba644a7f67.dat' '/galaxy/server/database/objects/0/6/1/dataset_061480fd-66bb-4382-b3e4-70490daf9c28.dat'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"fastqsanger\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "reads": "{\"__current_case__\": 1, \"reads_coll\": {\"values\": [{\"id\": 19, \"src\": \"hdca\"}]}, \"reads_selector\": \"paired_collection\"}"}, "inputs": {"reads|reads_coll2": {"id": "1cd18935d5504101", "src": "hda", "uuid": "184da7e2-9b73-48d9-974e-b3de24d52431"}, "reads|reads_coll1": {"id": "d0b4ada06108d401", "src": "hda", "uuid": "03f1354f-a0bd-47d7-bd54-042738012571"}}, "outputs": {"outfile_pairs_from_coll": {"id": "047c29d7543a0b6d", "src": "hda", "uuid": "aa59c7ce-f1cd-4cb2-9f70-0dba644a7f67"}, "outfile_singles_from_coll": {"id": "beff140338e13f0a", "src": "hda", "uuid": "061480fd-66bb-4382-b3e4-70490daf9c28"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "There were 0 single reads.\nInterlaced 5 pairs of sequences.\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "There were 0 single reads.\nInterlaced 5 pairs of sequences.\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2025-01-02 06:42:16", "plugin": "core", "name": "end_epoch", "raw_value": "1735800136.0000000"}, {"title": "Job Start Time", "value": "2025-01-02 06:42:16", "plugin": "core", "name": "start_epoch", "raw_value": "1735800136.0000000"}, {"title": "Memory Allocated (MB)", "value": "32641", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "32641.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "ivar_removereads/1.4.3+galaxy0-0", "has_data": true, "data": {"tool_id": "ivar_removereads", "tool_version": "1.4.3+galaxy0", "test_index": 0, "time_seconds": 54.99241900444031, "inputs": {"input_bam": {"src": "hda", "id": "ca93c50cd636868f"}, "variants_tsv": {"src": "hda", "id": "14c4464341db5a14"}, "input_bed": {"src": "hda", "id": "5097bafce94bd332"}, "amplicons|amplicon_info": {"src": "hda", "id": "8393b4d5e4ea6e92"}, "amplicons|computed": "no"}, "job": {"model_class": "Job", "id": "c1dd574506e972da", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.4.3+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2025-01-02T07:38:20.153640", "update_time": "2025-01-02T07:38:41.315745", "galaxy_version": "24.1", "external_id": "gxy-v6k9x", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/b/2/9/dataset_b2931419-d315-43e5-9629-6cd8e175fc8c.dat' binding_sites.bed && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/5dc33613c288/ivar_removereads/sanitize_bed.py' binding_sites.bed && ln -s '/galaxy/server/database/objects/6/d/7/dataset_6d7b9017-1a99-453f-9047-411637415474.dat' amplicon_info.tsv && ivar getmasked -i '/galaxy/server/database/objects/8/1/9/dataset_819d825a-6297-41d8-b3e5-f5506b13af76.dat' -b binding_sites.bed -f amplicon_info.tsv -p masked_primers && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/5dc33613c288/ivar_removereads/completemask.py' masked_primers.txt amplicon_info.tsv && ln -s '/galaxy/server/database/objects/6/9/7/dataset_6971efa7-6705-43af-b2bc-e8ea1708f4a2.dat' sorted.bam && ln -s '/galaxy/server/database/objects/_metadata_files/3/1/3/metadata_3135f632-46d9-410d-85a4-8226bdb79228.dat' sorted.bam.bai && ivar removereads -i sorted.bam -b binding_sites.bed -p removed_reads.bam -t masked_primers.txt", "user_email": "tests@fake.org", "command_version": "iVar version 1.4.3", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "amplicons": "{\"__current_case__\": 1, \"amplicon_info\": {\"values\": [{\"id\": 377, \"src\": \"hda\"}]}, \"computed\": \"no\"}"}, "inputs": {"input_bed": {"id": "5097bafce94bd332", "src": "hda", "uuid": "b2931419-d315-43e5-9629-6cd8e175fc8c"}, "amplicons|amplicon_info": {"id": "8393b4d5e4ea6e92", "src": "hda", "uuid": "6d7b9017-1a99-453f-9047-411637415474"}, "input_bam": {"id": "ca93c50cd636868f", "src": "hda", "uuid": "6971efa7-6705-43af-b2bc-e8ea1708f4a2"}, "variants_tsv": {"id": "14c4464341db5a14", "src": "hda", "uuid": "819d825a-6297-41d8-b3e5-f5506b13af76"}}, "outputs": {"output_bam": {"id": "60d72e367fc793b0", "src": "hda", "uuid": "29af3af7-4f66-4f2a-8efe-075bdc01678e"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "400_18_out_L**\n400_23_out_R\n400_32_out_L\n400_18_out_L**\t400_18_out_R**\t400_23_out_R\t400_23_out_L\t400_32_out_L\t400_32_out_R\n\nRemoving reads primed with any of:\n400_18_out_L**\t400_18_out_R**\t400_23_out_L\t400_23_out_R\t400_32_out_L\t400_32_out_R\nWriting to removed_reads.bam\nNumber of references: 1\nReference Name: PRV\nReference Length: 10807\nUsing Region: PRV\nSorted By Coordinate\nResults:\n2035 reads were removed.\n", "tool_stderr": "Found 67 primers in BED file\nPrimer pair for 400_1_out_R not found in BED file.\nPrimer pair for 400_34_out_L* not found in BED file.\nPrimer pair for 400_35_out_L not found in BED file.\nFound 67 primers in BED file\n", "job_stdout": "", "job_stderr": "", "stdout": "400_18_out_L**\n400_23_out_R\n400_32_out_L\n400_18_out_L**\t400_18_out_R**\t400_23_out_R\t400_23_out_L\t400_32_out_L\t400_32_out_R\n\nRemoving reads primed with any of:\n400_18_out_L**\t400_18_out_R**\t400_23_out_L\t400_23_out_R\t400_32_out_L\t400_32_out_R\nWriting to removed_reads.bam\nNumber of references: 1\nReference Name: PRV\nReference Length: 10807\nUsing Region: PRV\nSorted By Coordinate\nResults:\n2035 reads were removed.\n", "stderr": "Found 67 primers in BED file\nPrimer pair for 400_1_out_R not found in BED file.\nPrimer pair for 400_34_out_L* not found in BED file.\nPrimer pair for 400_35_out_L not found in BED file.\nFound 67 primers in BED file\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}, {"title": "Job End Time", "value": "2025-01-02 07:38:28", "plugin": "core", "name": "end_epoch", "raw_value": "1735803508.0000000"}, {"title": "Job Start Time", "value": "2025-01-02 07:38:26", "plugin": "core", "name": "start_epoch", "raw_value": "1735803506.0000000"}, {"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": "ivar_removereads/1.4.3+galaxy0-1", "has_data": true, "data": {"tool_id": "ivar_removereads", "tool_version": "1.4.3+galaxy0", "test_index": 1, "time_seconds": 41.23703360557556, "inputs": {"input_bam": {"src": "hda", "id": "19c5579ec08b407e"}, "variants_tsv": {"src": "hda", "id": "71090e9efed1bdcf"}, "input_bed": {"src": "hda", "id": "fb19e0153b8d71e2"}, "amplicons|computed": "yes"}, "job": {"model_class": "Job", "id": "8688d9f2b42bcb18", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.4.3+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2025-01-02T07:39:07.324765", "update_time": "2025-01-02T07:39:22.392431", "galaxy_version": "24.1", "external_id": "gxy-jt527", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/6/6/f/dataset_66f91b10-d1a4-4d62-9ee1-ca92e2beaae7.dat' binding_sites.bed && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/5dc33613c288/ivar_removereads/sanitize_bed.py' binding_sites.bed && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/5dc33613c288/ivar_removereads/write_amplicon_info_file.py' binding_sites.bed amplicon_info.tsv && ivar getmasked -i '/galaxy/server/database/objects/3/1/7/dataset_3178c707-4ac7-40bd-87de-afaa8d15fc45.dat' -b binding_sites.bed -f amplicon_info.tsv -p masked_primers && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/5dc33613c288/ivar_removereads/completemask.py' masked_primers.txt amplicon_info.tsv && ln -s '/galaxy/server/database/objects/e/7/c/dataset_e7c858e9-aec3-41c6-887d-c25fa04e2e87.dat' sorted.bam && ln -s '/galaxy/server/database/objects/_metadata_files/3/6/a/metadata_36a8d92f-4629-41de-a0be-5481e18b04c9.dat' sorted.bam.bai && ivar removereads -i sorted.bam -b binding_sites.bed -p removed_reads.bam -t masked_primers.txt", "user_email": "tests@fake.org", "command_version": "iVar version 1.4.3", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "amplicons": "{\"__current_case__\": 0, \"computed\": \"yes\"}"}, "inputs": {"variants_tsv": {"id": "71090e9efed1bdcf", "src": "hda", "uuid": "3178c707-4ac7-40bd-87de-afaa8d15fc45"}, "input_bed": {"id": "fb19e0153b8d71e2", "src": "hda", "uuid": "66f91b10-d1a4-4d62-9ee1-ca92e2beaae7"}, "input_bam": {"id": "19c5579ec08b407e", "src": "hda", "uuid": "e7c858e9-aec3-41c6-887d-c25fa04e2e87"}}, "outputs": {"output_bam": {"id": "9602d928fa3d3c41", "src": "hda", "uuid": "d2cc803e-a0ce-4c9d-a289-f6060b8b5f20"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "400_18_out_L**\n400_23_out_R\n400_32_out_L\n400_18_out_L**\t400_18_out_R**\t400_23_out_R\t400_23_out_L\t400_32_out_L\t400_32_out_R\n\nRemoving reads primed with any of:\n400_18_out_L**\t400_18_out_R**\t400_23_out_L\t400_23_out_R\t400_32_out_L\t400_32_out_R\nWriting to removed_reads.bam\nNumber of references: 1\nReference Name: PRV\nReference Length: 10807\nUsing Region: PRV\nSorted By Coordinate\nResults:\n2035 reads were removed.\n", "tool_stderr": "Found 67 primers in BED file\nPrimer pair is empty.\nPrimer pair is empty.\nPrimer pair is empty.\nFound 67 primers in BED file\n", "job_stdout": "", "job_stderr": "", "stdout": "400_18_out_L**\n400_23_out_R\n400_32_out_L\n400_18_out_L**\t400_18_out_R**\t400_23_out_R\t400_23_out_L\t400_32_out_L\t400_32_out_R\n\nRemoving reads primed with any of:\n400_18_out_L**\t400_18_out_R**\t400_23_out_L\t400_23_out_R\t400_32_out_L\t400_32_out_R\nWriting to removed_reads.bam\nNumber of references: 1\nReference Name: PRV\nReference Length: 10807\nUsing Region: PRV\nSorted By Coordinate\nResults:\n2035 reads were removed.\n", "stderr": "Found 67 primers in BED file\nPrimer pair is empty.\nPrimer pair is empty.\nPrimer pair is empty.\nFound 67 primers in BED file\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2025-01-02 07:39:10", "plugin": "core", "name": "end_epoch", "raw_value": "1735803550.0000000"}, {"title": "Job Start Time", "value": "2025-01-02 07:39:09", "plugin": "core", "name": "start_epoch", "raw_value": "1735803549.0000000"}, {"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": "jbrowse/1.16.11+galaxy1-0", "has_data": true, "data": {"tool_id": "jbrowse", "tool_version": "1.16.11+galaxy1", "test_index": 0, "time_seconds": 52.17535638809204, "inputs": {"reference_genome|genome": {"src": "hda", "id": "c067909e5f63b4bf"}, "reference_genome|genome_type_select": "history", "standalone": "data", "gencode": "1", "uglyTestingHack": "enabled"}, "job": {"model_class": "Job", "id": "1e96e1d58f839ce0", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2025-01-02T06:42:47.856525", "update_time": "2025-01-02T06:43:21.190962", "galaxy_version": "24.1", "external_id": "gxy-2hlgj", "handler": null, "job_runner_name": null, "command_line": "mkdir -p /galaxy/server/database/objects/a/a/4/dataset_aa49e30c-e46b-4fa6-8b15-e63346766bd7_files && cp /galaxy/server/database/jobs_directory/000/58/configs/tmpbh04di79 /galaxy/server/database/objects/a/a/4/dataset_aa49e30c-e46b-4fa6-8b15-e63346766bd7_files/galaxy.xml && export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'data' --outdir /galaxy/server/database/objects/a/a/4/dataset_aa49e30c-e46b-4fa6-8b15-e63346766bd7_files /galaxy/server/database/jobs_directory/000/58/configs/tmpbh04di79 && cp /galaxy/server/database/jobs_directory/000/58/configs/tmpr6q18nlj /galaxy/server/database/objects/a/a/4/dataset_aa49e30c-e46b-4fa6-8b15-e63346766bd7.dat; cp /galaxy/server/database/jobs_directory/000/58/configs/tmpbh04di79 /galaxy/server/database/objects/a/a/4/dataset_aa49e30c-e46b-4fa6-8b15-e63346766bd7.dat", "user_email": "tests@fake.org", "command_version": "jbrowse.py 0.8.0", "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "uglyTestingHack": "\"enabled\"", "plugins": "{\"BlastView\": true, \"ComboTrackSelector\": false, \"GCContent\": false}", "jbgen": "{\"aboutDescription\": \"\", \"defaultLocation\": \"\", \"hideGenomeOptions\": false, \"shareLink\": true, \"show_menu\": true, \"show_nav\": true, \"show_overview\": true, \"show_tracklist\": true, \"trackPadding\": \"20\"}", "track_groups": "[]", "action": "{\"__current_case__\": 0, \"action_select\": \"create\"}", "gencode": "\"1\"", "standalone": "\"data\"", "reference_genome": "{\"__current_case__\": 1, \"genome\": {\"values\": [{\"id\": 102, \"src\": \"hda\"}]}, \"genome_type_select\": \"history\"}"}, "inputs": {"reference_genome|genome": {"id": "c067909e5f63b4bf", "src": "hda", "uuid": "46488c7f-76c9-48d7-ac82-e17059697e58"}}, "outputs": {"output": {"id": "127b7060f892c121", "src": "hda", "uuid": "aa49e30c-e46b-4fa6-8b15-e63346766bd7"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "WARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "WARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2025-01-02 06:43:04", "plugin": "core", "name": "end_epoch", "raw_value": "1735800184.0000000"}, {"title": "Job Start Time", "value": "2025-01-02 06:43:04", "plugin": "core", "name": "start_epoch", "raw_value": "1735800184.0000000"}, {"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": "jbrowse/1.16.11+galaxy1-0", "has_data": true, "data": {"tool_id": "jbrowse", "tool_version": "1.16.11+galaxy1", "test_index": 0, "time_seconds": 25.339773893356323, "inputs": {"reference_genome|genome": {"src": "hda", "id": "27c7c932589d02a8"}, "reference_genome|genome_type_select": "history", "standalone": "data", "gencode": "1", "uglyTestingHack": "enabled"}, "job": {"model_class": "Job", "id": "fc56de97fc753237", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1", "state": "error", "exit_code": null, "create_time": "2025-01-02T06:49:17.448574", "update_time": "2025-01-02T06:49:23.287877", "galaxy_version": "24.1", "external_id": "gxy-6wbkl", "handler": null, "job_runner_name": null, "command_line": "mkdir -p /galaxy/server/database/objects/1/e/4/dataset_1e47a883-be24-495d-9a82-6d19c876453c_files && cp /galaxy/server/database/jobs_directory/000/89/configs/tmpdaik8q5d /galaxy/server/database/objects/1/e/4/dataset_1e47a883-be24-495d-9a82-6d19c876453c_files/galaxy.xml && export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'data' --outdir /galaxy/server/database/objects/1/e/4/dataset_1e47a883-be24-495d-9a82-6d19c876453c_files /galaxy/server/database/jobs_directory/000/89/configs/tmpdaik8q5d && cp /galaxy/server/database/jobs_directory/000/89/configs/tmplxq90css /galaxy/server/database/objects/1/e/4/dataset_1e47a883-be24-495d-9a82-6d19c876453c.dat; cp /galaxy/server/database/jobs_directory/000/89/configs/tmpdaik8q5d /galaxy/server/database/objects/1/e/4/dataset_1e47a883-be24-495d-9a82-6d19c876453c.dat", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "uglyTestingHack": "\"enabled\"", "plugins": "{\"BlastView\": true, \"ComboTrackSelector\": false, \"GCContent\": false}", "jbgen": "{\"aboutDescription\": \"\", \"defaultLocation\": \"\", \"hideGenomeOptions\": false, \"shareLink\": true, \"show_menu\": true, \"show_nav\": true, \"show_overview\": true, \"show_tracklist\": true, \"trackPadding\": \"20\"}", "track_groups": "[]", "action": "{\"__current_case__\": 0, \"action_select\": \"create\"}", "gencode": "\"1\"", "standalone": "\"data\"", "reference_genome": "{\"__current_case__\": 1, \"genome\": {\"values\": [{\"id\": 133, \"src\": \"hda\"}]}, \"genome_type_select\": \"history\"}"}, "inputs": {"reference_genome|genome": {"id": "27c7c932589d02a8", "src": "hda", "uuid": "4a0d2ccb-6139-457a-b293-0f27bbdfdebe"}}, "outputs": {"output": {"id": "040f59f1ef394007", "src": "hda", "uuid": "1e47a883-be24-495d-9a82-6d19c876453c"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "WARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "job_stdout": null, "job_stderr": null, "stdout": "", "stderr": "WARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1, exit_code: None, stderr: WARNING: No feature names found for indexing, only reference sequence names will be indexed.\n.", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1, exit_code: None, stderr: WARNING: No feature names found for indexing, only reference sequence names will be indexed.\n."], "status": "failure"}}, {"id": "jbrowse/1.16.11+galaxy1-1", "has_data": true, "data": {"tool_id": "jbrowse", "tool_version": "1.16.11+galaxy1", "test_index": 1, "time_seconds": 25.296777963638306, "inputs": {"reference_genome|genome": {"src": "hda", "id": "59e7f7bb0c0090a3"}, "reference_genome|genome_type_select": "history", "standalone": "data", "gencode": "11", "uglyTestingHack": "enabled"}, "job": {"model_class": "Job", "id": "24611f45b2c6f4c6", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1", "state": "error", "exit_code": null, "create_time": "2025-01-02T06:43:40.627763", "update_time": "2025-01-02T06:43:46.594588", "galaxy_version": "24.1", "external_id": "gxy-vgq6z", "handler": null, "job_runner_name": null, "command_line": "mkdir -p /galaxy/server/database/objects/d/1/b/dataset_d1bb7e69-77ec-4295-853d-fa8a94c59224_files && cp /galaxy/server/database/jobs_directory/000/60/configs/tmprwvpsk2e /galaxy/server/database/objects/d/1/b/dataset_d1bb7e69-77ec-4295-853d-fa8a94c59224_files/galaxy.xml && export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'data' --outdir /galaxy/server/database/objects/d/1/b/dataset_d1bb7e69-77ec-4295-853d-fa8a94c59224_files /galaxy/server/database/jobs_directory/000/60/configs/tmprwvpsk2e && cp /galaxy/server/database/jobs_directory/000/60/configs/tmpghdqxa_n /galaxy/server/database/objects/d/1/b/dataset_d1bb7e69-77ec-4295-853d-fa8a94c59224.dat; cp /galaxy/server/database/jobs_directory/000/60/configs/tmprwvpsk2e /galaxy/server/database/objects/d/1/b/dataset_d1bb7e69-77ec-4295-853d-fa8a94c59224.dat", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "uglyTestingHack": "\"enabled\"", "plugins": "{\"BlastView\": true, \"ComboTrackSelector\": false, \"GCContent\": false}", "jbgen": "{\"aboutDescription\": \"\", \"defaultLocation\": \"\", \"hideGenomeOptions\": false, \"shareLink\": true, \"show_menu\": true, \"show_nav\": true, \"show_overview\": true, \"show_tracklist\": true, \"trackPadding\": \"20\"}", "track_groups": "[]", "action": "{\"__current_case__\": 0, \"action_select\": \"create\"}", "gencode": "\"11\"", "standalone": "\"data\"", "reference_genome": "{\"__current_case__\": 1, \"genome\": {\"values\": [{\"id\": 104, \"src\": \"hda\"}]}, \"genome_type_select\": \"history\"}"}, "inputs": {"reference_genome|genome": {"id": "59e7f7bb0c0090a3", "src": "hda", "uuid": "f078e412-c1c9-4650-be7b-e5e1e28f0ac9"}}, "outputs": {"output": {"id": "86e3335ea84ed5fd", "src": "hda", "uuid": "d1bb7e69-77ec-4295-853d-fa8a94c59224"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "WARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "job_stdout": null, "job_stderr": null, "stdout": "", "stderr": "WARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1, exit_code: None, stderr: WARNING: No feature names found for indexing, only reference sequence names will be indexed.\n.", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1, exit_code: None, stderr: WARNING: No feature names found for indexing, only reference sequence names will be indexed.\n."], "status": "failure"}}, {"id": "jbrowse/1.16.11+galaxy1-1", "has_data": true, "data": {"tool_id": "jbrowse", "tool_version": "1.16.11+galaxy1", "test_index": 1, "time_seconds": 32.90899181365967, "inputs": {"reference_genome|genome": {"src": "hda", "id": "dbe845cfdafc6fb2"}, "reference_genome|genome_type_select": "history", "standalone": "data", "gencode": "11", "uglyTestingHack": "enabled"}, "job": {"model_class": "Job", "id": "d8e297280a597dec", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2025-01-02T06:49:41.864367", "update_time": "2025-01-02T06:49:55.927591", "galaxy_version": "24.1", "external_id": "gxy-hv7b2", "handler": null, "job_runner_name": null, "command_line": "mkdir -p /galaxy/server/database/objects/8/d/3/dataset_8d32d820-00e7-4369-beb5-797c3856297b_files && cp /galaxy/server/database/jobs_directory/000/91/configs/tmpewcp4474 /galaxy/server/database/objects/8/d/3/dataset_8d32d820-00e7-4369-beb5-797c3856297b_files/galaxy.xml && export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'data' --outdir /galaxy/server/database/objects/8/d/3/dataset_8d32d820-00e7-4369-beb5-797c3856297b_files /galaxy/server/database/jobs_directory/000/91/configs/tmpewcp4474 && cp /galaxy/server/database/jobs_directory/000/91/configs/tmpgm3rwid1 /galaxy/server/database/objects/8/d/3/dataset_8d32d820-00e7-4369-beb5-797c3856297b.dat; cp /galaxy/server/database/jobs_directory/000/91/configs/tmpewcp4474 /galaxy/server/database/objects/8/d/3/dataset_8d32d820-00e7-4369-beb5-797c3856297b.dat", "user_email": "tests@fake.org", "command_version": "jbrowse.py 0.8.0", "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "uglyTestingHack": "\"enabled\"", "plugins": "{\"BlastView\": true, \"ComboTrackSelector\": false, \"GCContent\": false}", "jbgen": "{\"aboutDescription\": \"\", \"defaultLocation\": \"\", \"hideGenomeOptions\": false, \"shareLink\": true, \"show_menu\": true, \"show_nav\": true, \"show_overview\": true, \"show_tracklist\": true, \"trackPadding\": \"20\"}", "track_groups": "[]", "action": "{\"__current_case__\": 0, \"action_select\": \"create\"}", "gencode": "\"11\"", "standalone": "\"data\"", "reference_genome": "{\"__current_case__\": 1, \"genome\": {\"values\": [{\"id\": 135, \"src\": \"hda\"}]}, \"genome_type_select\": \"history\"}"}, "inputs": {"reference_genome|genome": {"id": "dbe845cfdafc6fb2", "src": "hda", "uuid": "ef3fad6e-a1ff-4e8e-a0ad-942721414b8e"}}, "outputs": {"output": {"id": "1aa6b9331aa13111", "src": "hda", "uuid": "8d32d820-00e7-4369-beb5-797c3856297b"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "WARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "WARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2025-01-02 06:49:44", "plugin": "core", "name": "end_epoch", "raw_value": "1735800584.0000000"}, {"title": "Job Start Time", "value": "2025-01-02 06:49:44", "plugin": "core", "name": "start_epoch", "raw_value": "1735800584.0000000"}, {"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": "jbrowse/1.16.11+galaxy1-2", "has_data": true, "data": {"tool_id": "jbrowse", "tool_version": "1.16.11+galaxy1", "test_index": 2, "time_seconds": 38.17183542251587, "inputs": {"reference_genome|genome": {"src": "hda", "id": "e25c262d60016a05"}, "reference_genome|genome_type_select": "history", "standalone": "data", "gencode": "11", "track_groups_0|category": "Default", "track_groups_0|data_tracks_0|data_format|annotation": [{"src": "hda", "id": "7e902eabb9a394c6"}, {"src": "hda", "id": "abb7871dbf6325f9"}], "track_groups_0|data_tracks_0|data_format|data_format_select": "gene_calls", "uglyTestingHack": "enabled"}, "job": {"model_class": "Job", "id": "2862c9a90cb5fc49", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2025-01-02T06:44:10.802610", "update_time": "2025-01-02T06:44:24.679039", "galaxy_version": "24.1", "external_id": "gxy-8fc7j", "handler": null, "job_runner_name": null, "command_line": "mkdir -p /galaxy/server/database/objects/b/1/0/dataset_b1094681-49e6-4312-99a5-41a1006c8e74_files && cp /galaxy/server/database/jobs_directory/000/64/configs/tmpnn4821lt /galaxy/server/database/objects/b/1/0/dataset_b1094681-49e6-4312-99a5-41a1006c8e74_files/galaxy.xml && export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'data' --outdir /galaxy/server/database/objects/b/1/0/dataset_b1094681-49e6-4312-99a5-41a1006c8e74_files /galaxy/server/database/jobs_directory/000/64/configs/tmpnn4821lt && cp /galaxy/server/database/jobs_directory/000/64/configs/tmpdtr7zt_4 /galaxy/server/database/objects/b/1/0/dataset_b1094681-49e6-4312-99a5-41a1006c8e74.dat; cp /galaxy/server/database/jobs_directory/000/64/configs/tmpnn4821lt /galaxy/server/database/objects/b/1/0/dataset_b1094681-49e6-4312-99a5-41a1006c8e74.dat", "user_email": "tests@fake.org", "command_version": "jbrowse.py 0.8.0", "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "uglyTestingHack": "\"enabled\"", "plugins": "{\"BlastView\": true, \"ComboTrackSelector\": false, \"GCContent\": false}", "jbgen": "{\"aboutDescription\": \"\", \"defaultLocation\": \"\", \"hideGenomeOptions\": false, \"shareLink\": true, \"show_menu\": true, \"show_nav\": true, \"show_overview\": true, \"show_tracklist\": true, \"trackPadding\": \"20\"}", "track_groups": "[{\"__index__\": 0, \"category\": \"Default\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"__current_case__\": 2, \"annotation\": {\"values\": [{\"id\": 107, \"src\": \"hda\"}, {\"id\": 108, \"src\": \"hda\"}]}, \"data_format_select\": \"gene_calls\", \"index\": false, \"jb_custom_config\": {\"option\": []}, \"jbcolor_scale\": {\"color_score\": {\"__current_case__\": 0, \"color\": {\"__current_case__\": 0, \"color_select\": \"automatic\"}, \"color_score_select\": \"none\"}}, \"jbmenu\": {\"track_menu\": []}, \"jbstyle\": {\"max_height\": \"600\", \"style_classname\": \"feature\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"style_label\": \"product,name,id\"}, \"match_part\": {\"__current_case__\": 1, \"match_part_select\": false}, \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"track_config\": {\"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": null}, \"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\"}, \"track_visibility\": \"default_off\"}}]}]", "action": "{\"__current_case__\": 0, \"action_select\": \"create\"}", "gencode": "\"11\"", "standalone": "\"data\"", "reference_genome": "{\"__current_case__\": 1, \"genome\": {\"values\": [{\"id\": 106, \"src\": \"hda\"}]}, \"genome_type_select\": \"history\"}"}, "inputs": {"reference_genome|genome": {"id": "e25c262d60016a05", "src": "hda", "uuid": "7f87b84b-e4ad-4616-be18-c6cb2eb2f49c"}, "track_groups_0|data_tracks_0|data_format|annotation1": {"id": "7e902eabb9a394c6", "src": "hda", "uuid": "db5471a6-477f-47c6-9c85-fa8f548b82ff"}, "track_groups_0|data_tracks_0|data_format|annotation": {"id": "7e902eabb9a394c6", "src": "hda", "uuid": "db5471a6-477f-47c6-9c85-fa8f548b82ff"}, "track_groups_0|data_tracks_0|data_format|annotation2": {"id": "abb7871dbf6325f9", "src": "hda", "uuid": "8f680134-046a-4766-9f02-f637116d8906"}}, "outputs": {"output": {"id": "ff8c65f5f2aaf055", "src": "hda", "uuid": "b1094681-49e6-4312-99a5-41a1006c8e74"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "INFO:jbrowse:Processing Default / test-3.bed\nINFO:jbrowse:Processing Default / test-6.bed\nWARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "INFO:jbrowse:Processing Default / test-3.bed\nINFO:jbrowse:Processing Default / test-6.bed\nWARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2025-01-02 06:44:13", "plugin": "core", "name": "end_epoch", "raw_value": "1735800253.0000000"}, {"title": "Job Start Time", "value": "2025-01-02 06:44:12", "plugin": "core", "name": "start_epoch", "raw_value": "1735800252.0000000"}, {"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": "jbrowse/1.16.11+galaxy1-2", "has_data": true, "data": {"tool_id": "jbrowse", "tool_version": "1.16.11+galaxy1", "test_index": 2, "time_seconds": 39.00832796096802, "inputs": {"reference_genome|genome": {"src": "hda", "id": "fad5685674975133"}, "reference_genome|genome_type_select": "history", "standalone": "data", "gencode": "11", "track_groups_0|category": "Default", "track_groups_0|data_tracks_0|data_format|annotation": [{"src": "hda", "id": "9dfb9ab628f00936"}, {"src": "hda", "id": "fdca54d393a7a551"}], "track_groups_0|data_tracks_0|data_format|data_format_select": "gene_calls", "uglyTestingHack": "enabled"}, "job": {"model_class": "Job", "id": "4efedd6493da126f", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2025-01-02T06:50:20.761881", "update_time": "2025-01-02T06:50:35.040970", "galaxy_version": "24.1", "external_id": "gxy-g4wtx", "handler": null, "job_runner_name": null, "command_line": "mkdir -p /galaxy/server/database/objects/5/b/8/dataset_5b88e608-6fd5-469d-9ee6-5482bbae456b_files && cp /galaxy/server/database/jobs_directory/000/95/configs/tmpbdewavdf /galaxy/server/database/objects/5/b/8/dataset_5b88e608-6fd5-469d-9ee6-5482bbae456b_files/galaxy.xml && export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'data' --outdir /galaxy/server/database/objects/5/b/8/dataset_5b88e608-6fd5-469d-9ee6-5482bbae456b_files /galaxy/server/database/jobs_directory/000/95/configs/tmpbdewavdf && cp /galaxy/server/database/jobs_directory/000/95/configs/tmpraih_o3a /galaxy/server/database/objects/5/b/8/dataset_5b88e608-6fd5-469d-9ee6-5482bbae456b.dat; cp /galaxy/server/database/jobs_directory/000/95/configs/tmpbdewavdf /galaxy/server/database/objects/5/b/8/dataset_5b88e608-6fd5-469d-9ee6-5482bbae456b.dat", "user_email": "tests@fake.org", "command_version": "jbrowse.py 0.8.0", "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "uglyTestingHack": "\"enabled\"", "plugins": "{\"BlastView\": true, \"ComboTrackSelector\": false, \"GCContent\": false}", "jbgen": "{\"aboutDescription\": \"\", \"defaultLocation\": \"\", \"hideGenomeOptions\": false, \"shareLink\": true, \"show_menu\": true, \"show_nav\": true, \"show_overview\": true, \"show_tracklist\": true, \"trackPadding\": \"20\"}", "track_groups": "[{\"__index__\": 0, \"category\": \"Default\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"__current_case__\": 2, \"annotation\": {\"values\": [{\"id\": 138, \"src\": \"hda\"}, {\"id\": 139, \"src\": \"hda\"}]}, \"data_format_select\": \"gene_calls\", \"index\": false, \"jb_custom_config\": {\"option\": []}, \"jbcolor_scale\": {\"color_score\": {\"__current_case__\": 0, \"color\": {\"__current_case__\": 0, \"color_select\": \"automatic\"}, \"color_score_select\": \"none\"}}, \"jbmenu\": {\"track_menu\": []}, \"jbstyle\": {\"max_height\": \"600\", \"style_classname\": \"feature\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"style_label\": \"product,name,id\"}, \"match_part\": {\"__current_case__\": 1, \"match_part_select\": false}, \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"track_config\": {\"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": null}, \"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\"}, \"track_visibility\": \"default_off\"}}]}]", "action": "{\"__current_case__\": 0, \"action_select\": \"create\"}", "gencode": "\"11\"", "standalone": "\"data\"", "reference_genome": "{\"__current_case__\": 1, \"genome\": {\"values\": [{\"id\": 137, \"src\": \"hda\"}]}, \"genome_type_select\": \"history\"}"}, "inputs": {"reference_genome|genome": {"id": "fad5685674975133", "src": "hda", "uuid": "5fd41435-81eb-453e-8a01-af481e632b51"}, "track_groups_0|data_tracks_0|data_format|annotation": {"id": "9dfb9ab628f00936", "src": "hda", "uuid": "c3285de7-7736-468c-8d4f-5646b45a0b52"}, "track_groups_0|data_tracks_0|data_format|annotation1": {"id": "9dfb9ab628f00936", "src": "hda", "uuid": "c3285de7-7736-468c-8d4f-5646b45a0b52"}, "track_groups_0|data_tracks_0|data_format|annotation2": {"id": "fdca54d393a7a551", "src": "hda", "uuid": "82f37fe7-2dc7-468a-915d-1e9dcf979d9f"}}, "outputs": {"output": {"id": "43b711b8ef0c5e46", "src": "hda", "uuid": "5b88e608-6fd5-469d-9ee6-5482bbae456b"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "INFO:jbrowse:Processing Default / test-3.bed\nINFO:jbrowse:Processing Default / test-6.bed\nWARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "INFO:jbrowse:Processing Default / test-3.bed\nINFO:jbrowse:Processing Default / test-6.bed\nWARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2025-01-02 06:50:24", "plugin": "core", "name": "end_epoch", "raw_value": "1735800624.0000000"}, {"title": "Job Start Time", "value": "2025-01-02 06:50:23", "plugin": "core", "name": "start_epoch", "raw_value": "1735800623.0000000"}, {"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": "jbrowse/1.16.11+galaxy1-3", "has_data": true, "data": {"tool_id": "jbrowse", "tool_version": "1.16.11+galaxy1", "test_index": 3, "time_seconds": 22.498799562454224, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "jbrowse/1.16.11+galaxy1-3", "has_data": true, "data": {"tool_id": "jbrowse", "tool_version": "1.16.11+galaxy1", "test_index": 3, "time_seconds": 63.26656413078308, "inputs": {"reference_genome|genome": {"src": "hda", "id": "a5284223a1f64a54"}, "reference_genome|genome_type_select": "history", "standalone": "data", "gencode": "11", "track_groups_0|category": "Auto Coloured", "track_groups_0|data_tracks_0|data_format|annotation": [{"src": "hda", "id": "ee896aa35de40137"}, {"src": "hda", "id": "1f3136644b950c4e"}, {"src": "hda", "id": "f30b2a399ca810d7"}, {"src": "hda", "id": "9c7ffa381ed047d5"}], "track_groups_0|data_tracks_0|data_format|match_part|match_part_select": false, "track_groups_0|data_tracks_0|data_format|jbcolor_scale|color_score|color_score_select": "none", "track_groups_0|data_tracks_0|data_format|data_format_select": "gene_calls", "track_groups_1|category": "Ignore Scale", "track_groups_1|data_tracks_0|data_format|annotation": {"src": "hda", "id": "63595e06f91e4c77"}, "track_groups_1|data_tracks_0|data_format|match_part|match_part_select": false, "track_groups_1|data_tracks_0|data_format|jbcolor_scale|color_score|color|style_color": "#ff00ff", "track_groups_1|data_tracks_0|data_format|jbcolor_scale|color_score|color|color_select": "manual", "track_groups_1|data_tracks_0|data_format|jbcolor_scale|color_score|color_score_select": "none", "track_groups_1|data_tracks_0|data_format|data_format_select": "gene_calls", "track_groups_2|category": "Scaled Colour", "track_groups_2|data_tracks_0|data_format|annotation": {"src": "hda", "id": "63595e06f91e4c77"}, "track_groups_2|data_tracks_0|data_format|match_part|match_part_select": false, "track_groups_2|data_tracks_0|data_format|jbcolor_scale|color_score|score_scaling": "linear", "track_groups_2|data_tracks_0|data_format|jbcolor_scale|color_score|score_scales|scale_select": "automatic", "track_groups_2|data_tracks_0|data_format|jbcolor_scale|color_score|color_scheme|color|color_select": "automatic", "track_groups_2|data_tracks_0|data_format|jbcolor_scale|color_score|color_scheme|score_scheme": "opacity", "track_groups_2|data_tracks_0|data_format|jbcolor_scale|color_score|color_score_select": "score", "track_groups_2|data_tracks_0|data_format|data_format_select": "gene_calls", "track_groups_2|data_tracks_1|data_format|annotation": {"src": "hda", "id": "63595e06f91e4c77"}, "track_groups_2|data_tracks_1|data_format|match_part|match_part_select": false, "track_groups_2|data_tracks_1|data_format|jbcolor_scale|color_score|score_scaling": "linear", "track_groups_2|data_tracks_1|data_format|jbcolor_scale|color_score|score_scales|scale_select": "automatic", "track_groups_2|data_tracks_1|data_format|jbcolor_scale|color_score|color_scheme|color|style_color": "#0000ff", "track_groups_2|data_tracks_1|data_format|jbcolor_scale|color_score|color_scheme|color|color_select": "manual", "track_groups_2|data_tracks_1|data_format|jbcolor_scale|color_score|color_scheme|score_scheme": "opacity", "track_groups_2|data_tracks_1|data_format|jbcolor_scale|color_score|color_score_select": "score", "track_groups_2|data_tracks_1|data_format|data_format_select": "gene_calls", "track_groups_2|data_tracks_2|data_format|annotation": {"src": "hda", "id": "63595e06f91e4c77"}, "track_groups_2|data_tracks_2|data_format|match_part|match_part_select": false, "track_groups_2|data_tracks_2|data_format|jbcolor_scale|color_score|score_scaling": "linear", "track_groups_2|data_tracks_2|data_format|jbcolor_scale|color_score|score_scales|minimum": "0", "track_groups_2|data_tracks_2|data_format|jbcolor_scale|color_score|score_scales|maximum": "1000", "track_groups_2|data_tracks_2|data_format|jbcolor_scale|color_score|score_scales|scale_select": "manual", "track_groups_2|data_tracks_2|data_format|jbcolor_scale|color_score|color_scheme|color|color_select": "automatic", "track_groups_2|data_tracks_2|data_format|jbcolor_scale|color_score|color_scheme|score_scheme": "opacity", "track_groups_2|data_tracks_2|data_format|jbcolor_scale|color_score|color_score_select": "score", "track_groups_2|data_tracks_2|data_format|data_format_select": "gene_calls", "track_groups_2|data_tracks_3|data_format|annotation": {"src": "hda", "id": "63595e06f91e4c77"}, "track_groups_2|data_tracks_3|data_format|match_part|match_part_select": false, "track_groups_2|data_tracks_3|data_format|jbcolor_scale|color_score|score_scaling": "linear", "track_groups_2|data_tracks_3|data_format|jbcolor_scale|color_score|score_scales|minimum": "0", "track_groups_2|data_tracks_3|data_format|jbcolor_scale|color_score|score_scales|maximum": "1000", "track_groups_2|data_tracks_3|data_format|jbcolor_scale|color_score|score_scales|scale_select": "manual", "track_groups_2|data_tracks_3|data_format|jbcolor_scale|color_score|color_scheme|color|style_color": "#ff0000", "track_groups_2|data_tracks_3|data_format|jbcolor_scale|color_score|color_scheme|color|color_select": "manual", "track_groups_2|data_tracks_3|data_format|jbcolor_scale|color_score|color_scheme|score_scheme": "opacity", "track_groups_2|data_tracks_3|data_format|jbcolor_scale|color_score|color_score_select": "score", "track_groups_2|data_tracks_3|data_format|data_format_select": "gene_calls", "track_groups_3|category": "Realistic", "track_groups_3|data_tracks_0|data_format|annotation": {"src": "hda", "id": "45b5f63126351244"}, "track_groups_3|data_tracks_0|data_format|match_part|match_part_select": false, "track_groups_3|data_tracks_0|data_format|jbcolor_scale|color_score|color_score_select": "none", "track_groups_3|data_tracks_0|data_format|data_format_select": "gene_calls", "track_groups_3|data_tracks_1|data_format|annotation": {"src": "hda", "id": "f2efca6f659a474b"}, "track_groups_3|data_tracks_1|data_format|match_part|name": "cDNA_match", "track_groups_3|data_tracks_1|data_format|match_part|match_part_select": true, "track_groups_3|data_tracks_1|data_format|jbcolor_scale|color_score|color_score_select": "none", "track_groups_3|data_tracks_1|data_format|data_format_select": "gene_calls", "uglyTestingHack": "enabled"}, "job": {"model_class": "Job", "id": "59e7f7bb0c0090a3", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2025-01-02T06:51:22.414931", "update_time": "2025-01-02T06:51:38.398318", "galaxy_version": "24.1", "external_id": "gxy-8wkj7", "handler": null, "job_runner_name": null, "command_line": "mkdir -p /galaxy/server/database/objects/1/0/2/dataset_1022f186-52e1-467f-b777-792d897dba96_files && cp /galaxy/server/database/jobs_directory/000/104/configs/tmp1c41wso4 /galaxy/server/database/objects/1/0/2/dataset_1022f186-52e1-467f-b777-792d897dba96_files/galaxy.xml && export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'data' --outdir /galaxy/server/database/objects/1/0/2/dataset_1022f186-52e1-467f-b777-792d897dba96_files /galaxy/server/database/jobs_directory/000/104/configs/tmp1c41wso4 && cp /galaxy/server/database/jobs_directory/000/104/configs/tmpy65s35t3 /galaxy/server/database/objects/1/0/2/dataset_1022f186-52e1-467f-b777-792d897dba96.dat; cp /galaxy/server/database/jobs_directory/000/104/configs/tmp1c41wso4 /galaxy/server/database/objects/1/0/2/dataset_1022f186-52e1-467f-b777-792d897dba96.dat", "user_email": "tests@fake.org", "command_version": "jbrowse.py 0.8.0", "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "uglyTestingHack": "\"enabled\"", "plugins": "{\"BlastView\": true, \"ComboTrackSelector\": false, \"GCContent\": false}", "jbgen": "{\"aboutDescription\": \"\", \"defaultLocation\": \"\", \"hideGenomeOptions\": false, \"shareLink\": true, \"show_menu\": true, \"show_nav\": true, \"show_overview\": true, \"show_tracklist\": true, \"trackPadding\": \"20\"}", "track_groups": "[{\"__index__\": 0, \"category\": \"Auto Coloured\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"__current_case__\": 2, \"annotation\": {\"values\": [{\"id\": 142, \"src\": \"hda\"}, {\"id\": 143, \"src\": \"hda\"}, {\"id\": 144, \"src\": \"hda\"}, {\"id\": 145, \"src\": \"hda\"}]}, \"data_format_select\": \"gene_calls\", \"index\": false, \"jb_custom_config\": {\"option\": []}, \"jbcolor_scale\": {\"color_score\": {\"__current_case__\": 0, \"color\": {\"__current_case__\": 0, \"color_select\": \"automatic\"}, \"color_score_select\": \"none\"}}, \"jbmenu\": {\"track_menu\": []}, \"jbstyle\": {\"max_height\": \"600\", \"style_classname\": \"feature\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"style_label\": \"product,name,id\"}, \"match_part\": {\"__current_case__\": 1, \"match_part_select\": false}, \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"track_config\": {\"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": null}, \"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\"}, \"track_visibility\": \"default_off\"}}]}, {\"__index__\": 1, \"category\": \"Ignore Scale\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"__current_case__\": 2, \"annotation\": {\"values\": [{\"id\": 146, \"src\": \"hda\"}]}, \"data_format_select\": \"gene_calls\", \"index\": false, \"jb_custom_config\": {\"option\": []}, \"jbcolor_scale\": {\"color_score\": {\"__current_case__\": 0, \"color\": {\"__current_case__\": 1, \"color_select\": \"manual\", \"style_color\": \"#ff00ff\"}, \"color_score_select\": \"none\"}}, \"jbmenu\": {\"track_menu\": []}, \"jbstyle\": {\"max_height\": \"600\", \"style_classname\": \"feature\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"style_label\": \"product,name,id\"}, \"match_part\": {\"__current_case__\": 1, \"match_part_select\": false}, \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"track_config\": {\"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": null}, \"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\"}, \"track_visibility\": \"default_off\"}}]}, {\"__index__\": 2, \"category\": \"Scaled Colour\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"__current_case__\": 2, \"annotation\": {\"values\": [{\"id\": 146, \"src\": \"hda\"}]}, \"data_format_select\": \"gene_calls\", \"index\": false, \"jb_custom_config\": {\"option\": []}, \"jbcolor_scale\": {\"color_score\": {\"__current_case__\": 1, \"color_scheme\": {\"__current_case__\": 0, \"color\": {\"__current_case__\": 0, \"color_select\": \"automatic\"}, \"score_scheme\": \"opacity\"}, \"color_score_select\": \"score\", \"score_scales\": {\"__current_case__\": 0, \"scale_select\": \"automatic\"}, \"score_scaling\": \"linear\"}}, \"jbmenu\": {\"track_menu\": []}, \"jbstyle\": {\"max_height\": \"600\", \"style_classname\": \"feature\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"style_label\": \"product,name,id\"}, \"match_part\": {\"__current_case__\": 1, \"match_part_select\": false}, \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"track_config\": {\"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": null}, \"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\"}, \"track_visibility\": \"default_off\"}}, {\"__index__\": 1, \"data_format\": {\"__current_case__\": 2, \"annotation\": {\"values\": [{\"id\": 146, \"src\": \"hda\"}]}, \"data_format_select\": \"gene_calls\", \"index\": false, \"jb_custom_config\": {\"option\": []}, \"jbcolor_scale\": {\"color_score\": {\"__current_case__\": 1, \"color_scheme\": {\"__current_case__\": 0, \"color\": {\"__current_case__\": 1, \"color_select\": \"manual\", \"style_color\": \"#0000ff\"}, \"score_scheme\": \"opacity\"}, \"color_score_select\": \"score\", \"score_scales\": {\"__current_case__\": 0, \"scale_select\": \"automatic\"}, \"score_scaling\": \"linear\"}}, \"jbmenu\": {\"track_menu\": []}, \"jbstyle\": {\"max_height\": \"600\", \"style_classname\": \"feature\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"style_label\": \"product,name,id\"}, \"match_part\": {\"__current_case__\": 1, \"match_part_select\": false}, \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"track_config\": {\"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": null}, \"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\"}, \"track_visibility\": \"default_off\"}}, {\"__index__\": 2, \"data_format\": {\"__current_case__\": 2, \"annotation\": {\"values\": [{\"id\": 146, \"src\": \"hda\"}]}, \"data_format_select\": \"gene_calls\", \"index\": false, \"jb_custom_config\": {\"option\": []}, \"jbcolor_scale\": {\"color_score\": {\"__current_case__\": 1, \"color_scheme\": {\"__current_case__\": 0, \"color\": {\"__current_case__\": 0, \"color_select\": \"automatic\"}, \"score_scheme\": \"opacity\"}, \"color_score_select\": \"score\", \"score_scales\": {\"__current_case__\": 1, \"maximum\": \"1000\", \"minimum\": \"0\", \"scale_select\": \"manual\"}, \"score_scaling\": \"linear\"}}, \"jbmenu\": {\"track_menu\": []}, \"jbstyle\": {\"max_height\": \"600\", \"style_classname\": \"feature\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"style_label\": \"product,name,id\"}, \"match_part\": {\"__current_case__\": 1, \"match_part_select\": false}, \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"track_config\": {\"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": null}, \"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\"}, \"track_visibility\": \"default_off\"}}, {\"__index__\": 3, \"data_format\": {\"__current_case__\": 2, \"annotation\": {\"values\": [{\"id\": 146, \"src\": \"hda\"}]}, \"data_format_select\": \"gene_calls\", \"index\": false, \"jb_custom_config\": {\"option\": []}, \"jbcolor_scale\": {\"color_score\": {\"__current_case__\": 1, \"color_scheme\": {\"__current_case__\": 0, \"color\": {\"__current_case__\": 1, \"color_select\": \"manual\", \"style_color\": \"#ff0000\"}, \"score_scheme\": \"opacity\"}, \"color_score_select\": \"score\", \"score_scales\": {\"__current_case__\": 1, \"maximum\": \"1000\", \"minimum\": \"0\", \"scale_select\": \"manual\"}, \"score_scaling\": \"linear\"}}, \"jbmenu\": {\"track_menu\": []}, \"jbstyle\": {\"max_height\": \"600\", \"style_classname\": \"feature\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"style_label\": \"product,name,id\"}, \"match_part\": {\"__current_case__\": 1, \"match_part_select\": false}, \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"track_config\": {\"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": null}, \"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\"}, \"track_visibility\": \"default_off\"}}]}, {\"__index__\": 3, \"category\": \"Realistic\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"__current_case__\": 2, \"annotation\": {\"values\": [{\"id\": 147, \"src\": \"hda\"}]}, \"data_format_select\": \"gene_calls\", \"index\": false, \"jb_custom_config\": {\"option\": []}, \"jbcolor_scale\": {\"color_score\": {\"__current_case__\": 0, \"color\": {\"__current_case__\": 0, \"color_select\": \"automatic\"}, \"color_score_select\": \"none\"}}, \"jbmenu\": {\"track_menu\": []}, \"jbstyle\": {\"max_height\": \"600\", \"style_classname\": \"feature\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"style_label\": \"product,name,id\"}, \"match_part\": {\"__current_case__\": 1, \"match_part_select\": false}, \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"track_config\": {\"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": null}, \"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\"}, \"track_visibility\": \"default_off\"}}, {\"__index__\": 1, \"data_format\": {\"__current_case__\": 2, \"annotation\": {\"values\": [{\"id\": 148, \"src\": \"hda\"}]}, \"data_format_select\": \"gene_calls\", \"index\": false, \"jb_custom_config\": {\"option\": []}, \"jbcolor_scale\": {\"color_score\": {\"__current_case__\": 0, \"color\": {\"__current_case__\": 0, \"color_select\": \"automatic\"}, \"color_score_select\": \"none\"}}, \"jbmenu\": {\"track_menu\": []}, \"jbstyle\": {\"max_height\": \"600\", \"style_classname\": \"feature\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"style_label\": \"product,name,id\"}, \"match_part\": {\"__current_case__\": 0, \"match_part_select\": true, \"name\": \"cDNA_match\"}, \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"track_config\": {\"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": null}, \"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\"}, \"track_visibility\": \"default_off\"}}]}]", "action": "{\"__current_case__\": 0, \"action_select\": \"create\"}", "gencode": "\"11\"", "standalone": "\"data\"", "reference_genome": "{\"__current_case__\": 1, \"genome\": {\"values\": [{\"id\": 141, \"src\": \"hda\"}]}, \"genome_type_select\": \"history\"}"}, "inputs": {"reference_genome|genome": {"id": "a5284223a1f64a54", "src": "hda", "uuid": "bcdacb6f-1f32-4ce8-bf69-ba298a7d6362"}, "track_groups_0|data_tracks_0|data_format|annotation": {"id": "ee896aa35de40137", "src": "hda", "uuid": "5f42a473-05dd-4c59-a0ac-0ce27b1c22dc"}, "track_groups_0|data_tracks_0|data_format|annotation1": {"id": "ee896aa35de40137", "src": "hda", "uuid": "5f42a473-05dd-4c59-a0ac-0ce27b1c22dc"}, "track_groups_0|data_tracks_0|data_format|annotation2": {"id": "1f3136644b950c4e", "src": "hda", "uuid": "c557994f-061d-4b32-bb74-fd0a8f92db91"}, "track_groups_0|data_tracks_0|data_format|annotation3": {"id": "f30b2a399ca810d7", "src": "hda", "uuid": "634bd562-c6d6-4f11-9c91-382f878c963f"}, "track_groups_0|data_tracks_0|data_format|annotation4": {"id": "9c7ffa381ed047d5", "src": "hda", "uuid": "d22bcd8d-e39e-45a2-adc3-6bd68cc09c23"}, "track_groups_1|data_tracks_0|data_format|annotation": {"id": "63595e06f91e4c77", "src": "hda", "uuid": "c23b3f47-802c-4a98-bd83-88a4c2dc0f33"}, "track_groups_1|data_tracks_0|data_format|annotation1": {"id": "63595e06f91e4c77", "src": "hda", "uuid": "c23b3f47-802c-4a98-bd83-88a4c2dc0f33"}, "track_groups_2|data_tracks_0|data_format|annotation": {"id": "63595e06f91e4c77", "src": "hda", "uuid": "c23b3f47-802c-4a98-bd83-88a4c2dc0f33"}, "track_groups_2|data_tracks_0|data_format|annotation1": {"id": "63595e06f91e4c77", "src": "hda", "uuid": "c23b3f47-802c-4a98-bd83-88a4c2dc0f33"}, "track_groups_2|data_tracks_1|data_format|annotation": {"id": "63595e06f91e4c77", "src": "hda", "uuid": "c23b3f47-802c-4a98-bd83-88a4c2dc0f33"}, "track_groups_2|data_tracks_1|data_format|annotation1": {"id": "63595e06f91e4c77", "src": "hda", "uuid": "c23b3f47-802c-4a98-bd83-88a4c2dc0f33"}, "track_groups_2|data_tracks_2|data_format|annotation": {"id": "63595e06f91e4c77", "src": "hda", "uuid": "c23b3f47-802c-4a98-bd83-88a4c2dc0f33"}, "track_groups_2|data_tracks_2|data_format|annotation1": {"id": "63595e06f91e4c77", "src": "hda", "uuid": "c23b3f47-802c-4a98-bd83-88a4c2dc0f33"}, "track_groups_2|data_tracks_3|data_format|annotation": {"id": "63595e06f91e4c77", "src": "hda", "uuid": "c23b3f47-802c-4a98-bd83-88a4c2dc0f33"}, "track_groups_2|data_tracks_3|data_format|annotation1": {"id": "63595e06f91e4c77", "src": "hda", "uuid": "c23b3f47-802c-4a98-bd83-88a4c2dc0f33"}, "track_groups_3|data_tracks_0|data_format|annotation": {"id": "45b5f63126351244", "src": "hda", "uuid": "24ef5b7a-f9d2-4866-a2f7-1fbee7933f54"}, "track_groups_3|data_tracks_0|data_format|annotation1": {"id": "45b5f63126351244", "src": "hda", "uuid": "24ef5b7a-f9d2-4866-a2f7-1fbee7933f54"}, "track_groups_3|data_tracks_1|data_format|annotation": {"id": "f2efca6f659a474b", "src": "hda", "uuid": "3735e6f1-5a20-4876-88ef-e12e55d6b2be"}, "track_groups_3|data_tracks_1|data_format|annotation1": {"id": "f2efca6f659a474b", "src": "hda", "uuid": "3735e6f1-5a20-4876-88ef-e12e55d6b2be"}}, "outputs": {"output": {"id": "d42319a28dee733d", "src": "hda", "uuid": "1022f186-52e1-467f-b777-792d897dba96"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "INFO:jbrowse:Processing Auto Coloured / A.gff\nINFO:jbrowse:Processing Auto Coloured / B.gff\nINFO:jbrowse:Processing Auto Coloured / C.gff\nINFO:jbrowse:Processing Auto Coloured / D.gff\nINFO:jbrowse:Processing Ignore Scale / 1.gff\nINFO:jbrowse:Processing Scaled Colour / 1.gff\nINFO:jbrowse:Processing Scaled Colour / 1.gff\nINFO:jbrowse:Processing Scaled Colour / 1.gff\nINFO:jbrowse:Processing Scaled Colour / 1.gff\nINFO:jbrowse:Processing Realistic / interpro.gff\nINFO:jbrowse:Processing Realistic / 2.gff\nWARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "INFO:jbrowse:Processing Auto Coloured / A.gff\nINFO:jbrowse:Processing Auto Coloured / B.gff\nINFO:jbrowse:Processing Auto Coloured / C.gff\nINFO:jbrowse:Processing Auto Coloured / D.gff\nINFO:jbrowse:Processing Ignore Scale / 1.gff\nINFO:jbrowse:Processing Scaled Colour / 1.gff\nINFO:jbrowse:Processing Scaled Colour / 1.gff\nINFO:jbrowse:Processing Scaled Colour / 1.gff\nINFO:jbrowse:Processing Scaled Colour / 1.gff\nINFO:jbrowse:Processing Realistic / interpro.gff\nINFO:jbrowse:Processing Realistic / 2.gff\nWARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "3 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "3.0000000"}, {"title": "Job End Time", "value": "2025-01-02 06:51:27", "plugin": "core", "name": "end_epoch", "raw_value": "1735800687.0000000"}, {"title": "Job Start Time", "value": "2025-01-02 06:51:24", "plugin": "core", "name": "start_epoch", "raw_value": "1735800684.0000000"}, {"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": "jbrowse/1.16.11+galaxy1-4", "has_data": true, "data": {"tool_id": "jbrowse", "tool_version": "1.16.11+galaxy1", "test_index": 4, "time_seconds": 41.58414006233215, "inputs": {"reference_genome|genome": {"src": "hda", "id": "1e77095bebc3b3c7"}, "reference_genome|genome_type_select": "history", "standalone": "data", "gencode": "11", "track_groups_0|category": "With menu or index", "track_groups_0|data_tracks_0|data_format|annotation": {"src": "hda", "id": "fc72c3209ee3fe87"}, "track_groups_0|data_tracks_0|data_format|match_part|match_part_select": false, "track_groups_0|data_tracks_0|data_format|jbcolor_scale|color_score|color_score_select": "none", "track_groups_0|data_tracks_0|data_format|jbmenu|track_menu_0|menu_action": "iframeDialog", "track_groups_0|data_tracks_0|data_format|jbmenu|track_menu_0|menu_label": "Some menu item", "track_groups_0|data_tracks_0|data_format|jbmenu|track_menu_0|menu_title": "Frame title", "track_groups_0|data_tracks_0|data_format|jbmenu|track_menu_0|menu_url": "https://example.com/#!/?id={name}&q={type}&z=\"{end}\"", "track_groups_0|data_tracks_0|data_format|jbmenu|track_menu_0|menu_icon": "dijitIconNewTask", "track_groups_0|data_tracks_0|data_format|jbmenu|track_menu_1|menu_action": "newWindow", "track_groups_0|data_tracks_0|data_format|jbmenu|track_menu_1|menu_label": "Another menu item", "track_groups_0|data_tracks_0|data_format|jbmenu|track_menu_1|menu_title": "Frame title 2", "track_groups_0|data_tracks_0|data_format|jbmenu|track_menu_1|menu_url": "https://example.com/#!/?id={name}&q={type}&z=\"{end}\"", "track_groups_0|data_tracks_0|data_format|data_format_select": "gene_calls", "track_groups_0|data_tracks_1|data_format|annotation": {"src": "hda", "id": "fc72c3209ee3fe87"}, "track_groups_0|data_tracks_1|data_format|match_part|match_part_select": false, "track_groups_0|data_tracks_1|data_format|index": true, "track_groups_0|data_tracks_1|data_format|jbcolor_scale|color_score|color_score_select": "none", "track_groups_0|data_tracks_1|data_format|data_format_select": "gene_calls", "uglyTestingHack": "enabled"}, "job": {"model_class": "Job", "id": "3765a9dbf6de90a8", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2025-01-02T06:45:14.369374", "update_time": "2025-01-02T06:45:28.831540", "galaxy_version": "24.1", "external_id": "gxy-2bfzn", "handler": null, "job_runner_name": null, "command_line": "mkdir -p /galaxy/server/database/objects/4/a/a/dataset_4aa45a0f-5133-429a-95d5-2c700fa5c620_files && cp /galaxy/server/database/jobs_directory/000/75/configs/tmpb68nutcn /galaxy/server/database/objects/4/a/a/dataset_4aa45a0f-5133-429a-95d5-2c700fa5c620_files/galaxy.xml && export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'data' --outdir /galaxy/server/database/objects/4/a/a/dataset_4aa45a0f-5133-429a-95d5-2c700fa5c620_files /galaxy/server/database/jobs_directory/000/75/configs/tmpb68nutcn && cp /galaxy/server/database/jobs_directory/000/75/configs/tmpuhjjel89 /galaxy/server/database/objects/4/a/a/dataset_4aa45a0f-5133-429a-95d5-2c700fa5c620.dat; cp /galaxy/server/database/jobs_directory/000/75/configs/tmpb68nutcn /galaxy/server/database/objects/4/a/a/dataset_4aa45a0f-5133-429a-95d5-2c700fa5c620.dat", "user_email": "tests@fake.org", "command_version": "jbrowse.py 0.8.0", "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "uglyTestingHack": "\"enabled\"", "plugins": "{\"BlastView\": true, \"ComboTrackSelector\": false, \"GCContent\": false}", "jbgen": "{\"aboutDescription\": \"\", \"defaultLocation\": \"\", \"hideGenomeOptions\": false, \"shareLink\": true, \"show_menu\": true, \"show_nav\": true, \"show_overview\": true, \"show_tracklist\": true, \"trackPadding\": \"20\"}", "track_groups": "[{\"__index__\": 0, \"category\": \"With menu or index\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"__current_case__\": 2, \"annotation\": {\"values\": [{\"id\": 119, \"src\": \"hda\"}]}, \"data_format_select\": \"gene_calls\", \"index\": false, \"jb_custom_config\": {\"option\": []}, \"jbcolor_scale\": {\"color_score\": {\"__current_case__\": 0, \"color\": {\"__current_case__\": 0, \"color_select\": \"automatic\"}, \"color_score_select\": \"none\"}}, \"jbmenu\": {\"track_menu\": [{\"__index__\": 0, \"menu_action\": \"iframeDialog\", \"menu_icon\": \"dijitIconNewTask\", \"menu_label\": \"Some menu item\", \"menu_title\": \"Frame title\", \"menu_url\": \"https://example.com/#!/?id={name}&q={type}&z=\\\"{end}\\\"\"}, {\"__index__\": 1, \"menu_action\": \"newWindow\", \"menu_icon\": \"dijitIconBookmark\", \"menu_label\": \"Another menu item\", \"menu_title\": \"Frame title 2\", \"menu_url\": \"https://example.com/#!/?id={name}&q={type}&z=\\\"{end}\\\"\"}]}, \"jbstyle\": {\"max_height\": \"600\", \"style_classname\": \"feature\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"style_label\": \"product,name,id\"}, \"match_part\": {\"__current_case__\": 1, \"match_part_select\": false}, \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"track_config\": {\"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": null}, \"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\"}, \"track_visibility\": \"default_off\"}}, {\"__index__\": 1, \"data_format\": {\"__current_case__\": 2, \"annotation\": {\"values\": [{\"id\": 119, \"src\": \"hda\"}]}, \"data_format_select\": \"gene_calls\", \"index\": true, \"jb_custom_config\": {\"option\": []}, \"jbcolor_scale\": {\"color_score\": {\"__current_case__\": 0, \"color\": {\"__current_case__\": 0, \"color_select\": \"automatic\"}, \"color_score_select\": \"none\"}}, \"jbmenu\": {\"track_menu\": []}, \"jbstyle\": {\"max_height\": \"600\", \"style_classname\": \"feature\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"style_label\": \"product,name,id\"}, \"match_part\": {\"__current_case__\": 1, \"match_part_select\": false}, \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"track_config\": {\"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": null}, \"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\"}, \"track_visibility\": \"default_off\"}}]}]", "action": "{\"__current_case__\": 0, \"action_select\": \"create\"}", "gencode": "\"11\"", "standalone": "\"data\"", "reference_genome": "{\"__current_case__\": 1, \"genome\": {\"values\": [{\"id\": 118, \"src\": \"hda\"}]}, \"genome_type_select\": \"history\"}"}, "inputs": {"reference_genome|genome": {"id": "1e77095bebc3b3c7", "src": "hda", "uuid": "aacd3260-fee3-4940-afc1-5fe2a7b3ca66"}, "track_groups_0|data_tracks_0|data_format|annotation": {"id": "fc72c3209ee3fe87", "src": "hda", "uuid": "d03723df-3fc8-44b8-a228-9e857032fecf"}, "track_groups_0|data_tracks_0|data_format|annotation1": {"id": "fc72c3209ee3fe87", "src": "hda", "uuid": "d03723df-3fc8-44b8-a228-9e857032fecf"}, "track_groups_0|data_tracks_1|data_format|annotation": {"id": "fc72c3209ee3fe87", "src": "hda", "uuid": "d03723df-3fc8-44b8-a228-9e857032fecf"}, "track_groups_0|data_tracks_1|data_format|annotation1": {"id": "fc72c3209ee3fe87", "src": "hda", "uuid": "d03723df-3fc8-44b8-a228-9e857032fecf"}}, "outputs": {"output": {"id": "ced3cbd85f71829a", "src": "hda", "uuid": "4aa45a0f-5133-429a-95d5-2c700fa5c620"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "INFO:jbrowse:Processing With menu or index / 1.gff\nINFO:jbrowse:Processing With menu or index / 1.gff\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "INFO:jbrowse:Processing With menu or index / 1.gff\nINFO:jbrowse:Processing With menu or index / 1.gff\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}, {"title": "Job End Time", "value": "2025-01-02 06:45:18", "plugin": "core", "name": "end_epoch", "raw_value": "1735800318.0000000"}, {"title": "Job Start Time", "value": "2025-01-02 06:45:16", "plugin": "core", "name": "start_epoch", "raw_value": "1735800316.0000000"}, {"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": "jbrowse/1.16.11+galaxy1-4", "has_data": true, "data": {"tool_id": "jbrowse", "tool_version": "1.16.11+galaxy1", "test_index": 4, "time_seconds": 26.343416690826416, "inputs": {"reference_genome|genome": {"src": "hda", "id": "bfa7fc5290d195fc"}, "reference_genome|genome_type_select": "history", "standalone": "data", "gencode": "11", "track_groups_0|category": "With menu or index", "track_groups_0|data_tracks_0|data_format|annotation": {"src": "hda", "id": "54d4553682370391"}, "track_groups_0|data_tracks_0|data_format|match_part|match_part_select": false, "track_groups_0|data_tracks_0|data_format|jbcolor_scale|color_score|color_score_select": "none", "track_groups_0|data_tracks_0|data_format|jbmenu|track_menu_0|menu_action": "iframeDialog", "track_groups_0|data_tracks_0|data_format|jbmenu|track_menu_0|menu_label": "Some menu item", "track_groups_0|data_tracks_0|data_format|jbmenu|track_menu_0|menu_title": "Frame title", "track_groups_0|data_tracks_0|data_format|jbmenu|track_menu_0|menu_url": "https://example.com/#!/?id={name}&q={type}&z=\"{end}\"", "track_groups_0|data_tracks_0|data_format|jbmenu|track_menu_0|menu_icon": "dijitIconNewTask", "track_groups_0|data_tracks_0|data_format|jbmenu|track_menu_1|menu_action": "newWindow", "track_groups_0|data_tracks_0|data_format|jbmenu|track_menu_1|menu_label": "Another menu item", "track_groups_0|data_tracks_0|data_format|jbmenu|track_menu_1|menu_title": "Frame title 2", "track_groups_0|data_tracks_0|data_format|jbmenu|track_menu_1|menu_url": "https://example.com/#!/?id={name}&q={type}&z=\"{end}\"", "track_groups_0|data_tracks_0|data_format|data_format_select": "gene_calls", "track_groups_0|data_tracks_1|data_format|annotation": {"src": "hda", "id": "54d4553682370391"}, "track_groups_0|data_tracks_1|data_format|match_part|match_part_select": false, "track_groups_0|data_tracks_1|data_format|index": true, "track_groups_0|data_tracks_1|data_format|jbcolor_scale|color_score|color_score_select": "none", "track_groups_0|data_tracks_1|data_format|data_format_select": "gene_calls", "uglyTestingHack": "enabled"}, "job": {"model_class": "Job", "id": "7e902eabb9a394c6", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1", "state": "error", "exit_code": null, "create_time": "2025-01-02T06:51:57.581066", "update_time": "2025-01-02T06:52:04.717107", "galaxy_version": "24.1", "external_id": "gxy-j9hk4", "handler": null, "job_runner_name": null, "command_line": "mkdir -p /galaxy/server/database/objects/6/a/d/dataset_6ad5f93f-7e06-49fb-9ce4-e26ca54cfa65_files && cp /galaxy/server/database/jobs_directory/000/107/configs/tmp3dvoatg_ /galaxy/server/database/objects/6/a/d/dataset_6ad5f93f-7e06-49fb-9ce4-e26ca54cfa65_files/galaxy.xml && export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'data' --outdir /galaxy/server/database/objects/6/a/d/dataset_6ad5f93f-7e06-49fb-9ce4-e26ca54cfa65_files /galaxy/server/database/jobs_directory/000/107/configs/tmp3dvoatg_ && cp /galaxy/server/database/jobs_directory/000/107/configs/tmpjyjqcxe6 /galaxy/server/database/objects/6/a/d/dataset_6ad5f93f-7e06-49fb-9ce4-e26ca54cfa65.dat; cp /galaxy/server/database/jobs_directory/000/107/configs/tmp3dvoatg_ /galaxy/server/database/objects/6/a/d/dataset_6ad5f93f-7e06-49fb-9ce4-e26ca54cfa65.dat", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "uglyTestingHack": "\"enabled\"", "plugins": "{\"BlastView\": true, \"ComboTrackSelector\": false, \"GCContent\": false}", "jbgen": "{\"aboutDescription\": \"\", \"defaultLocation\": \"\", \"hideGenomeOptions\": false, \"shareLink\": true, \"show_menu\": true, \"show_nav\": true, \"show_overview\": true, \"show_tracklist\": true, \"trackPadding\": \"20\"}", "track_groups": "[{\"__index__\": 0, \"category\": \"With menu or index\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"__current_case__\": 2, \"annotation\": {\"values\": [{\"id\": 151, \"src\": \"hda\"}]}, \"data_format_select\": \"gene_calls\", \"index\": false, \"jb_custom_config\": {\"option\": []}, \"jbcolor_scale\": {\"color_score\": {\"__current_case__\": 0, \"color\": {\"__current_case__\": 0, \"color_select\": \"automatic\"}, \"color_score_select\": \"none\"}}, \"jbmenu\": {\"track_menu\": [{\"__index__\": 0, \"menu_action\": \"iframeDialog\", \"menu_icon\": \"dijitIconNewTask\", \"menu_label\": \"Some menu item\", \"menu_title\": \"Frame title\", \"menu_url\": \"https://example.com/#!/?id={name}&q={type}&z=\\\"{end}\\\"\"}, {\"__index__\": 1, \"menu_action\": \"newWindow\", \"menu_icon\": \"dijitIconBookmark\", \"menu_label\": \"Another menu item\", \"menu_title\": \"Frame title 2\", \"menu_url\": \"https://example.com/#!/?id={name}&q={type}&z=\\\"{end}\\\"\"}]}, \"jbstyle\": {\"max_height\": \"600\", \"style_classname\": \"feature\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"style_label\": \"product,name,id\"}, \"match_part\": {\"__current_case__\": 1, \"match_part_select\": false}, \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"track_config\": {\"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": null}, \"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\"}, \"track_visibility\": \"default_off\"}}, {\"__index__\": 1, \"data_format\": {\"__current_case__\": 2, \"annotation\": {\"values\": [{\"id\": 151, \"src\": \"hda\"}]}, \"data_format_select\": \"gene_calls\", \"index\": true, \"jb_custom_config\": {\"option\": []}, \"jbcolor_scale\": {\"color_score\": {\"__current_case__\": 0, \"color\": {\"__current_case__\": 0, \"color_select\": \"automatic\"}, \"color_score_select\": \"none\"}}, \"jbmenu\": {\"track_menu\": []}, \"jbstyle\": {\"max_height\": \"600\", \"style_classname\": \"feature\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"style_label\": \"product,name,id\"}, \"match_part\": {\"__current_case__\": 1, \"match_part_select\": false}, \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"track_config\": {\"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": null}, \"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\"}, \"track_visibility\": \"default_off\"}}]}]", "action": "{\"__current_case__\": 0, \"action_select\": \"create\"}", "gencode": "\"11\"", "standalone": "\"data\"", "reference_genome": "{\"__current_case__\": 1, \"genome\": {\"values\": [{\"id\": 150, \"src\": \"hda\"}]}, \"genome_type_select\": \"history\"}"}, "inputs": {"reference_genome|genome": {"id": "bfa7fc5290d195fc", "src": "hda", "uuid": "0feac21b-17ad-418a-8aaa-b9dfbda2c9f5"}, "track_groups_0|data_tracks_0|data_format|annotation": {"id": "54d4553682370391", "src": "hda", "uuid": "6bd31719-2a2c-491b-a446-d403a8d406eb"}, "track_groups_0|data_tracks_0|data_format|annotation1": {"id": "54d4553682370391", "src": "hda", "uuid": "6bd31719-2a2c-491b-a446-d403a8d406eb"}, "track_groups_0|data_tracks_1|data_format|annotation": {"id": "54d4553682370391", "src": "hda", "uuid": "6bd31719-2a2c-491b-a446-d403a8d406eb"}, "track_groups_0|data_tracks_1|data_format|annotation1": {"id": "54d4553682370391", "src": "hda", "uuid": "6bd31719-2a2c-491b-a446-d403a8d406eb"}}, "outputs": {"output": {"id": "25e804484ced14fc", "src": "hda", "uuid": "6ad5f93f-7e06-49fb-9ce4-e26ca54cfa65"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "INFO:jbrowse:Processing With menu or index / 1.gff\nINFO:jbrowse:Processing With menu or index / 1.gff\n", "job_stdout": null, "job_stderr": null, "stdout": "", "stderr": "INFO:jbrowse:Processing With menu or index / 1.gff\nINFO:jbrowse:Processing With menu or index / 1.gff\n", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1, exit_code: None, stderr: INFO:jbrowse:Processing With menu or index / 1.gff\nINFO:jbrowse:Processing With menu or index / 1.gff\n.", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1, exit_code: None, stderr: INFO:jbrowse:Processing With menu or index / 1.gff\nINFO:jbrowse:Processing With menu or index / 1.gff\n."], "status": "failure"}}, {"id": "jbrowse/1.16.11+galaxy1-5", "has_data": true, "data": {"tool_id": "jbrowse", "tool_version": "1.16.11+galaxy1", "test_index": 5, "time_seconds": 33.604830503463745, "inputs": {"reference_genome|genome": {"src": "hda", "id": "b0e95d401bc1ff67"}, "reference_genome|genome_type_select": "history", "standalone": "data", "gencode": "11", "track_groups_0|category": "With canvas config", "track_groups_0|data_tracks_0|data_format|annotation": {"src": "hda", "id": "7fd375b8233b3119"}, "track_groups_0|data_tracks_0|data_format|match_part|match_part_select": false, "track_groups_0|data_tracks_0|data_format|track_config|canvas_options|transcriptType": "transcript", "track_groups_0|data_tracks_0|data_format|track_config|canvas_options|subParts": "exon", "track_groups_0|data_tracks_0|data_format|track_config|canvas_options|impliedUTRs": true, "track_groups_0|data_tracks_0|data_format|track_config|track_class": "JBrowse/View/Track/CanvasFeatures", "track_groups_0|data_tracks_0|data_format|jbcolor_scale|color_score|color_score_select": "none", "track_groups_0|data_tracks_0|data_format|data_format_select": "gene_calls", "uglyTestingHack": "enabled"}, "job": {"model_class": "Job", "id": "57eaa0b8499f82dd", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2025-01-02T06:45:48.939153", "update_time": "2025-01-02T06:46:02.590161", "galaxy_version": "24.1", "external_id": "gxy-fvh87", "handler": null, "job_runner_name": null, "command_line": "mkdir -p /galaxy/server/database/objects/e/9/b/dataset_e9b92fb0-c476-401e-a97b-41dcf9d024c5_files && cp /galaxy/server/database/jobs_directory/000/78/configs/tmp1_gkrqu5 /galaxy/server/database/objects/e/9/b/dataset_e9b92fb0-c476-401e-a97b-41dcf9d024c5_files/galaxy.xml && export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'data' --outdir /galaxy/server/database/objects/e/9/b/dataset_e9b92fb0-c476-401e-a97b-41dcf9d024c5_files /galaxy/server/database/jobs_directory/000/78/configs/tmp1_gkrqu5 && cp /galaxy/server/database/jobs_directory/000/78/configs/tmp24bsd3qm /galaxy/server/database/objects/e/9/b/dataset_e9b92fb0-c476-401e-a97b-41dcf9d024c5.dat; cp /galaxy/server/database/jobs_directory/000/78/configs/tmp1_gkrqu5 /galaxy/server/database/objects/e/9/b/dataset_e9b92fb0-c476-401e-a97b-41dcf9d024c5.dat", "user_email": "tests@fake.org", "command_version": "jbrowse.py 0.8.0", "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "uglyTestingHack": "\"enabled\"", "plugins": "{\"BlastView\": true, \"ComboTrackSelector\": false, \"GCContent\": false}", "jbgen": "{\"aboutDescription\": \"\", \"defaultLocation\": \"\", \"hideGenomeOptions\": false, \"shareLink\": true, \"show_menu\": true, \"show_nav\": true, \"show_overview\": true, \"show_tracklist\": true, \"trackPadding\": \"20\"}", "track_groups": "[{\"__index__\": 0, \"category\": \"With canvas config\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"__current_case__\": 2, \"annotation\": {\"values\": [{\"id\": 122, \"src\": \"hda\"}]}, \"data_format_select\": \"gene_calls\", \"index\": false, \"jb_custom_config\": {\"option\": []}, \"jbcolor_scale\": {\"color_score\": {\"__current_case__\": 0, \"color\": {\"__current_case__\": 0, \"color_select\": \"automatic\"}, \"color_score_select\": \"none\"}}, \"jbmenu\": {\"track_menu\": []}, \"jbstyle\": {\"max_height\": \"600\", \"style_classname\": \"feature\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"style_label\": \"product,name,id\"}, \"match_part\": {\"__current_case__\": 1, \"match_part_select\": false}, \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"track_config\": {\"__current_case__\": 0, \"canvas_options\": {\"impliedUTRs\": true, \"subParts\": \"exon\", \"transcriptType\": \"transcript\"}, \"track_class\": \"JBrowse/View/Track/CanvasFeatures\"}, \"track_visibility\": \"default_off\"}}]}]", "action": "{\"__current_case__\": 0, \"action_select\": \"create\"}", "gencode": "\"11\"", "standalone": "\"data\"", "reference_genome": "{\"__current_case__\": 1, \"genome\": {\"values\": [{\"id\": 121, \"src\": \"hda\"}]}, \"genome_type_select\": \"history\"}"}, "inputs": {"reference_genome|genome": {"id": "b0e95d401bc1ff67", "src": "hda", "uuid": "2d935240-0fdd-4f15-b6a5-0f55b38474a5"}, "track_groups_0|data_tracks_0|data_format|annotation": {"id": "7fd375b8233b3119", "src": "hda", "uuid": "4d2e0eff-d391-4511-a36b-456f6dd827b5"}, "track_groups_0|data_tracks_0|data_format|annotation1": {"id": "7fd375b8233b3119", "src": "hda", "uuid": "4d2e0eff-d391-4511-a36b-456f6dd827b5"}}, "outputs": {"output": {"id": "62a8ef6bb482441a", "src": "hda", "uuid": "e9b92fb0-c476-401e-a97b-41dcf9d024c5"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "INFO:jbrowse:Processing With canvas config / 1.gff\nWARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "INFO:jbrowse:Processing With canvas config / 1.gff\nWARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2025-01-02 06:45:51", "plugin": "core", "name": "end_epoch", "raw_value": "1735800351.0000000"}, {"title": "Job Start Time", "value": "2025-01-02 06:45:50", "plugin": "core", "name": "start_epoch", "raw_value": "1735800350.0000000"}, {"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": "jbrowse/1.16.11+galaxy1-5", "has_data": true, "data": {"tool_id": "jbrowse", "tool_version": "1.16.11+galaxy1", "test_index": 5, "time_seconds": 25.70210075378418, "inputs": {"reference_genome|genome": {"src": "hda", "id": "bbe5504370b59d77"}, "reference_genome|genome_type_select": "history", "standalone": "data", "gencode": "11", "track_groups_0|category": "With canvas config", "track_groups_0|data_tracks_0|data_format|annotation": {"src": "hda", "id": "af6c4fd171b336e0"}, "track_groups_0|data_tracks_0|data_format|match_part|match_part_select": false, "track_groups_0|data_tracks_0|data_format|track_config|canvas_options|transcriptType": "transcript", "track_groups_0|data_tracks_0|data_format|track_config|canvas_options|subParts": "exon", "track_groups_0|data_tracks_0|data_format|track_config|canvas_options|impliedUTRs": true, "track_groups_0|data_tracks_0|data_format|track_config|track_class": "JBrowse/View/Track/CanvasFeatures", "track_groups_0|data_tracks_0|data_format|jbcolor_scale|color_score|color_score_select": "none", "track_groups_0|data_tracks_0|data_format|data_format_select": "gene_calls", "uglyTestingHack": "enabled"}, "job": {"model_class": "Job", "id": "55cbbbefccf62e5d", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1", "state": "error", "exit_code": null, "create_time": "2025-01-02T06:52:25.269427", "update_time": "2025-01-02T06:52:30.510140", "galaxy_version": "24.1", "external_id": "gxy-7xdf9", "handler": null, "job_runner_name": null, "command_line": "mkdir -p /galaxy/server/database/objects/2/2/7/dataset_2274b1b4-c97d-4e21-afd9-5753a52565c3_files && cp /galaxy/server/database/jobs_directory/000/110/configs/tmpwhxq0acu /galaxy/server/database/objects/2/2/7/dataset_2274b1b4-c97d-4e21-afd9-5753a52565c3_files/galaxy.xml && export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'data' --outdir /galaxy/server/database/objects/2/2/7/dataset_2274b1b4-c97d-4e21-afd9-5753a52565c3_files /galaxy/server/database/jobs_directory/000/110/configs/tmpwhxq0acu && cp /galaxy/server/database/jobs_directory/000/110/configs/tmp_jc7em4p /galaxy/server/database/objects/2/2/7/dataset_2274b1b4-c97d-4e21-afd9-5753a52565c3.dat; cp /galaxy/server/database/jobs_directory/000/110/configs/tmpwhxq0acu /galaxy/server/database/objects/2/2/7/dataset_2274b1b4-c97d-4e21-afd9-5753a52565c3.dat", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "uglyTestingHack": "\"enabled\"", "plugins": "{\"BlastView\": true, \"ComboTrackSelector\": false, \"GCContent\": false}", "jbgen": "{\"aboutDescription\": \"\", \"defaultLocation\": \"\", \"hideGenomeOptions\": false, \"shareLink\": true, \"show_menu\": true, \"show_nav\": true, \"show_overview\": true, \"show_tracklist\": true, \"trackPadding\": \"20\"}", "track_groups": "[{\"__index__\": 0, \"category\": \"With canvas config\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"__current_case__\": 2, \"annotation\": {\"values\": [{\"id\": 154, \"src\": \"hda\"}]}, \"data_format_select\": \"gene_calls\", \"index\": false, \"jb_custom_config\": {\"option\": []}, \"jbcolor_scale\": {\"color_score\": {\"__current_case__\": 0, \"color\": {\"__current_case__\": 0, \"color_select\": \"automatic\"}, \"color_score_select\": \"none\"}}, \"jbmenu\": {\"track_menu\": []}, \"jbstyle\": {\"max_height\": \"600\", \"style_classname\": \"feature\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"style_label\": \"product,name,id\"}, \"match_part\": {\"__current_case__\": 1, \"match_part_select\": false}, \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"track_config\": {\"__current_case__\": 0, \"canvas_options\": {\"impliedUTRs\": true, \"subParts\": \"exon\", \"transcriptType\": \"transcript\"}, \"track_class\": \"JBrowse/View/Track/CanvasFeatures\"}, \"track_visibility\": \"default_off\"}}]}]", "action": "{\"__current_case__\": 0, \"action_select\": \"create\"}", "gencode": "\"11\"", "standalone": "\"data\"", "reference_genome": "{\"__current_case__\": 1, \"genome\": {\"values\": [{\"id\": 153, \"src\": \"hda\"}]}, \"genome_type_select\": \"history\"}"}, "inputs": {"reference_genome|genome": {"id": "bbe5504370b59d77", "src": "hda", "uuid": "3ae56a62-a01f-4787-b723-06dd2d0cc18b"}, "track_groups_0|data_tracks_0|data_format|annotation": {"id": "af6c4fd171b336e0", "src": "hda", "uuid": "d214596b-e006-4110-866d-f4557616e26f"}, "track_groups_0|data_tracks_0|data_format|annotation1": {"id": "af6c4fd171b336e0", "src": "hda", "uuid": "d214596b-e006-4110-866d-f4557616e26f"}}, "outputs": {"output": {"id": "6ac8f9c789c25e5a", "src": "hda", "uuid": "2274b1b4-c97d-4e21-afd9-5753a52565c3"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "INFO:jbrowse:Processing With canvas config / 1.gff\nWARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "job_stdout": null, "job_stderr": null, "stdout": "", "stderr": "INFO:jbrowse:Processing With canvas config / 1.gff\nWARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1, exit_code: None, stderr: INFO:jbrowse:Processing With canvas config / 1.gff\nWARNING: No feature names found for indexing, only reference sequence names will be indexed.\n.", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1, exit_code: None, stderr: INFO:jbrowse:Processing With canvas config / 1.gff\nWARNING: No feature names found for indexing, only reference sequence names will be indexed.\n."], "status": "failure"}}, {"id": "jbrowse/1.16.11+galaxy1-6", "has_data": true, "data": {"tool_id": "jbrowse", "tool_version": "1.16.11+galaxy1", "test_index": 6, "time_seconds": 33.2950713634491, "inputs": {"reference_genome|genome": {"src": "hda", "id": "e76cff200bf710f5"}, "reference_genome|genome_type_select": "history", "standalone": "data", "gencode": "11", "track_groups_0|category": "With custom track config", "track_groups_0|data_tracks_0|data_format|annotation": {"src": "hda", "id": "f17becfa74bb10c7"}, "track_groups_0|data_tracks_0|data_format|match_part|match_part_select": false, "track_groups_0|data_tracks_0|data_format|jb_custom_config|option_0|opt_key": "displayMode", "track_groups_0|data_tracks_0|data_format|jb_custom_config|option_0|opt_value|val": "collapsed", "track_groups_0|data_tracks_0|data_format|jb_custom_config|option_0|opt_value|val_type": "text", "track_groups_0|data_tracks_0|data_format|jb_custom_config|option_1|opt_key": "histograms.height", "track_groups_0|data_tracks_0|data_format|jb_custom_config|option_1|opt_value|val": "150", "track_groups_0|data_tracks_0|data_format|jb_custom_config|option_1|opt_value|val_type": "integer", "track_groups_0|data_tracks_0|data_format|jb_custom_config|option_2|opt_key": "maxFeatureScreenDensity", "track_groups_0|data_tracks_0|data_format|jb_custom_config|option_2|opt_value|val": "0.1", "track_groups_0|data_tracks_0|data_format|jb_custom_config|option_2|opt_value|val_type": "float", "track_groups_0|data_tracks_0|data_format|jb_custom_config|option_3|opt_key": "style.strandArrow", "track_groups_0|data_tracks_0|data_format|jb_custom_config|option_3|opt_value|val": false, "track_groups_0|data_tracks_0|data_format|jb_custom_config|option_3|opt_value|val_type": "boolean", "track_groups_0|data_tracks_0|data_format|data_format_select": "gene_calls", "uglyTestingHack": "enabled"}, "job": {"model_class": "Job", "id": "1ee8d5aaf8a35324", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2025-01-02T06:46:22.373691", "update_time": "2025-01-02T06:46:35.934315", "galaxy_version": "24.1", "external_id": "gxy-m4grq", "handler": null, "job_runner_name": null, "command_line": "mkdir -p /galaxy/server/database/objects/1/7/5/dataset_17563f21-77f2-4658-a466-87d893a6b224_files && cp /galaxy/server/database/jobs_directory/000/81/configs/tmpxsv58prf /galaxy/server/database/objects/1/7/5/dataset_17563f21-77f2-4658-a466-87d893a6b224_files/galaxy.xml && export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'data' --outdir /galaxy/server/database/objects/1/7/5/dataset_17563f21-77f2-4658-a466-87d893a6b224_files /galaxy/server/database/jobs_directory/000/81/configs/tmpxsv58prf && cp /galaxy/server/database/jobs_directory/000/81/configs/tmpih_gisf_ /galaxy/server/database/objects/1/7/5/dataset_17563f21-77f2-4658-a466-87d893a6b224.dat; cp /galaxy/server/database/jobs_directory/000/81/configs/tmpxsv58prf /galaxy/server/database/objects/1/7/5/dataset_17563f21-77f2-4658-a466-87d893a6b224.dat", "user_email": "tests@fake.org", "command_version": "jbrowse.py 0.8.0", "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "uglyTestingHack": "\"enabled\"", "plugins": "{\"BlastView\": true, \"ComboTrackSelector\": false, \"GCContent\": false}", "jbgen": "{\"aboutDescription\": \"\", \"defaultLocation\": \"\", \"hideGenomeOptions\": false, \"shareLink\": true, \"show_menu\": true, \"show_nav\": true, \"show_overview\": true, \"show_tracklist\": true, \"trackPadding\": \"20\"}", "track_groups": "[{\"__index__\": 0, \"category\": \"With custom track config\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"__current_case__\": 2, \"annotation\": {\"values\": [{\"id\": 125, \"src\": \"hda\"}]}, \"data_format_select\": \"gene_calls\", \"index\": false, \"jb_custom_config\": {\"option\": [{\"__index__\": 0, \"opt_key\": \"displayMode\", \"opt_value\": {\"__current_case__\": 0, \"val\": \"collapsed\", \"val_type\": \"text\"}}, {\"__index__\": 1, \"opt_key\": \"histograms.height\", \"opt_value\": {\"__current_case__\": 1, \"val\": \"150\", \"val_type\": \"integer\"}}, {\"__index__\": 2, \"opt_key\": \"maxFeatureScreenDensity\", \"opt_value\": {\"__current_case__\": 2, \"val\": \"0.1\", \"val_type\": \"float\"}}, {\"__index__\": 3, \"opt_key\": \"style.strandArrow\", \"opt_value\": {\"__current_case__\": 3, \"val\": false, \"val_type\": \"boolean\"}}]}, \"jbcolor_scale\": {\"color_score\": {\"__current_case__\": 0, \"color\": {\"__current_case__\": 0, \"color_select\": \"automatic\"}, \"color_score_select\": \"none\"}}, \"jbmenu\": {\"track_menu\": []}, \"jbstyle\": {\"max_height\": \"600\", \"style_classname\": \"feature\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"style_label\": \"product,name,id\"}, \"match_part\": {\"__current_case__\": 1, \"match_part_select\": false}, \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"track_config\": {\"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": null}, \"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\"}, \"track_visibility\": \"default_off\"}}]}]", "action": "{\"__current_case__\": 0, \"action_select\": \"create\"}", "gencode": "\"11\"", "standalone": "\"data\"", "reference_genome": "{\"__current_case__\": 1, \"genome\": {\"values\": [{\"id\": 124, \"src\": \"hda\"}]}, \"genome_type_select\": \"history\"}"}, "inputs": {"reference_genome|genome": {"id": "e76cff200bf710f5", "src": "hda", "uuid": "260e8ab9-1dd8-4fb1-a231-56b82ea71b91"}, "track_groups_0|data_tracks_0|data_format|annotation": {"id": "f17becfa74bb10c7", "src": "hda", "uuid": "3eb57934-ddee-4a50-ace9-6124c2db66b3"}, "track_groups_0|data_tracks_0|data_format|annotation1": {"id": "f17becfa74bb10c7", "src": "hda", "uuid": "3eb57934-ddee-4a50-ace9-6124c2db66b3"}}, "outputs": {"output": {"id": "9fa5638ea7c7019e", "src": "hda", "uuid": "17563f21-77f2-4658-a466-87d893a6b224"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "INFO:jbrowse:Processing With custom track config / 1.gff\nWARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "INFO:jbrowse:Processing With custom track config / 1.gff\nWARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2025-01-02 06:46:24", "plugin": "core", "name": "end_epoch", "raw_value": "1735800384.0000000"}, {"title": "Job Start Time", "value": "2025-01-02 06:46:24", "plugin": "core", "name": "start_epoch", "raw_value": "1735800384.0000000"}, {"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": "jbrowse/1.16.11+galaxy1-6", "has_data": true, "data": {"tool_id": "jbrowse", "tool_version": "1.16.11+galaxy1", "test_index": 6, "time_seconds": 32.64648985862732, "inputs": {"reference_genome|genome": {"src": "hda", "id": "f209d4249397848c"}, "reference_genome|genome_type_select": "history", "standalone": "data", "gencode": "11", "track_groups_0|category": "With custom track config", "track_groups_0|data_tracks_0|data_format|annotation": {"src": "hda", "id": "ddc070378ca3ecf8"}, "track_groups_0|data_tracks_0|data_format|match_part|match_part_select": false, "track_groups_0|data_tracks_0|data_format|jb_custom_config|option_0|opt_key": "displayMode", "track_groups_0|data_tracks_0|data_format|jb_custom_config|option_0|opt_value|val": "collapsed", "track_groups_0|data_tracks_0|data_format|jb_custom_config|option_0|opt_value|val_type": "text", "track_groups_0|data_tracks_0|data_format|jb_custom_config|option_1|opt_key": "histograms.height", "track_groups_0|data_tracks_0|data_format|jb_custom_config|option_1|opt_value|val": "150", "track_groups_0|data_tracks_0|data_format|jb_custom_config|option_1|opt_value|val_type": "integer", "track_groups_0|data_tracks_0|data_format|jb_custom_config|option_2|opt_key": "maxFeatureScreenDensity", "track_groups_0|data_tracks_0|data_format|jb_custom_config|option_2|opt_value|val": "0.1", "track_groups_0|data_tracks_0|data_format|jb_custom_config|option_2|opt_value|val_type": "float", "track_groups_0|data_tracks_0|data_format|jb_custom_config|option_3|opt_key": "style.strandArrow", "track_groups_0|data_tracks_0|data_format|jb_custom_config|option_3|opt_value|val": false, "track_groups_0|data_tracks_0|data_format|jb_custom_config|option_3|opt_value|val_type": "boolean", "track_groups_0|data_tracks_0|data_format|data_format_select": "gene_calls", "uglyTestingHack": "enabled"}, "job": {"model_class": "Job", "id": "27e96da2ddad3da3", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2025-01-02T06:52:49.719418", "update_time": "2025-01-02T06:53:03.378073", "galaxy_version": "24.1", "external_id": "gxy-zzm27", "handler": null, "job_runner_name": null, "command_line": "mkdir -p /galaxy/server/database/objects/e/f/4/dataset_ef4c75ae-d6d8-45fb-8aba-6c883f6b81ce_files && cp /galaxy/server/database/jobs_directory/000/113/configs/tmp6id2xv6_ /galaxy/server/database/objects/e/f/4/dataset_ef4c75ae-d6d8-45fb-8aba-6c883f6b81ce_files/galaxy.xml && export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'data' --outdir /galaxy/server/database/objects/e/f/4/dataset_ef4c75ae-d6d8-45fb-8aba-6c883f6b81ce_files /galaxy/server/database/jobs_directory/000/113/configs/tmp6id2xv6_ && cp /galaxy/server/database/jobs_directory/000/113/configs/tmprr22qqam /galaxy/server/database/objects/e/f/4/dataset_ef4c75ae-d6d8-45fb-8aba-6c883f6b81ce.dat; cp /galaxy/server/database/jobs_directory/000/113/configs/tmp6id2xv6_ /galaxy/server/database/objects/e/f/4/dataset_ef4c75ae-d6d8-45fb-8aba-6c883f6b81ce.dat", "user_email": "tests@fake.org", "command_version": "jbrowse.py 0.8.0", "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "uglyTestingHack": "\"enabled\"", "plugins": "{\"BlastView\": true, \"ComboTrackSelector\": false, \"GCContent\": false}", "jbgen": "{\"aboutDescription\": \"\", \"defaultLocation\": \"\", \"hideGenomeOptions\": false, \"shareLink\": true, \"show_menu\": true, \"show_nav\": true, \"show_overview\": true, \"show_tracklist\": true, \"trackPadding\": \"20\"}", "track_groups": "[{\"__index__\": 0, \"category\": \"With custom track config\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"__current_case__\": 2, \"annotation\": {\"values\": [{\"id\": 157, \"src\": \"hda\"}]}, \"data_format_select\": \"gene_calls\", \"index\": false, \"jb_custom_config\": {\"option\": [{\"__index__\": 0, \"opt_key\": \"displayMode\", \"opt_value\": {\"__current_case__\": 0, \"val\": \"collapsed\", \"val_type\": \"text\"}}, {\"__index__\": 1, \"opt_key\": \"histograms.height\", \"opt_value\": {\"__current_case__\": 1, \"val\": \"150\", \"val_type\": \"integer\"}}, {\"__index__\": 2, \"opt_key\": \"maxFeatureScreenDensity\", \"opt_value\": {\"__current_case__\": 2, \"val\": \"0.1\", \"val_type\": \"float\"}}, {\"__index__\": 3, \"opt_key\": \"style.strandArrow\", \"opt_value\": {\"__current_case__\": 3, \"val\": false, \"val_type\": \"boolean\"}}]}, \"jbcolor_scale\": {\"color_score\": {\"__current_case__\": 0, \"color\": {\"__current_case__\": 0, \"color_select\": \"automatic\"}, \"color_score_select\": \"none\"}}, \"jbmenu\": {\"track_menu\": []}, \"jbstyle\": {\"max_height\": \"600\", \"style_classname\": \"feature\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"style_label\": \"product,name,id\"}, \"match_part\": {\"__current_case__\": 1, \"match_part_select\": false}, \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"track_config\": {\"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": null}, \"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\"}, \"track_visibility\": \"default_off\"}}]}]", "action": "{\"__current_case__\": 0, \"action_select\": \"create\"}", "gencode": "\"11\"", "standalone": "\"data\"", "reference_genome": "{\"__current_case__\": 1, \"genome\": {\"values\": [{\"id\": 156, \"src\": \"hda\"}]}, \"genome_type_select\": \"history\"}"}, "inputs": {"reference_genome|genome": {"id": "f209d4249397848c", "src": "hda", "uuid": "c6f9c6a1-d7ef-47ea-a6e0-d4ed66776bce"}, "track_groups_0|data_tracks_0|data_format|annotation1": {"id": "ddc070378ca3ecf8", "src": "hda", "uuid": "9a18f31e-9ed0-41ef-a10b-51f02de20aee"}, "track_groups_0|data_tracks_0|data_format|annotation": {"id": "ddc070378ca3ecf8", "src": "hda", "uuid": "9a18f31e-9ed0-41ef-a10b-51f02de20aee"}}, "outputs": {"output": {"id": "6e386b278832dd3b", "src": "hda", "uuid": "ef4c75ae-d6d8-45fb-8aba-6c883f6b81ce"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "INFO:jbrowse:Processing With custom track config / 1.gff\nWARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "INFO:jbrowse:Processing With custom track config / 1.gff\nWARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2025-01-02 06:52:52", "plugin": "core", "name": "end_epoch", "raw_value": "1735800772.0000000"}, {"title": "Job Start Time", "value": "2025-01-02 06:52:51", "plugin": "core", "name": "start_epoch", "raw_value": "1735800771.0000000"}, {"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": "jbrowse/1.16.11+galaxy1-7", "has_data": true, "data": {"tool_id": "jbrowse", "tool_version": "1.16.11+galaxy1", "test_index": 7, "time_seconds": 34.555591106414795, "inputs": {"reference_genome|genome": {"src": "hda", "id": "f90b805bacc4c138"}, "reference_genome|genome_type_select": "history", "standalone": "data", "gencode": "11", "track_groups_0|category": "Auto Coloured", "track_groups_0|data_tracks_0|data_format|annotation": {"src": "hda", "id": "5711a2960ca45e3c"}, "track_groups_0|data_tracks_0|data_format|data_format_select": "pileup", "uglyTestingHack": "enabled"}, "job": {"model_class": "Job", "id": "1d493d7b88012eee", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2025-01-02T06:46:56.982344", "update_time": "2025-01-02T06:47:10.570142", "galaxy_version": "24.1", "external_id": "gxy-grb9k", "handler": null, "job_runner_name": null, "command_line": "mkdir -p /galaxy/server/database/objects/a/5/9/dataset_a59f0901-51b1-492c-97fa-cc5995ea83ad_files && cp /galaxy/server/database/jobs_directory/000/84/configs/tmpxbhh9olw /galaxy/server/database/objects/a/5/9/dataset_a59f0901-51b1-492c-97fa-cc5995ea83ad_files/galaxy.xml && export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'data' --outdir /galaxy/server/database/objects/a/5/9/dataset_a59f0901-51b1-492c-97fa-cc5995ea83ad_files /galaxy/server/database/jobs_directory/000/84/configs/tmpxbhh9olw && cp /galaxy/server/database/jobs_directory/000/84/configs/tmpbpuc4_ib /galaxy/server/database/objects/a/5/9/dataset_a59f0901-51b1-492c-97fa-cc5995ea83ad.dat; cp /galaxy/server/database/jobs_directory/000/84/configs/tmpxbhh9olw /galaxy/server/database/objects/a/5/9/dataset_a59f0901-51b1-492c-97fa-cc5995ea83ad.dat", "user_email": "tests@fake.org", "command_version": "jbrowse.py 0.8.0", "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "uglyTestingHack": "\"enabled\"", "plugins": "{\"BlastView\": true, \"ComboTrackSelector\": false, \"GCContent\": false}", "jbgen": "{\"aboutDescription\": \"\", \"defaultLocation\": \"\", \"hideGenomeOptions\": false, \"shareLink\": true, \"show_menu\": true, \"show_nav\": true, \"show_overview\": true, \"show_tracklist\": true, \"trackPadding\": \"20\"}", "track_groups": "[{\"__index__\": 0, \"category\": \"Auto Coloured\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"__current_case__\": 3, \"annotation\": {\"values\": [{\"id\": 128, \"src\": \"hda\"}]}, \"auto_snp\": false, \"chunkSizeLimit\": \"5000000\", \"data_format_select\": \"pileup\", \"jb_custom_config\": {\"option\": []}, \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"track_visibility\": \"default_off\"}}]}]", "action": "{\"__current_case__\": 0, \"action_select\": \"create\"}", "gencode": "\"11\"", "standalone": "\"data\"", "reference_genome": "{\"__current_case__\": 1, \"genome\": {\"values\": [{\"id\": 127, \"src\": \"hda\"}]}, \"genome_type_select\": \"history\"}"}, "inputs": {"reference_genome|genome": {"id": "f90b805bacc4c138", "src": "hda", "uuid": "76c89812-21dd-4b99-a45c-b876b20867c5"}, "track_groups_0|data_tracks_0|data_format|annotation": {"id": "5711a2960ca45e3c", "src": "hda", "uuid": "b8896886-c6db-4e8a-9278-a8a4bf1bd501"}, "track_groups_0|data_tracks_0|data_format|annotation1": {"id": "5711a2960ca45e3c", "src": "hda", "uuid": "b8896886-c6db-4e8a-9278-a8a4bf1bd501"}}, "outputs": {"output": {"id": "ad7cdefb17e24f31", "src": "hda", "uuid": "a59f0901-51b1-492c-97fa-cc5995ea83ad"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "INFO:jbrowse:Processing Auto Coloured / merlin-sample.bam\nWARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "INFO:jbrowse:Processing Auto Coloured / merlin-sample.bam\nWARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2025-01-02 06:46:59", "plugin": "core", "name": "end_epoch", "raw_value": "1735800419.0000000"}, {"title": "Job Start Time", "value": "2025-01-02 06:46:58", "plugin": "core", "name": "start_epoch", "raw_value": "1735800418.0000000"}, {"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": "jbrowse/1.16.11+galaxy1-7", "has_data": true, "data": {"tool_id": "jbrowse", "tool_version": "1.16.11+galaxy1", "test_index": 7, "time_seconds": 16.104151010513306, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "jbrowse/1.16.11+galaxy1-8", "has_data": true, "data": {"tool_id": "jbrowse", "tool_version": "1.16.11+galaxy1", "test_index": 8, "time_seconds": 73.4549663066864, "inputs": {"reference_genome|genome_type_select": "indexed", "standalone": "data", "gencode": "1", "uglyTestingHack": "enabled"}, "job": {"model_class": "Job", "id": "7ef2d158ca9ba41c", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2025-01-02T06:47:11.179932", "update_time": "2025-01-02T06:48:24.116224", "galaxy_version": "24.1", "external_id": "gxy-vqwxn", "handler": null, "job_runner_name": null, "command_line": "mkdir -p /galaxy/server/database/objects/7/d/3/dataset_7d3a4dfb-d5c3-4aef-a524-8fdd248a15f3_files && cp /galaxy/server/database/jobs_directory/000/85/configs/tmpn07iopzq /galaxy/server/database/objects/7/d/3/dataset_7d3a4dfb-d5c3-4aef-a524-8fdd248a15f3_files/galaxy.xml && export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'data' --outdir /galaxy/server/database/objects/7/d/3/dataset_7d3a4dfb-d5c3-4aef-a524-8fdd248a15f3_files /galaxy/server/database/jobs_directory/000/85/configs/tmpn07iopzq && cp /galaxy/server/database/jobs_directory/000/85/configs/tmpnhid2jns /galaxy/server/database/objects/7/d/3/dataset_7d3a4dfb-d5c3-4aef-a524-8fdd248a15f3.dat; cp /galaxy/server/database/jobs_directory/000/85/configs/tmpn07iopzq /galaxy/server/database/objects/7/d/3/dataset_7d3a4dfb-d5c3-4aef-a524-8fdd248a15f3.dat", "user_email": "tests@fake.org", "command_version": "jbrowse.py 0.8.0", "params": {"__input_ext": "\"data\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "uglyTestingHack": "\"enabled\"", "plugins": "{\"BlastView\": true, \"ComboTrackSelector\": false, \"GCContent\": false}", "jbgen": "{\"aboutDescription\": \"\", \"defaultLocation\": \"\", \"hideGenomeOptions\": false, \"shareLink\": true, \"show_menu\": true, \"show_nav\": true, \"show_overview\": true, \"show_tracklist\": true, \"trackPadding\": \"20\"}", "track_groups": "[]", "action": "{\"__current_case__\": 0, \"action_select\": \"create\"}", "gencode": "\"1\"", "standalone": "\"data\"", "reference_genome": "{\"__current_case__\": 0, \"genome_type_select\": \"indexed\", \"genomes\": \"apiMel4\"}"}, "inputs": {}, "outputs": {"output": {"id": "2ba188dd08e677d1", "src": "hda", "uuid": "7d3a4dfb-d5c3-4aef-a524-8fdd248a15f3"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "WARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "WARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "54 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "54.0000000"}, {"title": "Job End Time", "value": "2025-01-02 06:48:06", "plugin": "core", "name": "end_epoch", "raw_value": "1735800486.0000000"}, {"title": "Job Start Time", "value": "2025-01-02 06:47:12", "plugin": "core", "name": "start_epoch", "raw_value": "1735800432.0000000"}, {"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"}]}, "output_problems": ["Output output: different than expected\nExpected text 'merlin.fa' in output ('\n\n \n 1\n \n \n \n s\n \n \n \n 20\n\n true\n \n true\n true\n true\n true\n false\n \n http://localhost:8080\n \n \n \n \n\n')"], "status": "failure"}}, {"id": "jbrowse/1.16.11+galaxy1-8", "has_data": true, "data": {"tool_id": "jbrowse", "tool_version": "1.16.11+galaxy1", "test_index": 8, "time_seconds": 65.3822500705719, "inputs": {"reference_genome|genome_type_select": "indexed", "standalone": "data", "gencode": "1", "uglyTestingHack": "enabled"}, "job": {"model_class": "Job", "id": "4963a0f517e742b4", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2025-01-02T06:53:20.067580", "update_time": "2025-01-02T06:54:24.879678", "galaxy_version": "24.1", "external_id": "gxy-p84k9", "handler": null, "job_runner_name": null, "command_line": "mkdir -p /galaxy/server/database/objects/7/2/3/dataset_723eff4c-a87b-4c3b-a674-457db995a504_files && cp /galaxy/server/database/jobs_directory/000/116/configs/tmpcicbrr73 /galaxy/server/database/objects/7/2/3/dataset_723eff4c-a87b-4c3b-a674-457db995a504_files/galaxy.xml && export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'data' --outdir /galaxy/server/database/objects/7/2/3/dataset_723eff4c-a87b-4c3b-a674-457db995a504_files /galaxy/server/database/jobs_directory/000/116/configs/tmpcicbrr73 && cp /galaxy/server/database/jobs_directory/000/116/configs/tmp63umx3b5 /galaxy/server/database/objects/7/2/3/dataset_723eff4c-a87b-4c3b-a674-457db995a504.dat; cp /galaxy/server/database/jobs_directory/000/116/configs/tmpcicbrr73 /galaxy/server/database/objects/7/2/3/dataset_723eff4c-a87b-4c3b-a674-457db995a504.dat", "user_email": "tests@fake.org", "command_version": "jbrowse.py 0.8.0", "params": {"__input_ext": "\"data\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "uglyTestingHack": "\"enabled\"", "plugins": "{\"BlastView\": true, \"ComboTrackSelector\": false, \"GCContent\": false}", "jbgen": "{\"aboutDescription\": \"\", \"defaultLocation\": \"\", \"hideGenomeOptions\": false, \"shareLink\": true, \"show_menu\": true, \"show_nav\": true, \"show_overview\": true, \"show_tracklist\": true, \"trackPadding\": \"20\"}", "track_groups": "[]", "action": "{\"__current_case__\": 0, \"action_select\": \"create\"}", "gencode": "\"1\"", "standalone": "\"data\"", "reference_genome": "{\"__current_case__\": 0, \"genome_type_select\": \"indexed\", \"genomes\": \"apiMel4\"}"}, "inputs": {}, "outputs": {"output": {"id": "8f3aaede24ad8be6", "src": "hda", "uuid": "723eff4c-a87b-4c3b-a674-457db995a504"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "WARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "WARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "44 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "44.0000000"}, {"title": "Job End Time", "value": "2025-01-02 06:54:06", "plugin": "core", "name": "end_epoch", "raw_value": "1735800846.0000000"}, {"title": "Job Start Time", "value": "2025-01-02 06:53:22", "plugin": "core", "name": "start_epoch", "raw_value": "1735800802.0000000"}, {"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"}]}, "output_problems": ["Output output: different than expected\nExpected text 'merlin.fa' in output ('\n\n \n 1\n \n \n \n s\n \n \n \n 20\n\n true\n \n true\n true\n true\n true\n false\n \n http://localhost:8080\n \n \n \n \n\n')"], "status": "failure"}}, {"id": "jbrowse/1.16.11+galaxy1-9", "has_data": true, "data": {"tool_id": "jbrowse", "tool_version": "1.16.11+galaxy1", "test_index": 9, "time_seconds": 32.67509341239929, "inputs": {"reference_genome|genome": {"src": "hda", "id": "0bbec1c4b4ec8188"}, "reference_genome|genome_type_select": "history", "standalone": "data", "gencode": "11", "track_groups_0|category": "External endpoints", "track_groups_0|data_tracks_0|data_format|url": "http://example.org.external/rest_api/", "track_groups_0|data_tracks_0|data_format|label": "Rest api", "track_groups_0|data_tracks_0|data_format|data_format_select": "rest", "track_groups_0|data_tracks_1|data_format|url": "http://example.org.external/sparql/", "track_groups_0|data_tracks_1|data_format|label": "Sparql endpoint", "track_groups_0|data_tracks_1|data_format|query": " DEFINE sql:select-option 'order' prefix rdf: select ?start, ?end, IF( ?faldo_type = faldo:ForwardStrandPosition, 1, IF( ?faldo_type = faldo:ReverseStrandPosition, -1, 0 ) ) as ?strand, str(?obj_type_name) as ?type, str(?label) as ?name, str(?obj_name) as ?description, ?obj as ?uniqueID, ?parent as ?parentUniqueID where { values ?faldo_type { faldo:ForwardStrandPosition faldo:ReverseStrandPosition faldo:BothStrandsPosition } }", "track_groups_0|data_tracks_1|data_format|data_format_select": "sparql", "uglyTestingHack": "enabled"}, "job": {"model_class": "Job", "id": "dc8e9e6b8f2166c0", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2025-01-02T06:48:43.822995", "update_time": "2025-01-02T06:48:56.930087", "galaxy_version": "24.1", "external_id": "gxy-7lrxz", "handler": null, "job_runner_name": null, "command_line": "mkdir -p /galaxy/server/database/objects/5/c/d/dataset_5cd80b1a-586f-420c-8632-61cb8a11be1f_files && cp /galaxy/server/database/jobs_directory/000/87/configs/tmplv5iqt9s /galaxy/server/database/objects/5/c/d/dataset_5cd80b1a-586f-420c-8632-61cb8a11be1f_files/galaxy.xml && export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'data' --outdir /galaxy/server/database/objects/5/c/d/dataset_5cd80b1a-586f-420c-8632-61cb8a11be1f_files /galaxy/server/database/jobs_directory/000/87/configs/tmplv5iqt9s && cp /galaxy/server/database/jobs_directory/000/87/configs/tmpb9h5zfgt /galaxy/server/database/objects/5/c/d/dataset_5cd80b1a-586f-420c-8632-61cb8a11be1f.dat; cp /galaxy/server/database/jobs_directory/000/87/configs/tmplv5iqt9s /galaxy/server/database/objects/5/c/d/dataset_5cd80b1a-586f-420c-8632-61cb8a11be1f.dat", "user_email": "tests@fake.org", "command_version": "jbrowse.py 0.8.0", "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "uglyTestingHack": "\"enabled\"", "plugins": "{\"BlastView\": true, \"ComboTrackSelector\": false, \"GCContent\": false}", "jbgen": "{\"aboutDescription\": \"\", \"defaultLocation\": \"\", \"hideGenomeOptions\": false, \"shareLink\": true, \"show_menu\": true, \"show_nav\": true, \"show_overview\": true, \"show_tracklist\": true, \"trackPadding\": \"20\"}", "track_groups": "[{\"__index__\": 0, \"category\": \"External endpoints\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"__current_case__\": 5, \"data_format_select\": \"rest\", \"jbcolor_scale\": {\"color_score\": {\"__current_case__\": 0, \"color\": {\"__current_case__\": 0, \"color_select\": \"automatic\"}, \"color_score_select\": \"none\"}}, \"jbmenu\": {\"track_menu\": []}, \"jbstyle\": {\"max_height\": \"600\", \"style_classname\": \"feature\", \"style_description\": \"Hit_titles\", \"style_height\": \"600px\", \"style_label\": \"description\"}, \"label\": \"Rest api\", \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"track_visibility\": \"default_off\", \"url\": \"http://example.org.external/rest_api/\"}}, {\"__index__\": 1, \"data_format\": {\"__current_case__\": 6, \"data_format_select\": \"sparql\", \"jbcolor_scale\": {\"color_score\": {\"__current_case__\": 0, \"color\": {\"__current_case__\": 0, \"color_select\": \"automatic\"}, \"color_score_select\": \"none\"}}, \"jbmenu\": {\"track_menu\": []}, \"jbstyle\": {\"max_height\": \"600\", \"style_classname\": \"feature\", \"style_description\": \"Hit_titles\", \"style_height\": \"600px\", \"style_label\": \"description\"}, \"label\": \"Sparql endpoint\", \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"query\": \" DEFINE sql:select-option 'order' prefix rdf: select ?start, ?end, IF( ?faldo_type = faldo:ForwardStrandPosition, 1, IF( ?faldo_type = faldo:ReverseStrandPosition, -1, 0 ) ) as ?strand, str(?obj_type_name) as ?type, str(?label) as ?name, str(?obj_name) as ?description, ?obj as ?uniqueID, ?parent as ?parentUniqueID where { values ?faldo_type { faldo:ForwardStrandPosition faldo:ReverseStrandPosition faldo:BothStrandsPosition } }\", \"track_visibility\": \"default_off\", \"url\": \"http://example.org.external/sparql/\"}}]}]", "action": "{\"__current_case__\": 0, \"action_select\": \"create\"}", "gencode": "\"11\"", "standalone": "\"data\"", "reference_genome": "{\"__current_case__\": 1, \"genome\": {\"values\": [{\"id\": 131, \"src\": \"hda\"}]}, \"genome_type_select\": \"history\"}"}, "inputs": {"reference_genome|genome": {"id": "0bbec1c4b4ec8188", "src": "hda", "uuid": "9f398a04-6e26-4612-b4d2-8f4426587955"}}, "outputs": {"output": {"id": "babaa99004e96057", "src": "hda", "uuid": "5cd80b1a-586f-420c-8632-61cb8a11be1f"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "INFO:jbrowse:Processing External endpoints / Rest api\nINFO:jbrowse:Processing External endpoints / Sparql endpoint\nWARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "INFO:jbrowse:Processing External endpoints / Rest api\nINFO:jbrowse:Processing External endpoints / Sparql endpoint\nWARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2025-01-02 06:48:46", "plugin": "core", "name": "end_epoch", "raw_value": "1735800526.0000000"}, {"title": "Job Start Time", "value": "2025-01-02 06:48:45", "plugin": "core", "name": "start_epoch", "raw_value": "1735800525.0000000"}, {"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": "jbrowse/1.16.11+galaxy1-9", "has_data": true, "data": {"tool_id": "jbrowse", "tool_version": "1.16.11+galaxy1", "test_index": 9, "time_seconds": 32.69084572792053, "inputs": {"reference_genome|genome": {"src": "hda", "id": "c33db1863748b37d"}, "reference_genome|genome_type_select": "history", "standalone": "data", "gencode": "11", "track_groups_0|category": "External endpoints", "track_groups_0|data_tracks_0|data_format|url": "http://example.org.external/rest_api/", "track_groups_0|data_tracks_0|data_format|label": "Rest api", "track_groups_0|data_tracks_0|data_format|data_format_select": "rest", "track_groups_0|data_tracks_1|data_format|url": "http://example.org.external/sparql/", "track_groups_0|data_tracks_1|data_format|label": "Sparql endpoint", "track_groups_0|data_tracks_1|data_format|query": " DEFINE sql:select-option 'order' prefix rdf: select ?start, ?end, IF( ?faldo_type = faldo:ForwardStrandPosition, 1, IF( ?faldo_type = faldo:ReverseStrandPosition, -1, 0 ) ) as ?strand, str(?obj_type_name) as ?type, str(?label) as ?name, str(?obj_name) as ?description, ?obj as ?uniqueID, ?parent as ?parentUniqueID where { values ?faldo_type { faldo:ForwardStrandPosition faldo:ReverseStrandPosition faldo:BothStrandsPosition } }", "track_groups_0|data_tracks_1|data_format|data_format_select": "sparql", "uglyTestingHack": "enabled"}, "job": {"model_class": "Job", "id": "1e77095bebc3b3c7", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2025-01-02T06:54:43.422030", "update_time": "2025-01-02T06:54:57.540638", "galaxy_version": "24.1", "external_id": "gxy-sfjgm", "handler": null, "job_runner_name": null, "command_line": "mkdir -p /galaxy/server/database/objects/4/f/4/dataset_4f4b6174-201b-4b9c-a770-3254eb05652f_files && cp /galaxy/server/database/jobs_directory/000/118/configs/tmprfbdfbl_ /galaxy/server/database/objects/4/f/4/dataset_4f4b6174-201b-4b9c-a770-3254eb05652f_files/galaxy.xml && export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'data' --outdir /galaxy/server/database/objects/4/f/4/dataset_4f4b6174-201b-4b9c-a770-3254eb05652f_files /galaxy/server/database/jobs_directory/000/118/configs/tmprfbdfbl_ && cp /galaxy/server/database/jobs_directory/000/118/configs/tmp7ax5okgu /galaxy/server/database/objects/4/f/4/dataset_4f4b6174-201b-4b9c-a770-3254eb05652f.dat; cp /galaxy/server/database/jobs_directory/000/118/configs/tmprfbdfbl_ /galaxy/server/database/objects/4/f/4/dataset_4f4b6174-201b-4b9c-a770-3254eb05652f.dat", "user_email": "tests@fake.org", "command_version": "jbrowse.py 0.8.0", "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "uglyTestingHack": "\"enabled\"", "plugins": "{\"BlastView\": true, \"ComboTrackSelector\": false, \"GCContent\": false}", "jbgen": "{\"aboutDescription\": \"\", \"defaultLocation\": \"\", \"hideGenomeOptions\": false, \"shareLink\": true, \"show_menu\": true, \"show_nav\": true, \"show_overview\": true, \"show_tracklist\": true, \"trackPadding\": \"20\"}", "track_groups": "[{\"__index__\": 0, \"category\": \"External endpoints\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"__current_case__\": 5, \"data_format_select\": \"rest\", \"jbcolor_scale\": {\"color_score\": {\"__current_case__\": 0, \"color\": {\"__current_case__\": 0, \"color_select\": \"automatic\"}, \"color_score_select\": \"none\"}}, \"jbmenu\": {\"track_menu\": []}, \"jbstyle\": {\"max_height\": \"600\", \"style_classname\": \"feature\", \"style_description\": \"Hit_titles\", \"style_height\": \"600px\", \"style_label\": \"description\"}, \"label\": \"Rest api\", \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"track_visibility\": \"default_off\", \"url\": \"http://example.org.external/rest_api/\"}}, {\"__index__\": 1, \"data_format\": {\"__current_case__\": 6, \"data_format_select\": \"sparql\", \"jbcolor_scale\": {\"color_score\": {\"__current_case__\": 0, \"color\": {\"__current_case__\": 0, \"color_select\": \"automatic\"}, \"color_score_select\": \"none\"}}, \"jbmenu\": {\"track_menu\": []}, \"jbstyle\": {\"max_height\": \"600\", \"style_classname\": \"feature\", \"style_description\": \"Hit_titles\", \"style_height\": \"600px\", \"style_label\": \"description\"}, \"label\": \"Sparql endpoint\", \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"query\": \" DEFINE sql:select-option 'order' prefix rdf: select ?start, ?end, IF( ?faldo_type = faldo:ForwardStrandPosition, 1, IF( ?faldo_type = faldo:ReverseStrandPosition, -1, 0 ) ) as ?strand, str(?obj_type_name) as ?type, str(?label) as ?name, str(?obj_name) as ?description, ?obj as ?uniqueID, ?parent as ?parentUniqueID where { values ?faldo_type { faldo:ForwardStrandPosition faldo:ReverseStrandPosition faldo:BothStrandsPosition } }\", \"track_visibility\": \"default_off\", \"url\": \"http://example.org.external/sparql/\"}}]}]", "action": "{\"__current_case__\": 0, \"action_select\": \"create\"}", "gencode": "\"11\"", "standalone": "\"data\"", "reference_genome": "{\"__current_case__\": 1, \"genome\": {\"values\": [{\"id\": 162, \"src\": \"hda\"}]}, \"genome_type_select\": \"history\"}"}, "inputs": {"reference_genome|genome": {"id": "c33db1863748b37d", "src": "hda", "uuid": "75732317-6248-4513-9838-75b92c060fc2"}}, "outputs": {"output": {"id": "6337d112ca25c320", "src": "hda", "uuid": "4f4b6174-201b-4b9c-a770-3254eb05652f"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "INFO:jbrowse:Processing External endpoints / Rest api\nINFO:jbrowse:Processing External endpoints / Sparql endpoint\nWARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "INFO:jbrowse:Processing External endpoints / Rest api\nINFO:jbrowse:Processing External endpoints / Sparql endpoint\nWARNING: No 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"\"-q\"", "min_length": "\"0\"", "min_identity": "\"0.0\"", "alignment": "\"-m\""}, "inputs": {"delta": {"id": "667e5431a134908a", "src": "hda", "uuid": "e181c66c-2ac5-4916-b36c-3406611a66a2"}}, "outputs": {"output": {"id": "a9062a17810006ff", "src": "hda", "uuid": "df386579-c9d0-46ad-ae24-f683be7415e5"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2025-01-02 06:55:24", "plugin": "core", "name": "end_epoch", "raw_value": "1735800924.0000000"}, {"title": "Job Start Time", "value": "2025-01-02 06:55:24", "plugin": "core", "name": "start_epoch", "raw_value": "1735800924.0000000"}, {"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_winner/0.6.1a1.0-0", "has_data": true, "data": {"tool_id": "poretools_winner", "tool_version": "0.6.1a1.0", "test_index": 0, "time_seconds": 46.40017533302307, "inputs": {"input": {"src": "hda", "id": "3bc6697b14d2f281"}, "type": "fwd"}, "job": {"model_class": "Job", "id": "7fd375b8233b3119", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/poretools_winner/poretools_winner/0.6.1a1.0", "state": "error", "exit_code": null, "create_time": "2025-01-02T06:55:55.397511", "update_time": "2025-01-02T06:56:23.316711", "galaxy_version": "24.1", "external_id": "gxy-4hk54", "handler": null, "job_runner_name": null, "command_line": "poretools winner --type fwd '/galaxy/server/database/objects/9/8/d/dataset_98d9e8e7-f47b-4f38-8b87-7dc9706b6c30.dat' > '/galaxy/server/database/objects/1/1/8/dataset_11823e5b-61db-4d8b-9dc0-7660c973cd70.dat'", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "type": "\"fwd\""}, "inputs": {"input": {"id": "3bc6697b14d2f281", "src": "hda", "uuid": "98d9e8e7-f47b-4f38-8b87-7dc9706b6c30"}}, "outputs": {"output": {"id": "c2ebd14675ce2289", "src": "hda", "uuid": "11823e5b-61db-4d8b-9dc0-7660c973cd70"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": null, "job_stderr": null, "stdout": "", "stderr": "", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_winner/poretools_winner/0.6.1a1.0, exit_code: None, stderr: .", "Job in error state.. tool_id: 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"toolshed.g2.bx.psu.edu/repos/iuc/poretools_winner/poretools_winner/0.6.1a1.0", "state": "ok", "exit_code": 0, "create_time": "2025-01-02T06:57:46.650897", "update_time": "2025-01-02T06:58:00.737534", "galaxy_version": "24.1", "external_id": "gxy-gx7hw", "handler": null, "job_runner_name": null, "command_line": "poretools winner --type best '/galaxy/server/database/objects/1/f/d/dataset_1fd07ee9-4ab5-42a1-af9e-2cbd836a2e26.dat' > '/galaxy/server/database/objects/e/5/1/dataset_e519f0ab-c66e-4f41-9964-ba1244f699a6.dat'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "type": "\"best\""}, "inputs": {"input": {"id": "fab6cb90ff6a0960", "src": "hda", "uuid": "1fd07ee9-4ab5-42a1-af9e-2cbd836a2e26"}}, "outputs": {"output": {"id": "96722cfa8e7f5f50", "src": "hda", "uuid": "e519f0ab-c66e-4f41-9964-ba1244f699a6"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2025-01-02 06:57:49", "plugin": "core", "name": "end_epoch", "raw_value": "1735801069.0000000"}, {"title": "Job Start Time", "value": "2025-01-02 06:57:48", "plugin": "core", "name": "start_epoch", "raw_value": "1735801068.0000000"}, {"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": "qualimap_multi_bamqc/2.3+galaxy0-0", "has_data": true, "data": {"tool_id": "qualimap_multi_bamqc", "tool_version": "2.3+galaxy0", "test_index": 0, "time_seconds": 108.7659981250763, "inputs": {"input|bam_qc_data_0|bam_qc_input": {"src": "hdca", "id": "b05369fb76ed1035"}, "input|bam_qc_data_1|bam_qc_input": {"src": "hdca", "id": "14b55797034a16ee"}, "input|mode": "individual"}, "job": {"model_class": "Job", "id": "004fc63303625c27", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/qualimap_multi_bamqc/qualimap_multi_bamqc/2.3+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2025-01-02T07:07:43.949436", "update_time": "2025-01-02T07:08:38.797956", "galaxy_version": "24.1", "external_id": "gxy-984qm", "handler": null, "job_runner_name": null, "command_line": "printf '%s\\tbam_qc_data%d\\t%d\\n' 'Unnamed_Collection' '0' '0' >> data_spec.txt && mkdir -p bam_qc_data0/raw_data_qualimapReport && ln -s '/galaxy/server/database/objects/8/1/c/dataset_81c5c614-0abe-40c4-89e2-a3aa9620d095.dat' 'bam_qc_data0/genome_results.txt' && ln -s '/galaxy/server/database/objects/6/9/f/dataset_69ff6db3-fcd5-4314-8846-99e5aa001c94.dat' 'bam_qc_data0/raw_data_qualimapReport/coverage_across_reference.txt' && ln -s '/galaxy/server/database/objects/5/f/8/dataset_5f8da3c0-d406-48dc-8785-03ef9c2f0b66.dat' 'bam_qc_data0/raw_data_qualimapReport/coverage_histogram.txt' && ln -s '/galaxy/server/database/objects/f/c/d/dataset_fcd338dc-e83c-433b-a529-a0757ff27abf.dat' 'bam_qc_data0/raw_data_qualimapReport/genome_fraction_coverage.txt' && ln -s '/galaxy/server/database/objects/5/4/5/dataset_54590bfb-1bbd-4dee-be9d-97024e057bdb.dat' 'bam_qc_data0/raw_data_qualimapReport/duplication_rate_histogram.txt' && ln -s '/galaxy/server/database/objects/d/a/9/dataset_da94644f-45d6-4285-a568-a3e336d5ded0.dat' 'bam_qc_data0/raw_data_qualimapReport/mapped_reads_clipping_profile.txt' && ln -s '/galaxy/server/database/objects/0/d/b/dataset_0dbb067f-2411-468b-9a68-9c46d29ff28f.dat' 'bam_qc_data0/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt' && ln -s '/galaxy/server/database/objects/3/4/5/dataset_345d4078-4660-4222-823f-f1a55a93991f.dat' 'bam_qc_data0/raw_data_qualimapReport/mapped_reads_nucleotide_content.txt' && ln -s '/galaxy/server/database/objects/a/8/3/dataset_a83d635c-0ece-4542-ab11-038b32bf52c2.dat' 'bam_qc_data0/raw_data_qualimapReport/mapping_quality_across_reference.txt' && ln -s '/galaxy/server/database/objects/7/1/5/dataset_715548e6-5785-4f38-9894-3ac3f77b2607.dat' 'bam_qc_data0/raw_data_qualimapReport/mapping_quality_histogram.txt' && printf '%s\\tbam_qc_data%d\\t%d\\n' 'Unnamed_Collection' '1' '1' >> data_spec.txt && mkdir -p bam_qc_data1/raw_data_qualimapReport && ln -s '/galaxy/server/database/objects/8/1/c/dataset_81c5c614-0abe-40c4-89e2-a3aa9620d095.dat' 'bam_qc_data1/genome_results.txt' && ln -s '/galaxy/server/database/objects/6/9/f/dataset_69ff6db3-fcd5-4314-8846-99e5aa001c94.dat' 'bam_qc_data1/raw_data_qualimapReport/coverage_across_reference.txt' && ln -s '/galaxy/server/database/objects/5/f/8/dataset_5f8da3c0-d406-48dc-8785-03ef9c2f0b66.dat' 'bam_qc_data1/raw_data_qualimapReport/coverage_histogram.txt' && ln -s '/galaxy/server/database/objects/f/c/d/dataset_fcd338dc-e83c-433b-a529-a0757ff27abf.dat' 'bam_qc_data1/raw_data_qualimapReport/genome_fraction_coverage.txt' && ln -s '/galaxy/server/database/objects/5/4/5/dataset_54590bfb-1bbd-4dee-be9d-97024e057bdb.dat' 'bam_qc_data1/raw_data_qualimapReport/duplication_rate_histogram.txt' && ln -s '/galaxy/server/database/objects/d/a/9/dataset_da94644f-45d6-4285-a568-a3e336d5ded0.dat' 'bam_qc_data1/raw_data_qualimapReport/mapped_reads_clipping_profile.txt' && ln -s '/galaxy/server/database/objects/0/d/b/dataset_0dbb067f-2411-468b-9a68-9c46d29ff28f.dat' 'bam_qc_data1/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt' && ln -s '/galaxy/server/database/objects/3/4/5/dataset_345d4078-4660-4222-823f-f1a55a93991f.dat' 'bam_qc_data1/raw_data_qualimapReport/mapped_reads_nucleotide_content.txt' && ln -s '/galaxy/server/database/objects/a/8/3/dataset_a83d635c-0ece-4542-ab11-038b32bf52c2.dat' 'bam_qc_data1/raw_data_qualimapReport/mapping_quality_across_reference.txt' && ln -s '/galaxy/server/database/objects/7/1/5/dataset_715548e6-5785-4f38-9894-3ac3f77b2607.dat' 'bam_qc_data1/raw_data_qualimapReport/mapping_quality_histogram.txt' && export JAVA_OPTS=\"-Djava.awt.headless=true -Xmx${GALAXY_MEMORY_MB:-1024}m\" && qualimap multi-bamqc --data data_spec.txt -outdir results -outformat html && sed 's|images_multisampleBamQcReport/||g;s|css/||g' results/multisampleBamQcReport.html > '/galaxy/server/database/objects/d/d/f/dataset_ddf76edc-dc21-4cf1-9972-e4f3c9c82072.dat' && mkdir '/galaxy/server/database/objects/d/d/f/dataset_ddf76edc-dc21-4cf1-9972-e4f3c9c82072_files' && mv results/css/*.css '/galaxy/server/database/objects/d/d/f/dataset_ddf76edc-dc21-4cf1-9972-e4f3c9c82072_files' && mv results/css/*.png '/galaxy/server/database/objects/d/d/f/dataset_ddf76edc-dc21-4cf1-9972-e4f3c9c82072_files' && if [ -d results/images_multisampleBamQcReport ]; then mv results/images_multisampleBamQcReport/* '/galaxy/server/database/objects/d/d/f/dataset_ddf76edc-dc21-4cf1-9972-e4f3c9c82072_files' && for file in $(ls -A results/raw_data_multisampleBamQcReport); do mv \"results/raw_data_multisampleBamQcReport/$file\" `echo \"results/$file\" | sed 's/(//;s/)//'`; done fi", "user_email": "tests@fake.org", "command_version": "2.3", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "input": "{\"__current_case__\": 0, \"bam_qc_data\": [{\"__index__\": 0, \"bam_qc_input\": {\"values\": [{\"id\": 32, \"src\": \"hdca\"}]}, \"sample_name\": null}, {\"__index__\": 1, \"bam_qc_input\": {\"values\": [{\"id\": 33, \"src\": \"hdca\"}]}, \"sample_name\": null}], \"mode\": \"individual\"}"}, "inputs": {"input|bam_qc_data_0|bam_qc_input1": {"id": "151e7c15b36f3fcc", "src": "hda", "uuid": "81c5c614-0abe-40c4-89e2-a3aa9620d095"}, "input|bam_qc_data_0|bam_qc_input2": {"id": "fe89dd5dd5f6d05a", "src": "hda", "uuid": "69ff6db3-fcd5-4314-8846-99e5aa001c94"}, "input|bam_qc_data_0|bam_qc_input3": {"id": "0fbb29ada91f1ed6", "src": "hda", "uuid": "5f8da3c0-d406-48dc-8785-03ef9c2f0b66"}, "input|bam_qc_data_0|bam_qc_input4": {"id": "ae1f53e2d55347a6", "src": "hda", "uuid": "fcd338dc-e83c-433b-a529-a0757ff27abf"}, "input|bam_qc_data_0|bam_qc_input5": {"id": "7b16b58549ce6ce8", "src": "hda", "uuid": "54590bfb-1bbd-4dee-be9d-97024e057bdb"}, "input|bam_qc_data_0|bam_qc_input6": {"id": "e65c1f732e51c060", "src": "hda", "uuid": "da94644f-45d6-4285-a568-a3e336d5ded0"}, "input|bam_qc_data_0|bam_qc_input7": {"id": "2661a54b91fc578a", "src": "hda", "uuid": "0dbb067f-2411-468b-9a68-9c46d29ff28f"}, "input|bam_qc_data_0|bam_qc_input8": {"id": "5412f832fa402412", "src": "hda", "uuid": "345d4078-4660-4222-823f-f1a55a93991f"}, "input|bam_qc_data_0|bam_qc_input9": {"id": "f23509e5c74c32af", "src": "hda", "uuid": "a83d635c-0ece-4542-ab11-038b32bf52c2"}, "input|bam_qc_data_0|bam_qc_input10": {"id": "b5b5b391681960d4", "src": "hda", "uuid": "715548e6-5785-4f38-9894-3ac3f77b2607"}, "input|bam_qc_data_1|bam_qc_input1": {"id": "151e7c15b36f3fcc", "src": "hda", "uuid": "81c5c614-0abe-40c4-89e2-a3aa9620d095"}, "input|bam_qc_data_1|bam_qc_input2": {"id": "fe89dd5dd5f6d05a", "src": "hda", "uuid": "69ff6db3-fcd5-4314-8846-99e5aa001c94"}, "input|bam_qc_data_1|bam_qc_input3": {"id": "0fbb29ada91f1ed6", "src": "hda", "uuid": "5f8da3c0-d406-48dc-8785-03ef9c2f0b66"}, "input|bam_qc_data_1|bam_qc_input4": {"id": "ae1f53e2d55347a6", "src": "hda", "uuid": "fcd338dc-e83c-433b-a529-a0757ff27abf"}, "input|bam_qc_data_1|bam_qc_input5": {"id": "7b16b58549ce6ce8", "src": "hda", "uuid": "54590bfb-1bbd-4dee-be9d-97024e057bdb"}, "input|bam_qc_data_1|bam_qc_input6": {"id": "e65c1f732e51c060", "src": "hda", "uuid": "da94644f-45d6-4285-a568-a3e336d5ded0"}, "input|bam_qc_data_1|bam_qc_input7": {"id": "2661a54b91fc578a", "src": "hda", "uuid": "0dbb067f-2411-468b-9a68-9c46d29ff28f"}, "input|bam_qc_data_1|bam_qc_input8": {"id": "5412f832fa402412", "src": "hda", "uuid": "345d4078-4660-4222-823f-f1a55a93991f"}, "input|bam_qc_data_1|bam_qc_input9": {"id": "f23509e5c74c32af", "src": "hda", "uuid": "a83d635c-0ece-4542-ab11-038b32bf52c2"}, "input|bam_qc_data_1|bam_qc_input10": {"id": "b5b5b391681960d4", "src": "hda", "uuid": "715548e6-5785-4f38-9894-3ac3f77b2607"}}, "outputs": {"output_html": {"id": "c7b13a91a66a40a3", "src": "hda", "uuid": "ddf76edc-dc21-4cf1-9972-e4f3c9c82072"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Java memory size is set to 1200M\nLaunching application...\n\ndetected environment java options -Djava.awt.headless=true -Xmx4080m\nQualiMap v.2.3\nBuilt on 2023-05-19 16:57\n\nSelected tool: multi-bamqc\nRunning multi-sample BAM QC\n\nChecking input paths\nLoading sample data\nCreating charts\n\nPreparing result report\nWriting HTML report...\nHTML report created successfully\n\nFinished\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "Java memory size is set to 1200M\nLaunching application...\n\ndetected environment java options -Djava.awt.headless=true -Xmx4080m\nQualiMap v.2.3\nBuilt on 2023-05-19 16:57\n\nSelected tool: multi-bamqc\nRunning multi-sample BAM QC\n\nChecking input paths\nLoading sample data\nCreating charts\n\nPreparing result report\nWriting HTML report...\nHTML report created successfully\n\nFinished\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "3 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "3.0000000"}, {"title": "Job End Time", "value": "2025-01-02 07:08:17", "plugin": "core", "name": "end_epoch", "raw_value": "1735801697.0000000"}, {"title": "Job Start Time", "value": "2025-01-02 07:08:14", "plugin": "core", "name": "start_epoch", "raw_value": "1735801694.0000000"}, {"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": "raceid_trajectory/0.2.3+galaxy3-0", "has_data": true, "data": {"tool_id": "raceid_trajectory", "tool_version": "0.2.3+galaxy3", "test_index": 0, "time_seconds": 63.31807732582092, "inputs": {"inputrds": {"src": "hda", "id": "0572c791ef6f2a4a"}}, "job": {"model_class": "Job", "id": "b378df587ddbec27", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/raceid_trajectory/raceid_trajectory/0.2.3+galaxy3", "state": "ok", "exit_code": 0, "create_time": "2025-01-02T07:13:44.335347", "update_time": "2025-01-02T07:14:25.956048", "galaxy_version": "24.1", "external_id": "gxy-xbzpc", "handler": null, "job_runner_name": null, "command_line": "Rscript '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/raceid_trajectory/2af7c5086a96/raceid_trajectory/scripts/pseudotemporal.R' '/galaxy/server/database/jobs_directory/000/199/configs/tmpm2gc8lqm' 2> 'XXXX'", "user_email": "tests@fake.org", "command_version": "0.1", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "use_log": "false", "compscore": "{\"nn\": \"1\", \"scthr\": \"0.0\"}", "plotgraph": "{\"scthr\": \"0.0\", \"showcells\": false, \"use\": {\"__current_case__\": 0, \"def\": \"yes\"}}", "comppval": "{\"pthr\": \"0.01\", \"sensitive\": false}", "projback": "{\"pdishuf\": \"2000\", \"use\": {\"__current_case__\": 0, \"def\": \"yes\"}}", "projcell": "{\"cthr\": \"5\", \"knn\": \"3\", \"use\": {\"__current_case__\": 0, \"def\": \"yes\"}}"}, "inputs": {"inputrds": {"id": "0572c791ef6f2a4a", "src": "hda", "uuid": "9a7eaeea-598f-4115-8408-b22e40cfe7ae"}}, "outputs": {"outpdf": {"id": "05af15a29458f6b6", "src": "hda", "uuid": "964ae84e-18cc-4847-9d7d-772130f1ce7d"}, "outrdat": {"id": "3dd41b1a5f63dc03", "src": "hda", "uuid": "eb428b55-6db0-4c14-8e5f-1fa271c6ab87"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Building tree: 1 \rBuilding tree: 2 \rBuilding tree: 3 \rBuilding tree: 4 \rBuilding tree: 5 \rBuilding tree: 6 \rBuilding tree: 7 \rBuilding tree: 8 \rBuilding tree: 9 \rBuilding tree: 10 \rBuilding tree: 11 \rBuilding tree: 12 \rBuilding tree: 13 \rBuilding tree: 14 \rBuilding tree: 15 \rBuilding tree: 16 \rBuilding tree: 17 \rBuilding tree: 18 \rBuilding tree: 19 \rBuilding tree: 20 \rBuilding tree: 21 \rBuilding tree: 22 \rBuilding tree: 23 \rBuilding tree: 24 \rBuilding tree: 25 \rBuilding tree: 26 \rBuilding tree: 27 \rBuilding tree: 28 \rBuilding tree: 29 \rBuilding tree: 30 \rBuilding tree: 31 \rBuilding tree: 32 \rBuilding tree: 33 \rBuilding tree: 34 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"false", "prim_key_cond": "{\"__current_case__\": 1, \"prim_key_select\": \"-n\"}"}, "inputs": {"input1": {"id": "fef920eed3b2bb9a", "src": "hda", "uuid": "e792e6e4-5ed2-416c-aaab-d861868aed0a"}}, "outputs": {"output1": {"id": "d4ba988d8114743a", "src": "hda", "uuid": "c2b9dc41-abd0-4bc4-9fac-4366a7c6a6c7"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2025-01-02 07:12:25", "plugin": "core", "name": "end_epoch", "raw_value": "1735801945.0000000"}, {"title": "Job Start Time", "value": "2025-01-02 07:12:25", "plugin": "core", "name": "start_epoch", "raw_value": "1735801945.0000000"}, {"title": "Memory Allocated (MB)", "value": "10737", "plugin": "core", "name": 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$addthreads -m $addmemory\"M\" -M -O bam -T \"${TMPDIR:-.}\" '/galaxy/server/database/objects/0/b/8/dataset_0b858c9c-ab87-44d4-905f-cb9a9e5b7b03.dat' > '/galaxy/server/database/objects/0/1/9/dataset_019f1a72-1e29-4871-968a-ff6e0ac58556.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.20 (using htslib 1.20)", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "minhash": "true", "prim_key_cond": "{\"__current_case__\": 0, \"prim_key_select\": \"\"}"}, "inputs": {"input1": {"id": "8512113d23d65e82", "src": "hda", "uuid": "0b858c9c-ab87-44d4-905f-cb9a9e5b7b03"}}, "outputs": {"output1": {"id": "f0ebfcddbd4eac17", "src": "hda", "uuid": "019f1a72-1e29-4871-968a-ff6e0ac58556"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": 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"scanpy_find_variable_genes/1.9.3+galaxy1-0", "has_data": true, "data": {"tool_id": "scanpy_find_variable_genes", "tool_version": "1.9.3+galaxy1", "test_index": 0, "time_seconds": 0.09946417808532715, "execution_problem": "Input staging problem: Test input file (normalise_data.h5) cannot be found.", "status": "error"}}, {"id": "scanpy_find_variable_genes/1.9.3+galaxy1-1", "has_data": true, "data": {"tool_id": "scanpy_find_variable_genes", "tool_version": "1.9.3+galaxy1", "test_index": 1, "time_seconds": 0.05225324630737305, "execution_problem": "Input staging problem: Test input file (normalise_data.h5) cannot be found.", "status": "error"}}, {"id": "scanpy_find_variable_genes/1.9.3+galaxy1-1", "has_data": true, "data": {"tool_id": "scanpy_find_variable_genes", "tool_version": "1.9.3+galaxy1", "test_index": 1, "time_seconds": 0.053173065185546875, "execution_problem": "Input staging problem: Test input file (normalise_data.h5) cannot be found.", "status": "error"}}, {"id": "scanpy_find_variable_genes/1.9.3+galaxy1-2", "has_data": true, "data": {"tool_id": "scanpy_find_variable_genes", "tool_version": "1.9.3+galaxy1", "test_index": 2, "time_seconds": 0.053546905517578125, "execution_problem": "Input staging problem: Test input file (normalise_data.h5) cannot be found.", "status": "error"}}, {"id": "scanpy_find_variable_genes/1.9.3+galaxy1-2", "has_data": true, "data": {"tool_id": "scanpy_find_variable_genes", "tool_version": "1.9.3+galaxy1", "test_index": 2, "time_seconds": 0.054247379302978516, "execution_problem": "Input staging problem: Test input file (normalise_data.h5) cannot be found.", "status": "error"}}, {"id": "scanpy_inspect/1.9.6+galaxy4-0", "has_data": true, "data": {"tool_id": "scanpy_inspect", "tool_version": "1.9.6+galaxy4", "test_index": 0, "time_seconds": 82.5081512928009, "inputs": {"adata": {"src": "hda", "id": "6668614524935375"}, "method|expr_type": "counts", "method|var_type": "genes", "method|qc_vars": "mito,negative", "method|percent_top": "", "method|method": "pp.calculate_qc_metrics", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "31e4f64964b79803", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.9.6+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2025-01-02T07:18:18.485341", "update_time": "2025-01-02T07:19:20.211038", "galaxy_version": "24.1", "external_id": "gxy-b2rrz", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/3/e/6/dataset_3e669c40-482a-4bbc-b0e7-81da6d669e0d.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/211/configs/tmpfjn8k05d' > '/galaxy/server/database/objects/2/a/4/dataset_2a4b5df8-d931-418b-8a27-76ca72562a48.dat' && python '/galaxy/server/database/jobs_directory/000/211/configs/tmpfjn8k05d' >> '/galaxy/server/database/objects/2/a/4/dataset_2a4b5df8-d931-418b-8a27-76ca72562a48.dat' && ls . >> '/galaxy/server/database/objects/2/a/4/dataset_2a4b5df8-d931-418b-8a27-76ca72562a48.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.9.6", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 0, \"expr_type\": \"counts\", \"method\": \"pp.calculate_qc_metrics\", \"percent_top\": \"\", \"qc_vars\": \"mito,negative\", \"var_type\": \"genes\"}"}, "inputs": {"adata": {"id": "6668614524935375", "src": "hda", "uuid": "3e669c40-482a-4bbc-b0e7-81da6d669e0d"}}, "outputs": {"hidden_output": {"id": "2d51f2fa00833d10", "src": "hda", "uuid": "2a4b5df8-d931-418b-8a27-76ca72562a48"}, "anndata_out": {"id": "264f5edb3170a95d", "src": "hda", "uuid": "5217ef16-5f46-4432-a7c4-0f788ac4524b"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "[n_obs \u00d7 n_vars]\n- 1000 \u00d7 1000\n[obs]\n- n_genes_by_counts\n- log1p_n_genes_by_counts\n- total_counts\n- log1p_total_counts\n- pct_counts_in_top_50_genes\n- pct_counts_in_top_100_genes\n- pct_counts_in_top_200_genes\n- pct_counts_in_top_500_genes\n- total_counts_mito\n- log1p_total_counts_mito\n- pct_counts_mito\n- total_counts_negative\n- log1p_total_counts_negative\n- pct_counts_negative\n[var]\n- mito\n- negative\n- n_cells_by_counts\n- mean_counts\n- log1p_mean_counts\n- pct_dropout_by_counts\n- total_counts\n- log1p_total_counts\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "[n_obs \u00d7 n_vars]\n- 1000 \u00d7 1000\n[obs]\n- n_genes_by_counts\n- log1p_n_genes_by_counts\n- total_counts\n- log1p_total_counts\n- pct_counts_in_top_50_genes\n- pct_counts_in_top_100_genes\n- pct_counts_in_top_200_genes\n- pct_counts_in_top_500_genes\n- total_counts_mito\n- log1p_total_counts_mito\n- pct_counts_mito\n- total_counts_negative\n- log1p_total_counts_negative\n- pct_counts_negative\n[var]\n- mito\n- negative\n- n_cells_by_counts\n- mean_counts\n- log1p_mean_counts\n- pct_dropout_by_counts\n- total_counts\n- log1p_total_counts\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "16 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "16.0000000"}, {"title": "Job End Time", "value": "2025-01-02 07:18:59", "plugin": "core", "name": "end_epoch", "raw_value": "1735802339.0000000"}, {"title": "Job Start Time", "value": "2025-01-02 07:18:43", "plugin": "core", "name": "start_epoch", "raw_value": "1735802323.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "output_problems": ["Output anndata_out: Test output file (pp.calculate_qc_metrics.sparce_csr_matrix.h5ad) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "scanpy_inspect/1.9.6+galaxy4-1", "has_data": true, "data": {"tool_id": "scanpy_inspect", "tool_version": "1.9.6+galaxy4", "test_index": 1, "time_seconds": 47.76577091217041, "inputs": {"adata": {"src": "hda", "id": "35993369f130fd6d"}, "method|n_neighbors": "15", "method|knn": true, "method|random_state": "0", "method|pp_neighbors_method": "umap", "method|metric": "euclidean", "method|method": "pp.neighbors", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "4ed835abe2c77037", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.9.6+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2025-01-02T07:19:41.395919", "update_time": "2025-01-02T07:20:07.932343", "galaxy_version": "24.1", "external_id": "gxy-dcpx5", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/3/8/a/dataset_38abefd0-29fe-4065-ab67-86d80784cadf.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/213/configs/tmp2clwma6f' > '/galaxy/server/database/objects/2/0/a/dataset_20aadca0-2e2b-4b7f-82b1-9a205f5c25d5.dat' && python '/galaxy/server/database/jobs_directory/000/213/configs/tmp2clwma6f' >> '/galaxy/server/database/objects/2/0/a/dataset_20aadca0-2e2b-4b7f-82b1-9a205f5c25d5.dat' && ls . >> '/galaxy/server/database/objects/2/0/a/dataset_20aadca0-2e2b-4b7f-82b1-9a205f5c25d5.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.9.6", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 1, \"knn\": true, \"method\": \"pp.neighbors\", \"metric\": \"euclidean\", \"n_neighbors\": \"15\", \"n_pcs\": \"\", \"pp_neighbors_method\": \"umap\", \"random_state\": \"0\", \"use_rep\": \"\"}"}, "inputs": {"adata": {"id": "35993369f130fd6d", "src": "hda", "uuid": "38abefd0-29fe-4065-ab67-86d80784cadf"}}, "outputs": {"hidden_output": {"id": "444b3d9caa993193", "src": "hda", "uuid": "20aadca0-2e2b-4b7f-82b1-9a205f5c25d5"}, "anndata_out": {"id": "6f0260484d355357", "src": "hda", "uuid": "a4d4ab3b-61ee-48ef-b085-2982c3084f38"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "[n_obs \u00d7 n_vars]\n- 100 \u00d7 1592\n[obs]\n- paul15_clusters\n[uns]\n- iroot\n- neighbors\n[obsm]\n- X_pca\n[obsp]\n- distances\n- connectivities\n", "tool_stderr": "WARNING: Root cell index [840] does not exist for 100 samples. It\u2019s ignored.\n", "job_stdout": "", "job_stderr": "", "stdout": "[n_obs \u00d7 n_vars]\n- 100 \u00d7 1592\n[obs]\n- paul15_clusters\n[uns]\n- iroot\n- neighbors\n[obsm]\n- X_pca\n[obsp]\n- distances\n- connectivities\n", "stderr": "WARNING: Root cell index [840] does not exist for 100 samples. It\u2019s ignored.\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "14 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "14.0000000"}, {"title": "Job End Time", "value": "2025-01-02 07:19:57", "plugin": "core", "name": "end_epoch", "raw_value": "1735802397.0000000"}, {"title": "Job Start Time", "value": "2025-01-02 07:19:43", "plugin": "core", "name": "start_epoch", "raw_value": "1735802383.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "scanpy_inspect/1.9.6+galaxy4-10", "has_data": true, "data": {"tool_id": "scanpy_inspect", "tool_version": "1.9.6+galaxy4", "test_index": 10, "time_seconds": 11.271416902542114, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "scanpy_inspect/1.9.6+galaxy4-11", "has_data": true, "data": {"tool_id": "scanpy_inspect", "tool_version": "1.9.6+galaxy4", "test_index": 11, "time_seconds": 36.48307514190674, "inputs": {"adata": {"src": "hda", "id": "8f1d8f88e0074a9b"}, "method|method": "pp.sqrt", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "1acd2e68eecded0a", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.9.6+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2025-01-02T07:24:51.983933", "update_time": "2025-01-02T07:25:09.103341", "galaxy_version": "24.1", "external_id": "gxy-ks2zq", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/d/3/6/dataset_d36b1908-7426-4b52-82ec-66a111fce543.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/230/configs/tmpntu3ch55' > '/galaxy/server/database/objects/8/6/9/dataset_869bc2f5-3ed4-4b85-89f8-a1514536ad2d.dat' && python '/galaxy/server/database/jobs_directory/000/230/configs/tmpntu3ch55' >> '/galaxy/server/database/objects/8/6/9/dataset_869bc2f5-3ed4-4b85-89f8-a1514536ad2d.dat' && ls . >> '/galaxy/server/database/objects/8/6/9/dataset_869bc2f5-3ed4-4b85-89f8-a1514536ad2d.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.9.6", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 7, \"method\": \"pp.sqrt\"}"}, "inputs": {"adata": {"id": "8f1d8f88e0074a9b", "src": "hda", "uuid": "d36b1908-7426-4b52-82ec-66a111fce543"}}, "outputs": {"hidden_output": {"id": "5fdf8e6d9841b46b", "src": "hda", "uuid": "869bc2f5-3ed4-4b85-89f8-a1514536ad2d"}, "anndata_out": {"id": "e55abe26d1fe37a4", "src": "hda", "uuid": "0776266a-9e48-4730-9d5f-623529de6604"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "[n_obs \u00d7 n_vars]\n- 640 \u00d7 11\n[obs]\n- cell_type\n[uns]\n- cell_type_colors\n- highlights\n- iroot\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "[n_obs \u00d7 n_vars]\n- 640 \u00d7 11\n[obs]\n- cell_type\n[uns]\n- cell_type_colors\n- highlights\n- iroot\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "4 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "4.0000000"}, {"title": "Job End Time", "value": "2025-01-02 07:24:58", "plugin": "core", "name": "end_epoch", "raw_value": "1735802698.0000000"}, {"title": "Job Start Time", "value": "2025-01-02 07:24:54", "plugin": "core", "name": "start_epoch", "raw_value": "1735802694.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "output_problems": ["Output anndata_out: Test output file (pp.sqrt.krumsiek11.h5ad) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "scanpy_inspect/1.9.6+galaxy4-12", "has_data": true, "data": {"tool_id": "scanpy_inspect", "tool_version": "1.9.6+galaxy4", "test_index": 12, "time_seconds": 48.61503267288208, "inputs": {"adata": {"src": "hda", "id": "39f05b2acc71e5fa"}, "method|expr_type": "counts", "method|var_type": "genes", "method|qc_vars": "mito,negative", "method|percent_top": "50,100,200,300", "method|method": "pp.calculate_qc_metrics", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "fe89dd5dd5f6d05a", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.9.6+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2025-01-02T07:25:28.406051", "update_time": "2025-01-02T07:25:57.646728", "galaxy_version": "24.1", "external_id": "gxy-c488k", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/6/6/7/dataset_6675120a-7d97-4687-a357-fcc364dcd09e.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/232/configs/tmpy_ocsn0z' > '/galaxy/server/database/objects/c/f/e/dataset_cfe7c85a-116e-4e01-9add-ca7dec75c7a0.dat' && python '/galaxy/server/database/jobs_directory/000/232/configs/tmpy_ocsn0z' >> '/galaxy/server/database/objects/c/f/e/dataset_cfe7c85a-116e-4e01-9add-ca7dec75c7a0.dat' && ls . >> '/galaxy/server/database/objects/c/f/e/dataset_cfe7c85a-116e-4e01-9add-ca7dec75c7a0.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.9.6", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 0, \"expr_type\": \"counts\", \"method\": \"pp.calculate_qc_metrics\", \"percent_top\": \"50,100,200,300\", \"qc_vars\": \"mito,negative\", \"var_type\": \"genes\"}"}, "inputs": {"adata": {"id": "39f05b2acc71e5fa", "src": "hda", "uuid": "6675120a-7d97-4687-a357-fcc364dcd09e"}}, "outputs": {"hidden_output": {"id": "6e5bf1e4a2b4fba8", "src": "hda", "uuid": "cfe7c85a-116e-4e01-9add-ca7dec75c7a0"}, "anndata_out": {"id": "fbc817b027150850", "src": "hda", "uuid": "e8f92fbd-ef77-4bb7-96a3-505da84c79db"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "[n_obs \u00d7 n_vars]\n- 1000 \u00d7 1000\n[obs]\n- n_genes_by_counts\n- log1p_n_genes_by_counts\n- total_counts\n- log1p_total_counts\n- pct_counts_in_top_50_genes\n- pct_counts_in_top_100_genes\n- pct_counts_in_top_200_genes\n- pct_counts_in_top_300_genes\n- total_counts_mito\n- log1p_total_counts_mito\n- pct_counts_mito\n- total_counts_negative\n- log1p_total_counts_negative\n- pct_counts_negative\n[var]\n- mito\n- negative\n- n_cells_by_counts\n- mean_counts\n- log1p_mean_counts\n- pct_dropout_by_counts\n- total_counts\n- log1p_total_counts\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "[n_obs \u00d7 n_vars]\n- 1000 \u00d7 1000\n[obs]\n- n_genes_by_counts\n- log1p_n_genes_by_counts\n- total_counts\n- log1p_total_counts\n- pct_counts_in_top_50_genes\n- pct_counts_in_top_100_genes\n- pct_counts_in_top_200_genes\n- pct_counts_in_top_300_genes\n- total_counts_mito\n- log1p_total_counts_mito\n- pct_counts_mito\n- total_counts_negative\n- log1p_total_counts_negative\n- pct_counts_negative\n[var]\n- mito\n- negative\n- n_cells_by_counts\n- mean_counts\n- log1p_mean_counts\n- pct_dropout_by_counts\n- total_counts\n- log1p_total_counts\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "16 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "16.0000000"}, {"title": "Job End Time", "value": "2025-01-02 07:25:46", "plugin": "core", "name": "end_epoch", "raw_value": "1735802746.0000000"}, {"title": "Job Start Time", "value": "2025-01-02 07:25:30", "plugin": "core", "name": "start_epoch", "raw_value": "1735802730.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "output_problems": ["Output anndata_out: Test output file (pp.calculate_qc_metrics.sparce_csr_matrix.h5ad) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "scanpy_inspect/1.9.6+galaxy4-2", "has_data": true, "data": {"tool_id": "scanpy_inspect", "tool_version": "1.9.6+galaxy4", "test_index": 2, "time_seconds": 48.69956970214844, "inputs": {"adata": {"src": "hda", "id": "262f6eccc3a9efd0"}, "method|n_neighbors": "15", "method|knn": true, "method|pp_neighbors_method": "gauss", "method|metric": "braycurtis", "method|method": "pp.neighbors", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "ea1b54aa52fefd80", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.9.6+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2025-01-02T07:20:27.567269", "update_time": "2025-01-02T07:20:56.780138", "galaxy_version": "24.1", "external_id": "gxy-hljbs", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/1/f/7/dataset_1f791fd0-2080-4ae5-bd27-3fec357770dd.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/215/configs/tmp6svcpjtv' > '/galaxy/server/database/objects/5/0/d/dataset_50d449d0-ad62-47ed-931a-10cc9a167210.dat' && python '/galaxy/server/database/jobs_directory/000/215/configs/tmp6svcpjtv' >> '/galaxy/server/database/objects/5/0/d/dataset_50d449d0-ad62-47ed-931a-10cc9a167210.dat' && ls . >> '/galaxy/server/database/objects/5/0/d/dataset_50d449d0-ad62-47ed-931a-10cc9a167210.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.9.6", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 1, \"knn\": true, \"method\": \"pp.neighbors\", \"metric\": \"braycurtis\", \"n_neighbors\": \"15\", \"n_pcs\": \"\", \"pp_neighbors_method\": \"gauss\", \"random_state\": \"0\", \"use_rep\": \"\"}"}, "inputs": {"adata": {"id": "262f6eccc3a9efd0", "src": "hda", "uuid": "1f791fd0-2080-4ae5-bd27-3fec357770dd"}}, "outputs": {"hidden_output": {"id": "cee70782e38f3ef6", "src": "hda", "uuid": "50d449d0-ad62-47ed-931a-10cc9a167210"}, "anndata_out": {"id": "1ef0d1ec9ee673a8", "src": "hda", "uuid": "5f3b1531-8b84-4bc4-b097-dd9539e6fbb0"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "[n_obs \u00d7 n_vars]\n- 100 \u00d7 1592\n[obs]\n- paul15_clusters\n[uns]\n- iroot\n- neighbors\n[obsm]\n- X_pca\n[obsp]\n- distances\n- connectivities\n", "tool_stderr": "WARNING: Root cell index [840] does not exist for 100 samples. It\u2019s ignored.\n", "job_stdout": "", "job_stderr": "", "stdout": "[n_obs \u00d7 n_vars]\n- 100 \u00d7 1592\n[obs]\n- paul15_clusters\n[uns]\n- iroot\n- neighbors\n[obsm]\n- X_pca\n[obsp]\n- distances\n- connectivities\n", "stderr": "WARNING: Root cell index [840] does not exist for 100 samples. It\u2019s ignored.\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "16 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "16.0000000"}, {"title": "Job End Time", "value": "2025-01-02 07:20:45", "plugin": "core", "name": "end_epoch", "raw_value": "1735802445.0000000"}, {"title": "Job Start Time", "value": "2025-01-02 07:20:29", "plugin": "core", "name": "start_epoch", "raw_value": "1735802429.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "scanpy_inspect/1.9.6+galaxy4-3", "has_data": true, "data": {"tool_id": "scanpy_inspect", "tool_version": "1.9.6+galaxy4", "test_index": 3, "time_seconds": 36.07694745063782, "inputs": {"adata": {"src": "hda", "id": "99525d77e9098735"}, "method|gene_list": "Gata2, Fog1", "method|ctrl_size": "2", "method|n_bins": "2", "method|random_state": "2", "method|use_raw": false, "method|score_name": "score", "method|method": "tl.score_genes", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "ef3f8a672fc014e8", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.9.6+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2025-01-02T07:21:16.338076", "update_time": "2025-01-02T07:21:33.073541", "galaxy_version": "24.1", "external_id": "gxy-fqtd8", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/4/6/f/dataset_46f373bb-3d27-45b2-be6e-83a86f4bf959.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/217/configs/tmpcqy4fglb' > '/galaxy/server/database/objects/5/d/f/dataset_5dfa5ff4-d5ba-425c-a818-6e472977b7f6.dat' && python '/galaxy/server/database/jobs_directory/000/217/configs/tmpcqy4fglb' >> '/galaxy/server/database/objects/5/d/f/dataset_5dfa5ff4-d5ba-425c-a818-6e472977b7f6.dat' && ls . >> '/galaxy/server/database/objects/5/d/f/dataset_5dfa5ff4-d5ba-425c-a818-6e472977b7f6.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.9.6", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 2, \"ctrl_size\": \"2\", \"gene_list\": \"Gata2, Fog1\", \"gene_pool\": \"\", \"method\": \"tl.score_genes\", \"n_bins\": \"2\", \"random_state\": \"2\", \"score_name\": \"score\", \"use_raw\": false}"}, "inputs": {"adata": {"id": "99525d77e9098735", "src": "hda", "uuid": "46f373bb-3d27-45b2-be6e-83a86f4bf959"}}, "outputs": {"hidden_output": {"id": "62deb1b52b351d52", "src": "hda", "uuid": "5dfa5ff4-d5ba-425c-a818-6e472977b7f6"}, "anndata_out": {"id": "985cff68b895fef7", "src": "hda", "uuid": "84796e48-3dab-458c-8b27-d0d888821d49"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "[n_obs \u00d7 n_vars]\n- 640 \u00d7 11\n[obs]\n- cell_type\n- score\n[uns]\n- cell_type_colors\n- highlights\n- iroot\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "[n_obs \u00d7 n_vars]\n- 640 \u00d7 11\n[obs]\n- cell_type\n- score\n[uns]\n- cell_type_colors\n- highlights\n- iroot\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "5 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "5.0000000"}, {"title": "Job End Time", "value": "2025-01-02 07:21:22", "plugin": "core", "name": "end_epoch", "raw_value": "1735802482.0000000"}, {"title": "Job Start Time", "value": "2025-01-02 07:21:17", "plugin": "core", "name": "start_epoch", "raw_value": "1735802477.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "output_problems": ["Output anndata_out: Test output file (tl.score_genes.krumsiek11.h5ad) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "scanpy_inspect/1.9.6+galaxy4-4", "has_data": true, "data": {"tool_id": "scanpy_inspect", "tool_version": "1.9.6+galaxy4", "test_index": 4, "time_seconds": 37.05776071548462, "inputs": {"adata": {"src": "hda", "id": "20b0fc0ea1c4682a"}, "method|s_genes|text": "Gata2, Fog1, EgrNab", "method|s_genes|format": "text", "method|g2m_genes|text": "Gata2, Fog1, EgrNab", "method|g2m_genes|format": "text", "method|n_bins": "2", "method|random_state": "1", "method|use_raw": false, "method|method": "tl.score_genes_cell_cycle", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "c00e3dad3855ea32", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.9.6+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2025-01-02T07:21:53.420296", "update_time": "2025-01-02T07:22:10.307923", "galaxy_version": "24.1", "external_id": "gxy-w7nl9", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/d/d/0/dataset_dd0b280c-c859-4c6a-9fc6-0db949cac5f4.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/219/configs/tmp_iqj865r' > '/galaxy/server/database/objects/c/b/c/dataset_cbcb4c35-c4f4-43be-a97a-ade980b603f9.dat' && python '/galaxy/server/database/jobs_directory/000/219/configs/tmp_iqj865r' >> '/galaxy/server/database/objects/c/b/c/dataset_cbcb4c35-c4f4-43be-a97a-ade980b603f9.dat' && ls . >> '/galaxy/server/database/objects/c/b/c/dataset_cbcb4c35-c4f4-43be-a97a-ade980b603f9.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.9.6", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 3, \"g2m_genes\": {\"__current_case__\": 0, \"format\": \"text\", \"text\": \"Gata2, Fog1, EgrNab\"}, \"method\": \"tl.score_genes_cell_cycle\", \"n_bins\": \"2\", \"random_state\": \"1\", \"s_genes\": {\"__current_case__\": 0, \"format\": \"text\", \"text\": \"Gata2, Fog1, EgrNab\"}, \"use_raw\": false}"}, "inputs": {"adata": {"id": "20b0fc0ea1c4682a", "src": "hda", "uuid": "dd0b280c-c859-4c6a-9fc6-0db949cac5f4"}}, "outputs": {"hidden_output": {"id": "295a4a07b0c126d8", "src": "hda", "uuid": "cbcb4c35-c4f4-43be-a97a-ade980b603f9"}, "anndata_out": {"id": "414408a001dd2431", "src": "hda", "uuid": "6122f740-79b3-4882-9ac4-d117ed15e7ed"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "[n_obs \u00d7 n_vars]\n- 640 \u00d7 11\n[obs]\n- cell_type\n- S_score\n- G2M_score\n- phase\n[uns]\n- cell_type_colors\n- highlights\n- iroot\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "[n_obs \u00d7 n_vars]\n- 640 \u00d7 11\n[obs]\n- cell_type\n- S_score\n- G2M_score\n- phase\n[uns]\n- cell_type_colors\n- highlights\n- iroot\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "4 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "4.0000000"}, {"title": "Job End Time", "value": "2025-01-02 07:21:59", "plugin": "core", "name": "end_epoch", "raw_value": "1735802519.0000000"}, {"title": "Job Start Time", "value": "2025-01-02 07:21:55", "plugin": "core", "name": "start_epoch", "raw_value": "1735802515.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "output_problems": ["Output anndata_out: Test output file (tl.score_genes_cell_cycle.krumsiek11.h5ad) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "scanpy_inspect/1.9.6+galaxy4-5", "has_data": true, "data": {"tool_id": "scanpy_inspect", "tool_version": "1.9.6+galaxy4", "test_index": 5, "time_seconds": 36.817076444625854, "inputs": {"adata": {"src": "hda", "id": "af900f0a581f1633"}, "method|groupby": "cell_type", "method|use_raw": false, "method|ref|rest": "rest", "method|n_genes": "100", "method|tl_rank_genes_groups_method|corr_method": "benjamini-hochberg", "method|tl_rank_genes_groups_method|method": "t-test_overestim_var", "method|method": "tl.rank_genes_groups", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "0fe28ee9e6a3131f", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.9.6+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2025-01-02T07:22:29.818048", "update_time": "2025-01-02T07:22:46.902846", "galaxy_version": "24.1", "external_id": "gxy-t2q5s", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/7/5/8/dataset_758540aa-117f-4d7e-a112-4729e038bcd2.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/221/configs/tmpd26v5du4' > '/galaxy/server/database/objects/9/3/a/dataset_93af7a71-034b-45a0-b6cd-6db8e3566c70.dat' && python '/galaxy/server/database/jobs_directory/000/221/configs/tmpd26v5du4' >> '/galaxy/server/database/objects/9/3/a/dataset_93af7a71-034b-45a0-b6cd-6db8e3566c70.dat' && ls . >> '/galaxy/server/database/objects/9/3/a/dataset_93af7a71-034b-45a0-b6cd-6db8e3566c70.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.9.6", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 4, \"groupby\": \"cell_type\", \"groups\": \"\", \"method\": \"tl.rank_genes_groups\", \"n_genes\": \"100\", \"ref\": {\"__current_case__\": 0, \"rest\": \"rest\"}, \"tl_rank_genes_groups_method\": {\"__current_case__\": 2, \"corr_method\": \"benjamini-hochberg\", \"method\": \"t-test_overestim_var\"}, \"use_raw\": false}"}, "inputs": {"adata": {"id": "af900f0a581f1633", "src": "hda", "uuid": "758540aa-117f-4d7e-a112-4729e038bcd2"}}, "outputs": {"hidden_output": {"id": "712d1f62bce5560d", "src": "hda", "uuid": "93af7a71-034b-45a0-b6cd-6db8e3566c70"}, "anndata_out": {"id": "7256dd95abde87fe", "src": "hda", "uuid": "0e89e13d-7ac1-4328-a11e-470476999c1f"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "[n_obs \u00d7 n_vars]\n- 640 \u00d7 11\n[obs]\n- cell_type\n[uns]\n- cell_type_colors\n- highlights\n- iroot\n- rank_genes_groups\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "[n_obs \u00d7 n_vars]\n- 640 \u00d7 11\n[obs]\n- cell_type\n[uns]\n- cell_type_colors\n- highlights\n- iroot\n- rank_genes_groups\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "4 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "4.0000000"}, {"title": "Job End Time", "value": "2025-01-02 07:22:35", "plugin": "core", "name": "end_epoch", "raw_value": "1735802555.0000000"}, {"title": "Job Start Time", "value": "2025-01-02 07:22:31", "plugin": "core", "name": "start_epoch", "raw_value": "1735802551.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "scanpy_inspect/1.9.6+galaxy4-6", "has_data": true, "data": {"tool_id": "scanpy_inspect", "tool_version": "1.9.6+galaxy4", "test_index": 6, "time_seconds": 11.239217281341553, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "scanpy_inspect/1.9.6+galaxy4-7", "has_data": true, "data": {"tool_id": "scanpy_inspect", "tool_version": "1.9.6+galaxy4", "test_index": 7, "time_seconds": 10.273878812789917, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "scanpy_inspect/1.9.6+galaxy4-8", "has_data": true, "data": {"tool_id": "scanpy_inspect", "tool_version": "1.9.6+galaxy4", "test_index": 8, "time_seconds": 36.04260325431824, "inputs": {"adata": {"src": "hda", "id": "1c347d26c54e7ae1"}, "method|method": "pp.log1p", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "2ed2c73882801fa0", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.9.6+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2025-01-02T07:23:28.024391", "update_time": "2025-01-02T07:23:44.773023", "galaxy_version": "24.1", "external_id": "gxy-f98s2", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/c/8/4/dataset_c8498ad7-60f3-443b-96ed-58cb6bbf1af7.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/225/configs/tmporhnk63j' > '/galaxy/server/database/objects/f/5/e/dataset_f5e93e60-ffb5-456a-a92d-75842de7cd46.dat' && python '/galaxy/server/database/jobs_directory/000/225/configs/tmporhnk63j' >> '/galaxy/server/database/objects/f/5/e/dataset_f5e93e60-ffb5-456a-a92d-75842de7cd46.dat' && ls . >> '/galaxy/server/database/objects/f/5/e/dataset_f5e93e60-ffb5-456a-a92d-75842de7cd46.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.9.6", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 5, \"method\": \"pp.log1p\"}"}, "inputs": {"adata": {"id": "1c347d26c54e7ae1", "src": "hda", "uuid": "c8498ad7-60f3-443b-96ed-58cb6bbf1af7"}}, "outputs": {"hidden_output": {"id": "c1dd574506e972da", "src": "hda", "uuid": "f5e93e60-ffb5-456a-a92d-75842de7cd46"}, "anndata_out": {"id": "a7de184b0c25821a", "src": "hda", "uuid": "07eca9db-fb80-438e-a48a-89b09420710c"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "[n_obs \u00d7 n_vars]\n- 640 \u00d7 11\n[obs]\n- cell_type\n[uns]\n- cell_type_colors\n- highlights\n- iroot\n- log1p\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "[n_obs \u00d7 n_vars]\n- 640 \u00d7 11\n[obs]\n- cell_type\n[uns]\n- cell_type_colors\n- highlights\n- iroot\n- log1p\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "4 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "4.0000000"}, {"title": "Job End Time", "value": "2025-01-02 07:23:34", "plugin": "core", "name": "end_epoch", "raw_value": "1735802614.0000000"}, {"title": "Job Start Time", "value": "2025-01-02 07:23:30", "plugin": "core", "name": "start_epoch", "raw_value": "1735802610.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "output_problems": ["Output anndata_out: Test output file (pp.log1p.krumsiek11.h5ad) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "scanpy_inspect/1.9.6+galaxy4-9", "has_data": true, "data": {"tool_id": "scanpy_inspect", "tool_version": "1.9.6+galaxy4", "test_index": 9, "time_seconds": 36.36564517021179, "inputs": {"adata": {"src": "hda", "id": "ccf74b2c8407aa5c"}, "method|zero_center": true, "method|method": "pp.scale", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "8d7000811c7fd8fe", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.9.6+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2025-01-02T07:24:04.140925", "update_time": "2025-01-02T07:24:21.208813", "galaxy_version": "24.1", "external_id": "gxy-htkgz", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/0/7/2/dataset_072b50a4-2d26-4c38-8ec7-f39d3c8ddc2d.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/227/configs/tmp6_0bxlxu' > '/galaxy/server/database/objects/5/6/3/dataset_563afa32-ec87-412f-b664-0019b604ec2a.dat' && python '/galaxy/server/database/jobs_directory/000/227/configs/tmp6_0bxlxu' >> '/galaxy/server/database/objects/5/6/3/dataset_563afa32-ec87-412f-b664-0019b604ec2a.dat' && ls . >> '/galaxy/server/database/objects/5/6/3/dataset_563afa32-ec87-412f-b664-0019b604ec2a.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.9.6", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 6, \"max_value\": \"\", \"method\": \"pp.scale\", \"zero_center\": true}"}, "inputs": {"adata": {"id": "ccf74b2c8407aa5c", "src": "hda", "uuid": "072b50a4-2d26-4c38-8ec7-f39d3c8ddc2d"}}, "outputs": {"hidden_output": {"id": "6c77337fd108ecdc", "src": "hda", "uuid": "563afa32-ec87-412f-b664-0019b604ec2a"}, "anndata_out": {"id": "0dd8f072b892687a", "src": "hda", "uuid": "08ebff36-de9e-4c52-8389-ecc4c34bc47c"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "[n_obs \u00d7 n_vars]\n- 640 \u00d7 11\n[obs]\n- cell_type\n[var]\n- mean\n- std\n[uns]\n- cell_type_colors\n- highlights\n- iroot\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "[n_obs \u00d7 n_vars]\n- 640 \u00d7 11\n[obs]\n- cell_type\n[var]\n- mean\n- std\n[uns]\n- cell_type_colors\n- highlights\n- iroot\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "4 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "4.0000000"}, {"title": "Job End Time", "value": "2025-01-02 07:24:09", "plugin": "core", "name": "end_epoch", "raw_value": "1735802649.0000000"}, {"title": "Job Start Time", "value": "2025-01-02 07:24:05", "plugin": "core", "name": "start_epoch", "raw_value": "1735802645.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "output_problems": ["Output anndata_out: Test output file (pp.scale.krumsiek11.h5ad) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "snpfreqplot/1.0+galaxy3-0", "has_data": true, "data": {"tool_id": "snpfreqplot", "tool_version": "1.0+galaxy3", "test_index": 0, "time_seconds": 47.62605571746826, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "snpfreqplot/1.0+galaxy3-1", "has_data": true, "data": {"tool_id": "snpfreqplot", "tool_version": "1.0+galaxy3", "test_index": 1, "time_seconds": 117.8009786605835, "inputs": {"sinputs": [{"src": "hda", "id": "280fa2eca83c1bec"}, {"src": "hda", "id": "775e3054b987573e"}, {"src": "hda", "id": "f36c2a512a4db02e"}, {"src": "hda", "id": "2c6fcca736093d75"}, {"src": "hda", "id": "bedfeddc1deb2f42"}, {"src": "hda", "id": "7d87f315d43308bc"}, {"src": "hda", "id": "d7a4d8aabad046e1"}, {"src": "hda", "id": "ea3b6f64fe68f4dc"}, {"src": "hda", "id": "b8e9463a205e97b5"}], "advanced|color": "Set2"}, "job": {"model_class": "Job", "id": "4a67f711d60438e3", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3", "state": "ok", "exit_code": 0, "create_time": "2025-01-02T07:27:51.288154", "update_time": "2025-01-02T07:28:47.536163", "galaxy_version": "24.1", "external_id": "gxy-q76xw", "handler": null, "job_runner_name": null, "command_line": "cat '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/3d0adeee3f2b/snpfreqplot/helperFunctions.R' > /dev/null && cat '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/3d0adeee3f2b/snpfreqplot/snpEffExtract.R' > /dev/null && cat '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/3d0adeee3f2b/snpfreqplot/heatmap_for_variants.R' > /dev/null && echo \"output file: tmp_output.pdf\" && Rscript '/galaxy/server/database/jobs_directory/000/251/configs/tmprmvohide'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "clustering": "{\"__current_case__\": 1, \"do\": \"FALSE\"}", "advanced": "{\"color\": \"Set2\", \"output_type\": \"pdf\", \"ratio\": \"0.67\"}", "varfreq": "\"0.1\""}, "inputs": {"sinputs": {"id": "280fa2eca83c1bec", "src": "hda", "uuid": "73931800-ca7f-4a02-9e8b-647eb050f436"}, "sinputs1": {"id": "280fa2eca83c1bec", "src": "hda", "uuid": "73931800-ca7f-4a02-9e8b-647eb050f436"}, "sinputs2": {"id": "775e3054b987573e", "src": "hda", "uuid": "1ee46cc9-a6aa-4098-bc10-24dbd4efe1a1"}, "sinputs3": {"id": "f36c2a512a4db02e", "src": "hda", "uuid": "04fb439d-3359-4e59-8d1a-c622fe51c1b7"}, "sinputs4": {"id": "2c6fcca736093d75", "src": "hda", "uuid": "b7cbf068-74b9-4a0f-afae-ac2e86d783d4"}, "sinputs5": {"id": "bedfeddc1deb2f42", "src": "hda", "uuid": "56fe570c-cad4-42bb-b40c-3099f3b4e1ea"}, "sinputs6": {"id": "7d87f315d43308bc", 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:\n n too large, allowed maximum for palette Set2 is 8\nReturning the palette you asked for with that many colors\n\n", "job_stdout": "", "job_stderr": "", "stdout": "output file: tmp_output.pdf\n", "stderr": "input436.tabular : already tabular\ninput437.tabular : already tabular\ninput438.tabular : already tabular\ninput439.tabular : already tabular\ninput440.tabular : already tabular\ninput441.tabular : already tabular\ninput442.tabular : already tabular\ninput443.tabular : already tabular\ninput444.tabular : already tabular\nWarning message:\nIn brewer.pal(brewer_color_gene_annotation, n = count) :\n n too large, allowed maximum for palette Set2 is 8\nReturning the palette you asked for with that many colors\n\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "14 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "14.0000000"}, {"title": "Job End Time", "value": "2025-01-02 07:28:28", "plugin": "core", "name": 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{"src": "hda", "id": "3c4e27964d9ff904"}, {"src": "hda", "id": "826fac6121d17d65"}, {"src": "hda", "id": "52f0293e5900e051"}, {"src": "hda", "id": "62ff7d0e73ef795a"}], "advanced|output_type": "svg", "advanced|ratio": "0.8", "advanced|color": "Greys", "clustering|do": "TRUE"}, "job": {"model_class": "Job", "id": "05af15a29458f6b6", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3", "state": "ok", "exit_code": 0, "create_time": "2025-01-02T07:29:41.039381", "update_time": "2025-01-02T07:30:40.920700", "galaxy_version": "24.1", "external_id": "gxy-hkh8p", "handler": null, "job_runner_name": null, "command_line": "cat '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/3d0adeee3f2b/snpfreqplot/helperFunctions.R' > /dev/null && cat '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/3d0adeee3f2b/snpfreqplot/snpEffExtract.R' > /dev/null && cat '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/3d0adeee3f2b/snpfreqplot/heatmap_for_variants.R' > /dev/null && echo \"output file: tmp_output.svg\" && Rscript '/galaxy/server/database/jobs_directory/000/261/configs/tmpmcnwuytf'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "clustering": "{\"__current_case__\": 0, \"do\": \"TRUE\", \"method\": \"ward.D2\", \"nclust\": \"1\"}", "advanced": "{\"color\": \"Greys\", \"output_type\": \"svg\", \"ratio\": \"0.8\"}", "varfreq": "\"0.1\""}, "inputs": {"sinputs": {"id": "9b22cecbbdc53fa2", "src": "hda", "uuid": "d7cd32bf-fde6-4fc2-af95-b8d3d129fc47"}, "sinputs1": {"id": "9b22cecbbdc53fa2", "src": "hda", "uuid": "d7cd32bf-fde6-4fc2-af95-b8d3d129fc47"}, "sinputs2": {"id": "3c4e27964d9ff904", "src": "hda", "uuid": "bd4e36d1-7664-40c5-a705-bd9e233ee5b0"}, "sinputs3": {"id": 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"error"}}, {"id": "snpfreqplot/1.0+galaxy3-5", "has_data": true, "data": {"tool_id": "snpfreqplot", "tool_version": "1.0+galaxy3", "test_index": 5, "time_seconds": 59.466283082962036, "inputs": {"sinputs": [{"src": "hda", "id": "2db384f9be12b8f6"}, {"src": "hda", "id": "75165c3f0e24177b"}, {"src": "hda", "id": "8531ce707a328625"}], "advanced|output_type": "pdf", "advanced|color": "PuBuGn"}, "job": {"model_class": "Job", "id": "c1edba9534a2ca62", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3", "state": "ok", "exit_code": 0, "create_time": "2025-01-02T07:31:31.946805", "update_time": "2025-01-02T07:32:00.061969", "galaxy_version": "24.1", "external_id": "gxy-dxns4", "handler": null, "job_runner_name": null, "command_line": "cat '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/3d0adeee3f2b/snpfreqplot/helperFunctions.R' > /dev/null && cat '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/3d0adeee3f2b/snpfreqplot/snpEffExtract.R' > /dev/null && cat '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/3d0adeee3f2b/snpfreqplot/heatmap_for_variants.R' > /dev/null && echo \"output file: tmp_output.pdf\" && Rscript '/galaxy/server/database/jobs_directory/000/269/configs/tmpmdko1vpy'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "clustering": "{\"__current_case__\": 1, \"do\": \"FALSE\"}", "advanced": "{\"color\": \"PuBuGn\", \"output_type\": \"pdf\", \"ratio\": \"0.67\"}", "varfreq": "\"0.1\""}, "inputs": {"sinputs": {"id": "2db384f9be12b8f6", "src": "hda", "uuid": "18f98e97-e11d-46d5-8518-f321717ed226"}, "sinputs1": {"id": "2db384f9be12b8f6", "src": "hda", "uuid": "18f98e97-e11d-46d5-8518-f321717ed226"}, "sinputs2": {"id": 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72.92811608314514, "inputs": {"sinputs": [{"src": "hda", "id": "7ea661e1e049bd18"}, {"src": "hda", "id": "00ccd1159a1d309c"}, {"src": "hda", "id": "5d1f1f5e288ba514"}, {"src": "hda", "id": "87f475194be60cd0"}, {"src": "hda", "id": "bb582d3de4271b0a"}], "advanced|output_type": "svg"}, "job": {"model_class": "Job", "id": "b38df5f4a534f8b3", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3", "state": "ok", "exit_code": 0, "create_time": "2025-01-02T07:32:44.952579", "update_time": "2025-01-02T07:33:18.405889", "galaxy_version": "24.1", "external_id": "gxy-7mpgb", "handler": null, "job_runner_name": null, "command_line": "cat '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/3d0adeee3f2b/snpfreqplot/helperFunctions.R' > /dev/null && cat '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/3d0adeee3f2b/snpfreqplot/snpEffExtract.R' > /dev/null && cat '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/3d0adeee3f2b/snpfreqplot/heatmap_for_variants.R' > /dev/null && echo \"output file: tmp_output.svg\" && Rscript '/galaxy/server/database/jobs_directory/000/275/configs/tmpu21vht29'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "clustering": "{\"__current_case__\": 1, \"do\": \"FALSE\"}", "advanced": "{\"color\": \"Set3\", \"output_type\": \"svg\", \"ratio\": \"0.67\"}", "varfreq": "\"0.1\""}, "inputs": {"sinputs": {"id": "7ea661e1e049bd18", "src": "hda", "uuid": "ddeb956e-3163-416e-8bdb-d5b4225ca908"}, "sinputs1": {"id": "7ea661e1e049bd18", "src": "hda", "uuid": "ddeb956e-3163-416e-8bdb-d5b4225ca908"}, "sinputs2": {"id": "00ccd1159a1d309c", "src": "hda", "uuid": "d615382d-5bc7-4076-a12a-8d2cf94d53f7"}, "sinputs3": {"id": "5d1f1f5e288ba514", "src": "hda", "uuid": 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"id": "feec5649a164216f"}, {"src": "hda", "id": "c9a8ffa21d8c0294"}, {"src": "hda", "id": "c725de5fd835b7b1"}, {"src": "hda", "id": "526e8d7e93930bf3"}], "varfreq": "0.0222", "advanced|output_type": "svg"}, "job": {"model_class": "Job", "id": "35993369f130fd6d", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3", "state": "ok", "exit_code": 0, "create_time": "2025-01-02T07:33:55.632762", "update_time": "2025-01-02T07:34:26.375103", "galaxy_version": "24.1", "external_id": "gxy-bh5dl", "handler": null, "job_runner_name": null, "command_line": "cat '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/3d0adeee3f2b/snpfreqplot/helperFunctions.R' > /dev/null && cat '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/3d0adeee3f2b/snpfreqplot/snpEffExtract.R' > /dev/null && cat '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/3d0adeee3f2b/snpfreqplot/heatmap_for_variants.R' > /dev/null && echo \"output file: tmp_output.svg\" && Rscript '/galaxy/server/database/jobs_directory/000/281/configs/tmpc1hh1g_a'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "clustering": "{\"__current_case__\": 1, \"do\": \"FALSE\"}", "advanced": "{\"color\": \"Set3\", \"output_type\": \"svg\", \"ratio\": \"0.67\"}", "varfreq": "\"0.0222\""}, "inputs": {"sinputs": {"id": "4e3414c55f70b233", "src": "hda", "uuid": "e563aa01-cee4-4002-bc98-0da45a3cf79c"}, "sinputs1": {"id": "4e3414c55f70b233", "src": "hda", "uuid": "e563aa01-cee4-4002-bc98-0da45a3cf79c"}, "sinputs2": {"id": "feec5649a164216f", "src": "hda", "uuid": "b71c8c86-f898-431b-ac3d-7f2292815fc3"}, "sinputs3": {"id": "c9a8ffa21d8c0294", "src": "hda", "uuid": 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tabular\nsingle_variant.vcf : converted from VCF to tabular\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "17 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "17.0000000"}, {"title": "Job End Time", "value": "2025-01-02 07:34:14", "plugin": "core", "name": "end_epoch", "raw_value": "1735803254.0000000"}, {"title": "Job Start Time", "value": "2025-01-02 07:33:57", "plugin": "core", "name": "start_epoch", "raw_value": "1735803237.0000000"}, {"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": "split_file_to_collection/0.5.2-0", "has_data": true, "data": {"tool_id": "split_file_to_collection", "tool_version": "0.5.2", "test_index": 0, "time_seconds": 61.84880971908569, "inputs": {"split_parms|input": {"src": "hda", "id": "417947348fdacb2d"}, "split_parms|top": "2", "split_parms|split_by|id_col": "1", "split_parms|split_by|match_regex": "(.*)\\.mgf", "split_parms|split_by|sub_regex": "\\1.tab", "split_parms|split_by|select_split_by": "col", "split_parms|select_ftype": "tabular"}, "job": {"model_class": "Job", "id": "804dcea5bbe17c90", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2", "state": "error", "exit_code": null, "create_time": "2025-01-02T06:28:56.100572", "update_time": "2025-01-02T06:29:30.542699", "galaxy_version": "24.1", "external_id": "gxy-kd8fq", "handler": null, "job_runner_name": null, "command_line": "mkdir ./out && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/2dae863c8f42/split_file_to_collection/split_file_to_collection.py' --out ./out --in '/galaxy/server/database/objects/7/7/3/dataset_7731d777-7741-4f81-a845-f70e1b18e559.dat' --ftype 'tabular' --top '2' --by 'col' --id_column '1' --match '(.*)__backslash__.mgf' --sub '__backslash__1.tab'", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "split_parms": "{\"__current_case__\": 0, \"input\": {\"values\": [{\"id\": 1, \"src\": \"hda\"}]}, \"select_ftype\": \"tabular\", \"split_by\": {\"__current_case__\": 0, \"id_col\": \"1\", \"match_regex\": \"(.*)\\\\.mgf\", \"select_split_by\": \"col\", \"sub_regex\": \"\\\\1.tab\"}, \"top\": \"2\"}"}, "inputs": {"split_parms|input": {"id": "417947348fdacb2d", "src": "hda", "uuid": "7731d777-7741-4f81-a845-f70e1b18e559"}}, "outputs": {}, "copied_from_job_id": null, "output_collections": {"list_output_tab": {"src": "hdca", "id": "417947348fdacb2d"}}, "tool_stdout": "", "tool_stderr": "", "job_stdout": null, "job_stderr": null, "stdout": "", "stderr": "", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2, exit_code: None, stderr: .", "Output collection 'list_output_tab': failed to find identifier 'foo.tab' in the tool generated elements []"], "status": "failure"}}, {"id": "split_file_to_collection/0.5.2-1", "has_data": true, "data": {"tool_id": "split_file_to_collection", "tool_version": "0.5.2", "test_index": 1, "time_seconds": 32.028618812561035, "inputs": {"split_parms|input": {"src": "hda", "id": "804dcea5bbe17c90"}, "split_parms|top": "2", "split_parms|split_by|select_mode|numnew": "2", "split_parms|split_by|select_mode|mode": "numnew", "split_parms|split_by|newfilenames": "test", "split_parms|split_by|select_split_by": "row", "split_parms|select_ftype": "tabular"}, "job": {"model_class": "Job", "id": "7ffebc1e07d84419", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2", "state": "ok", "exit_code": 0, "create_time": "2025-01-02T06:29:50.207827", "update_time": "2025-01-02T06:30:02.379337", "galaxy_version": "24.1", "external_id": "gxy-mlkdz", "handler": null, "job_runner_name": null, "command_line": "mkdir ./out && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/2dae863c8f42/split_file_to_collection/split_file_to_collection.py' --out ./out --in '/galaxy/server/database/objects/4/7/e/dataset_47ed77d7-71c8-4dce-8526-5bfd3871179e.dat' --ftype 'tabular' --top '2' --by 'row' --numnew '2' --file_names 'test' --file_ext 'tabular'", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "split_parms": "{\"__current_case__\": 0, \"input\": {\"values\": [{\"id\": 2, \"src\": \"hda\"}]}, \"select_ftype\": \"tabular\", \"split_by\": {\"__current_case__\": 1, \"newfilenames\": \"test\", \"select_allocate\": {\"__current_case__\": 2, \"allocate\": \"byrow\"}, \"select_mode\": {\"__current_case__\": 1, \"mode\": \"numnew\", \"numnew\": \"2\"}, \"select_split_by\": \"row\"}, \"top\": \"2\"}"}, "inputs": {"split_parms|input": {"id": "804dcea5bbe17c90", "src": "hda", "uuid": "47ed77d7-71c8-4dce-8526-5bfd3871179e"}}, "outputs": {"__new_primary_file_list_output_tab|test_000001.tabular__": {"id": "7ffebc1e07d84419", "src": "hda", "uuid": "5016549b-1471-4dea-9c5d-e52b65c290d3"}, "__new_primary_file_list_output_tab|test_000000.tabular__": {"id": "fa19a58c7eaf71b5", "src": "hda", "uuid": "d612fe74-8c0d-4635-a0e3-92794745eef6"}}, "copied_from_job_id": null, "output_collections": {"list_output_tab": {"src": "hdca", "id": "804dcea5bbe17c90"}}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2025-01-02 06:29:51", "plugin": "core", "name": "end_epoch", "raw_value": "1735799391.0000000"}, {"title": "Job Start Time", "value": "2025-01-02 06:29:51", "plugin": "core", "name": "start_epoch", "raw_value": "1735799391.0000000"}, {"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": "split_file_to_collection/0.5.2-10", "has_data": true, "data": {"tool_id": "split_file_to_collection", "tool_version": "0.5.2", "test_index": 10, "time_seconds": 32.00102138519287, "inputs": {"split_parms|input": {"src": "hda", "id": "33b124f4a0e08d37"}, "split_parms|split_method|record_length": "4", "split_parms|split_method|select_split_method": "number", "split_parms|select_mode|numnew": "2", "split_parms|select_mode|mode": "numnew", "split_parms|newfilenames": "test", "split_parms|select_ftype": "generic"}, "job": {"model_class": "Job", "id": "b691c7254e38a402", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2", "state": "ok", "exit_code": 0, "create_time": "2025-01-02T06:34:26.926563", "update_time": "2025-01-02T06:34:39.709222", "galaxy_version": "24.1", "external_id": "gxy-dnwnd", "handler": null, "job_runner_name": null, "command_line": "mkdir ./out && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/2dae863c8f42/split_file_to_collection/split_file_to_collection.py' --out ./out --in '/galaxy/server/database/objects/2/2/3/dataset_22340cd4-516c-4877-a4a5-f25e805b6c31.dat' --ftype 'generic' --generic_num 4 --numnew '2' --file_names 'test' --file_ext 'fastq'", "user_email": "tests@fake.org", "command_version": null, "params": {"split_parms": "{\"__current_case__\": 6, \"input\": {\"values\": [{\"id\": 52, \"src\": \"hda\"}]}, \"newfilenames\": \"test\", \"select_allocate\": {\"__current_case__\": 2, \"allocate\": \"byrow\"}, \"select_ftype\": \"generic\", \"select_mode\": {\"__current_case__\": 1, \"mode\": \"numnew\", \"numnew\": \"2\"}, \"split_method\": {\"__current_case__\": 1, \"record_length\": \"4\", \"select_split_method\": \"number\"}}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"fastq\""}, "inputs": {"split_parms|input": {"id": "33b124f4a0e08d37", "src": "hda", "uuid": "22340cd4-516c-4877-a4a5-f25e805b6c31"}}, "outputs": {"__new_primary_file_list_output_generic|test_000000__": {"id": "f31ba40a134f0e3c", "src": "hda", "uuid": "4e95ae3f-9b1a-47df-874e-3680ad973c9c"}, "__new_primary_file_list_output_generic|test_000001__": {"id": "9b787033c9052aa6", "src": "hda", "uuid": "94e5c1db-46e0-495c-8984-91152f921622"}}, "copied_from_job_id": null, "output_collections": {"list_output_generic": {"src": "hdca", "id": "2da80dd8d646d9cd"}}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Job Start Time", "value": "2025-01-02 06:34:28", "plugin": "core", "name": "start_epoch", "raw_value": "1735799668.0000000"}, {"title": "Job End Time", "value": "2025-01-02 06:34:28", "plugin": "core", "name": "end_epoch", "raw_value": "1735799668.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "split_file_to_collection/0.5.2-11", "has_data": true, "data": {"tool_id": "split_file_to_collection", "tool_version": "0.5.2", "test_index": 11, "time_seconds": 33.25705623626709, "inputs": {"split_parms|input": {"src": "hda", "id": "055bd6bd17ad1036"}, "split_parms|select_mode|numnew": "2", "split_parms|select_mode|mode": "numnew", "split_parms|newfilenames": "rand", "split_parms|select_allocate|seed": "1010", "split_parms|select_allocate|allocate": "random", "split_parms|select_ftype": "fasta"}, "job": {"model_class": "Job", "id": "1b77217c2414c23e", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2", "state": "ok", "exit_code": 0, "create_time": "2025-01-02T06:34:59.295128", "update_time": "2025-01-02T06:35:13.132434", "galaxy_version": "24.1", "external_id": "gxy-84pv9", "handler": null, "job_runner_name": null, "command_line": "mkdir ./out && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/2dae863c8f42/split_file_to_collection/split_file_to_collection.py' --out ./out --in '/galaxy/server/database/objects/e/d/3/dataset_ed3e5703-9bfd-4b02-aa5c-18fad3c3b3af.dat' --ftype 'fasta' --numnew '2' --rand --seed '1010' --file_names 'rand' --file_ext 'fasta'", "user_email": "tests@fake.org", "command_version": null, "params": {"split_parms": "{\"__current_case__\": 3, \"input\": {\"values\": [{\"id\": 55, \"src\": \"hda\"}]}, \"newfilenames\": \"rand\", \"select_allocate\": {\"__current_case__\": 0, \"allocate\": \"random\", \"seed\": \"1010\"}, \"select_ftype\": \"fasta\", \"select_mode\": {\"__current_case__\": 1, \"mode\": \"numnew\", \"numnew\": \"2\"}}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"fasta\""}, "inputs": {"split_parms|input": {"id": "055bd6bd17ad1036", "src": "hda", "uuid": "ed3e5703-9bfd-4b02-aa5c-18fad3c3b3af"}}, "outputs": {"__new_primary_file_list_output_fasta|rand_000000.fasta__": {"id": "b20a6f5b6dfc46b8", "src": "hda", "uuid": "042eaea1-0ba9-490a-9bfb-67c19255aa36"}, "__new_primary_file_list_output_fasta|rand_000001.fasta__": {"id": "f1e7ec6971c91b6c", "src": "hda", "uuid": "6564f51e-74d9-4ebc-8ee1-fb8f0f8a8a33"}}, "copied_from_job_id": null, "output_collections": {"list_output_fasta": {"src": "hdca", "id": "345f6aa96f8fc5bc"}}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Job Start Time", "value": "2025-01-02 06:35:01", "plugin": "core", "name": "start_epoch", "raw_value": "1735799701.0000000"}, {"title": "Job End Time", "value": "2025-01-02 06:35:01", "plugin": "core", "name": "end_epoch", "raw_value": "1735799701.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "split_file_to_collection/0.5.2-12", "has_data": true, "data": {"tool_id": "split_file_to_collection", "tool_version": "0.5.2", "test_index": 12, "time_seconds": 31.39319396018982, "inputs": {"split_parms|input": {"src": "hda", "id": "1e96e1d58f839ce0"}, "split_parms|select_mode|numnew": "2", "split_parms|select_mode|mode": "numnew", "split_parms|newfilenames": "fasta_batch", "split_parms|select_allocate|allocate": "batch", "split_parms|select_ftype": "fasta"}, "job": {"model_class": "Job", "id": "2dca843539d91a0d", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2", "state": "ok", "exit_code": 0, "create_time": "2025-01-02T06:35:31.652844", "update_time": "2025-01-02T06:35:44.637548", "galaxy_version": "24.1", "external_id": "gxy-qwxtm", "handler": null, "job_runner_name": null, "command_line": "mkdir ./out && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/2dae863c8f42/split_file_to_collection/split_file_to_collection.py' --out ./out --in '/galaxy/server/database/objects/b/e/b/dataset_beb66869-09ca-467c-ac36-b376e1ee2f04.dat' --ftype 'fasta' --numnew '2' --batch --file_names 'fasta_batch' --file_ext 'fasta'", "user_email": "tests@fake.org", "command_version": null, "params": {"split_parms": "{\"__current_case__\": 3, \"input\": {\"values\": [{\"id\": 58, \"src\": \"hda\"}]}, \"newfilenames\": \"fasta_batch\", \"select_allocate\": {\"__current_case__\": 1, \"allocate\": \"batch\"}, \"select_ftype\": \"fasta\", \"select_mode\": {\"__current_case__\": 1, \"mode\": \"numnew\", \"numnew\": \"2\"}}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"fasta\""}, "inputs": {"split_parms|input": {"id": "1e96e1d58f839ce0", "src": "hda", "uuid": "beb66869-09ca-467c-ac36-b376e1ee2f04"}}, "outputs": {"__new_primary_file_list_output_fasta|fasta_batch_000000.fasta__": {"id": "6e2017aab688e208", "src": "hda", "uuid": "5dca8e4d-94b9-4312-a995-3e5051693a8b"}, "__new_primary_file_list_output_fasta|fasta_batch_000001.fasta__": {"id": "24611f45b2c6f4c6", "src": "hda", "uuid": "ff7ae8e8-3643-481f-b3c5-00835323a5fe"}}, "copied_from_job_id": null, "output_collections": {"list_output_fasta": {"src": "hdca", "id": "ecd04b30e568d759"}}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Job Start Time", "value": "2025-01-02 06:35:33", "plugin": "core", "name": "start_epoch", "raw_value": "1735799733.0000000"}, {"title": "Job End Time", "value": "2025-01-02 06:35:33", "plugin": "core", "name": "end_epoch", "raw_value": "1735799733.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "split_file_to_collection/0.5.2-13", "has_data": true, "data": {"tool_id": "split_file_to_collection", "tool_version": "0.5.2", "test_index": 13, "time_seconds": 32.57814145088196, "inputs": {"split_parms|input": {"src": "hda", "id": "928abf10b09916b8"}, "split_parms|select_mode|numnew": "2", "split_parms|select_mode|mode": "numnew", "split_parms|newfilenames": "test", "split_parms|select_ftype": "txt"}, "job": {"model_class": "Job", "id": "8c6a9a635ccb6b1c", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2", "state": "ok", "exit_code": 0, "create_time": "2025-01-02T06:36:03.919894", "update_time": "2025-01-02T06:36:17.280552", "galaxy_version": "24.1", "external_id": "gxy-zfhsw", "handler": null, "job_runner_name": null, "command_line": "mkdir ./out && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/2dae863c8f42/split_file_to_collection/split_file_to_collection.py' --out ./out --in '/galaxy/server/database/objects/f/0/b/dataset_f0bbc17d-3a76-4b89-881f-c665a8b8b438.dat' --ftype 'txt' --numnew '2' --file_names 'test' --file_ext 'txt'", "user_email": "tests@fake.org", "command_version": null, "params": {"split_parms": "{\"__current_case__\": 5, \"input\": {\"values\": [{\"id\": 61, \"src\": \"hda\"}]}, \"newfilenames\": \"test\", \"select_allocate\": {\"__current_case__\": 2, \"allocate\": \"byrow\"}, \"select_ftype\": \"txt\", \"select_mode\": {\"__current_case__\": 1, \"mode\": \"numnew\", \"numnew\": \"2\"}}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"txt\""}, "inputs": {"split_parms|input": {"id": "928abf10b09916b8", "src": "hda", "uuid": "f0bbc17d-3a76-4b89-881f-c665a8b8b438"}}, "outputs": {"__new_primary_file_list_output_txt|test_000000.txt__": {"id": "12be6bb5ce7b2302", "src": "hda", "uuid": "7d1d49f7-97e3-4c21-9ea5-8daca396b387"}, "__new_primary_file_list_output_txt|test_000001.txt__": {"id": "2c6dddfa20f05e64", "src": "hda", "uuid": "f40a7ed7-6c2d-4c00-b322-3d2fe5b37b00"}}, "copied_from_job_id": null, "output_collections": {"list_output_txt": {"src": "hdca", "id": "9de504bc018e2949"}}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Job Start Time", "value": "2025-01-02 06:36:05", "plugin": "core", "name": "start_epoch", "raw_value": "1735799765.0000000"}, {"title": "Job End Time", "value": "2025-01-02 06:36:05", "plugin": "core", "name": "end_epoch", "raw_value": "1735799765.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "split_file_to_collection/0.5.2-14", "has_data": true, "data": {"tool_id": "split_file_to_collection", "tool_version": "0.5.2", "test_index": 14, "time_seconds": 22.594356060028076, "inputs": {"split_parms|input": {"src": "hda", "id": "2862c9a90cb5fc49"}, "split_parms|split_method|generic_regex": "^.*", "split_parms|split_method|select_split_method": "regex", "split_parms|select_mode|numnew": "2", "split_parms|select_mode|mode": "numnew", "split_parms|newfilenames": "test", "split_parms|select_ftype": "generic"}, "job": {"model_class": "Job", "id": "c2c9997c29a1ad4a", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2", "state": "error", "exit_code": null, "create_time": "2025-01-02T06:36:35.497964", "update_time": "2025-01-02T06:36:40.253026", "galaxy_version": "24.1", "external_id": "gxy-6w8zt", "handler": null, "job_runner_name": null, "command_line": "mkdir ./out && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/2dae863c8f42/split_file_to_collection/split_file_to_collection.py' --out ./out --in '/galaxy/server/database/objects/3/d/9/dataset_3d9ff423-ec48-4de4-9fa7-62c7d3e1213f.dat' --ftype 'generic' --generic_re '^.*' --numnew '2' --file_names 'test' --file_ext 'txt'", "user_email": "tests@fake.org", "command_version": null, "params": {"split_parms": "{\"__current_case__\": 6, \"input\": {\"values\": [{\"id\": 64, \"src\": \"hda\"}]}, \"newfilenames\": \"test\", \"select_allocate\": {\"__current_case__\": 2, \"allocate\": \"byrow\"}, \"select_ftype\": \"generic\", \"select_mode\": {\"__current_case__\": 1, \"mode\": \"numnew\", \"numnew\": \"2\"}, \"split_method\": {\"__current_case__\": 0, \"generic_regex\": \"^.*\", \"select_split_method\": \"regex\", \"split_after\": \"false\"}}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"txt\""}, "inputs": {"split_parms|input": {"id": "2862c9a90cb5fc49", "src": "hda", "uuid": "3d9ff423-ec48-4de4-9fa7-62c7d3e1213f"}}, "outputs": {}, "copied_from_job_id": null, "output_collections": {"list_output_generic": {"src": "hdca", "id": "b6825f59da9f7281"}}, "tool_stdout": "", "tool_stderr": "", "job_stdout": null, "job_stderr": null, "stdout": "", "stderr": "", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2, exit_code: None, stderr: .", "Output collection 'list_output_generic': failed to find identifier 'test_000000' in the tool generated elements []"], "status": "failure"}}, {"id": "split_file_to_collection/0.5.2-15", "has_data": true, "data": {"tool_id": "split_file_to_collection", "tool_version": "0.5.2", "test_index": 15, "time_seconds": 30.827760934829712, "inputs": {"split_parms|input": {"src": "hda", "id": "87de444ed74458c4"}, "split_parms|split_method|generic_regex": "^>.*", "split_parms|split_method|select_split_method": "regex", "split_parms|select_mode|numnew": "2", "split_parms|select_mode|mode": "numnew", "split_parms|newfilenames": "rand", "split_parms|select_allocate|seed": "1010", "split_parms|select_allocate|allocate": "random", "split_parms|select_ftype": "generic"}, "job": {"model_class": "Job", "id": "00fed3ded302320f", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2", "state": "ok", "exit_code": 0, "create_time": "2025-01-02T06:36:58.113483", "update_time": "2025-01-02T06:37:10.730574", "galaxy_version": "24.1", "external_id": "gxy-hbx6b", "handler": null, "job_runner_name": null, "command_line": "mkdir ./out && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/2dae863c8f42/split_file_to_collection/split_file_to_collection.py' --out ./out --in '/galaxy/server/database/objects/1/6/8/dataset_16819ef6-3c22-4a20-90ad-bd6c22b8351e.dat' --ftype 'generic' --generic_re '^>.*' --numnew '2' --rand --seed '1010' --file_names 'rand' --file_ext 'fasta'", "user_email": "tests@fake.org", "command_version": null, "params": {"split_parms": "{\"__current_case__\": 6, \"input\": {\"values\": [{\"id\": 65, \"src\": \"hda\"}]}, \"newfilenames\": \"rand\", \"select_allocate\": {\"__current_case__\": 0, \"allocate\": \"random\", \"seed\": \"1010\"}, \"select_ftype\": \"generic\", \"select_mode\": {\"__current_case__\": 1, \"mode\": \"numnew\", \"numnew\": \"2\"}, \"split_method\": {\"__current_case__\": 0, \"generic_regex\": \"^>.*\", \"select_split_method\": \"regex\", \"split_after\": \"false\"}}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"fasta\""}, "inputs": {"split_parms|input": {"id": "87de444ed74458c4", "src": "hda", "uuid": "16819ef6-3c22-4a20-90ad-bd6c22b8351e"}}, "outputs": {"__new_primary_file_list_output_generic|rand_000000__": {"id": "039e98ef7e07fc36", "src": "hda", "uuid": "518ded5a-ce0e-4238-871a-da0778c4916c"}, "__new_primary_file_list_output_generic|rand_000001__": {"id": "313ab96f9d8f8251", "src": "hda", "uuid": "1c99b564-17dc-45ea-8551-9313a185716e"}}, "copied_from_job_id": null, "output_collections": {"list_output_generic": {"src": "hdca", "id": "307e56616f72abf0"}}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Job Start Time", "value": "2025-01-02 06:36:59", "plugin": "core", "name": "start_epoch", "raw_value": "1735799819.0000000"}, {"title": "Job End Time", "value": "2025-01-02 06:36:59", "plugin": "core", "name": "end_epoch", "raw_value": "1735799819.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "split_file_to_collection/0.5.2-16", "has_data": true, "data": {"tool_id": "split_file_to_collection", "tool_version": "0.5.2", "test_index": 16, "time_seconds": 32.56169867515564, "inputs": {"split_parms|input": {"src": "hda", "id": "109483ea678a2726"}, "split_parms|select_mode|numnew": "10", "split_parms|select_mode|mode": "numnew", "split_parms|newfilenames": "mol", "split_parms|select_allocate|allocate": "batch", "split_parms|select_ftype": "sdf"}, "job": {"model_class": "Job", "id": "14b55797034a16ee", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2", "state": "ok", "exit_code": 0, "create_time": "2025-01-02T06:37:30.260793", "update_time": "2025-01-02T06:37:43.086472", "galaxy_version": "24.1", "external_id": "gxy-p6skm", "handler": null, "job_runner_name": null, "command_line": "mkdir ./out && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/2dae863c8f42/split_file_to_collection/split_file_to_collection.py' --out ./out --in '/galaxy/server/database/objects/3/e/7/dataset_3e7545cc-a88d-4b41-aa11-777e429b4e80.dat' --ftype 'sdf' --numnew '10' --batch --file_names 'mol' --file_ext 'sdf'", "user_email": "tests@fake.org", "command_version": null, "params": {"split_parms": "{\"__current_case__\": 4, \"input\": {\"values\": [{\"id\": 68, \"src\": \"hda\"}]}, \"newfilenames\": \"mol\", \"select_allocate\": {\"__current_case__\": 1, \"allocate\": \"batch\"}, \"select_ftype\": \"sdf\", \"select_mode\": {\"__current_case__\": 1, \"mode\": \"numnew\", \"numnew\": \"10\"}}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"sdf\""}, "inputs": {"split_parms|input": {"id": "109483ea678a2726", "src": "hda", "uuid": "3e7545cc-a88d-4b41-aa11-777e429b4e80"}}, "outputs": {"__new_primary_file_list_output_sdf|mol_000000.sdf__": {"id": "1adfc04efc82c30c", "src": "hda", "uuid": "63824a6a-ac21-43fc-ac10-8d163761f258"}, "__new_primary_file_list_output_sdf|mol_000001.sdf__": {"id": "23099d778d2eb38a", "src": "hda", "uuid": "a62b91f7-7a73-4eb6-9398-769852de9690"}, "__new_primary_file_list_output_sdf|mol_000002.sdf__": {"id": "3e8cd1fa93a54128", "src": "hda", "uuid": "f9f72d06-5cc8-44a4-8975-67697a0341ea"}}, "copied_from_job_id": null, "output_collections": {"list_output_sdf": {"src": "hdca", "id": "dcbf6c083c690e6e"}}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Job Start Time", "value": "2025-01-02 06:37:32", "plugin": "core", "name": "start_epoch", "raw_value": "1735799852.0000000"}, {"title": "Job End Time", "value": "2025-01-02 06:37:32", "plugin": "core", "name": "end_epoch", "raw_value": "1735799852.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "split_file_to_collection/0.5.2-17", "has_data": true, "data": {"tool_id": "split_file_to_collection", "tool_version": "0.5.2", "test_index": 17, "time_seconds": 10.504394769668579, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "split_file_to_collection/0.5.2-18", "has_data": true, "data": {"tool_id": "split_file_to_collection", "tool_version": "0.5.2", "test_index": 18, "time_seconds": 23.319425106048584, "inputs": {"split_parms|input": {"src": "hda", "id": "0e916bfa231d1662"}, "split_parms|split_method|generic_regex": "^[^>].*", "split_parms|split_method|split_after": "true", "split_parms|split_method|select_split_method": "regex", "split_parms|select_mode|numnew": "2", "split_parms|select_mode|mode": "numnew", "split_parms|newfilenames": "rand", "split_parms|select_allocate|seed": "1010", "split_parms|select_allocate|allocate": "random", "split_parms|select_ftype": "generic"}, "job": {"model_class": "Job", "id": "b5109b578da9c816", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2", "state": "error", "exit_code": null, "create_time": "2025-01-02T06:38:12.846820", "update_time": "2025-01-02T06:38:17.646409", "galaxy_version": "24.1", "external_id": "gxy-5v5rx", "handler": null, "job_runner_name": null, "command_line": "mkdir ./out && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/2dae863c8f42/split_file_to_collection/split_file_to_collection.py' --out ./out --in '/galaxy/server/database/objects/e/6/9/dataset_e690dc82-0c4d-4dc8-a731-0bc5ef17a552.dat' --ftype 'generic' --generic_re '^[^>].*' --split_after --numnew '2' --rand --seed '1010' --file_names 'rand' --file_ext 'fasta'", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "split_parms": "{\"__current_case__\": 6, \"input\": {\"values\": [{\"id\": 73, \"src\": \"hda\"}]}, \"newfilenames\": \"rand\", \"select_allocate\": {\"__current_case__\": 0, \"allocate\": \"random\", \"seed\": \"1010\"}, \"select_ftype\": \"generic\", \"select_mode\": {\"__current_case__\": 1, \"mode\": \"numnew\", \"numnew\": \"2\"}, \"split_method\": {\"__current_case__\": 0, \"generic_regex\": \"^[^>].*\", \"select_split_method\": \"regex\", \"split_after\": \"true\"}}"}, "inputs": {"split_parms|input": {"id": "0e916bfa231d1662", "src": "hda", "uuid": "e690dc82-0c4d-4dc8-a731-0bc5ef17a552"}}, "outputs": {}, "copied_from_job_id": null, "output_collections": {"list_output_generic": {"src": "hdca", "id": "81ab1de02ece1727"}}, "tool_stdout": "", "tool_stderr": "", "job_stdout": null, "job_stderr": null, "stdout": "", "stderr": "", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2, exit_code: None, stderr: .", "Output collection 'list_output_generic': failed to find identifier 'rand_000000' in the tool generated elements []"], "status": "failure"}}, {"id": "split_file_to_collection/0.5.2-19", "has_data": true, "data": {"tool_id": "split_file_to_collection", "tool_version": "0.5.2", "test_index": 19, "time_seconds": 33.23784279823303, "inputs": {"split_parms|input": {"src": "hda", "id": "e520b254cad009c5"}, "split_parms|top": "2", "split_parms|split_by|select_mode|chunksize": "1", "split_parms|split_by|select_mode|mode": "chunk", "split_parms|split_by|select_allocate|allocate": "batch", "split_parms|split_by|select_split_by": "row", "split_parms|select_ftype": "tabular"}, "job": {"model_class": "Job", "id": "8414badffa71b2a6", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2", "state": "ok", "exit_code": 0, "create_time": "2025-01-02T06:38:36.643719", "update_time": "2025-01-02T06:38:50.235035", "galaxy_version": "24.1", "external_id": "gxy-nb4bk", "handler": null, "job_runner_name": null, "command_line": "mkdir ./out && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/2dae863c8f42/split_file_to_collection/split_file_to_collection.py' --out ./out --in '/galaxy/server/database/objects/3/d/3/dataset_3d395a31-00d3-432a-a2b0-18e28a3748f6.dat' --ftype 'tabular' --top '2' --by 'row' --chunksize 1 --batch --file_names 'split_file' --file_ext 'tabular'", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "split_parms": "{\"__current_case__\": 0, \"input\": {\"values\": [{\"id\": 74, \"src\": \"hda\"}]}, \"select_ftype\": \"tabular\", \"split_by\": {\"__current_case__\": 1, \"newfilenames\": \"split_file\", \"select_allocate\": {\"__current_case__\": 1, \"allocate\": \"batch\"}, \"select_mode\": {\"__current_case__\": 0, \"chunksize\": \"1\", \"mode\": \"chunk\"}, \"select_split_by\": \"row\"}, \"top\": \"2\"}"}, "inputs": {"split_parms|input": {"id": "e520b254cad009c5", "src": "hda", "uuid": "3d395a31-00d3-432a-a2b0-18e28a3748f6"}}, "outputs": {"__new_primary_file_list_output_tab|split_file_000000.tabular__": {"id": "3765a9dbf6de90a8", "src": "hda", "uuid": "5ab80543-dcf1-4c05-8bb4-af0c5ec8d9d7"}, "__new_primary_file_list_output_tab|split_file_000001.tabular__": {"id": "4ae9ef01a8862b59", "src": "hda", "uuid": "bf769f90-e9cb-4566-8d44-9ee4c3e96036"}, "__new_primary_file_list_output_tab|split_file_000002.tabular__": {"id": "7d590e2aab35997b", "src": "hda", "uuid": "02837faf-8678-4f44-9d3f-aa09306f5460"}, "__new_primary_file_list_output_tab|split_file_000003.tabular__": {"id": "57eaa0b8499f82dd", "src": "hda", "uuid": "3d46b8ef-87ab-4abc-90ee-3341bd80175e"}}, "copied_from_job_id": null, "output_collections": {"list_output_tab": {"src": "hdca", "id": "4f527a71b6c9dd50"}}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Job Start Time", "value": "2025-01-02 06:38:39", "plugin": "core", "name": "start_epoch", "raw_value": "1735799919.0000000"}, {"title": "Job End Time", "value": "2025-01-02 06:38:39", "plugin": "core", "name": "end_epoch", "raw_value": "1735799919.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "split_file_to_collection/0.5.2-2", "has_data": true, "data": {"tool_id": "split_file_to_collection", "tool_version": "0.5.2", "test_index": 2, "time_seconds": 33.66924858093262, "inputs": {"split_parms|input": {"src": "hda", "id": "af6ecdbda415fbdd"}, "split_parms|top": "2", "split_parms|split_by|select_mode|numnew": "2", "split_parms|split_by|select_mode|mode": "numnew", "split_parms|split_by|newfilenames": "batch_tab", "split_parms|split_by|select_allocate|allocate": "batch", "split_parms|split_by|select_split_by": "row", "split_parms|select_ftype": "tabular"}, "job": {"model_class": "Job", "id": "eb32687926f00cfa", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2", "state": "ok", "exit_code": 0, "create_time": "2025-01-02T06:30:22.331308", "update_time": "2025-01-02T06:30:35.890365", "galaxy_version": "24.1", "external_id": "gxy-6fbmq", "handler": null, "job_runner_name": null, "command_line": "mkdir ./out && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/2dae863c8f42/split_file_to_collection/split_file_to_collection.py' --out ./out --in '/galaxy/server/database/objects/6/1/3/dataset_6130e9c0-d969-41e5-95e5-ce42e2c2af37.dat' --ftype 'tabular' --top '2' --by 'row' --numnew '2' --batch --file_names 'batch_tab' --file_ext 'tabular'", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "split_parms": "{\"__current_case__\": 0, \"input\": {\"values\": [{\"id\": 5, \"src\": \"hda\"}]}, \"select_ftype\": \"tabular\", \"split_by\": {\"__current_case__\": 1, \"newfilenames\": \"batch_tab\", \"select_allocate\": {\"__current_case__\": 1, \"allocate\": \"batch\"}, \"select_mode\": {\"__current_case__\": 1, \"mode\": \"numnew\", \"numnew\": \"2\"}, \"select_split_by\": \"row\"}, \"top\": \"2\"}"}, "inputs": {"split_parms|input": {"id": "af6ecdbda415fbdd", "src": "hda", "uuid": "6130e9c0-d969-41e5-95e5-ce42e2c2af37"}}, "outputs": {"__new_primary_file_list_output_tab|batch_tab_000001.tabular__": {"id": "86525e5b18646427", "src": "hda", "uuid": "b9b0d2f8-757f-42de-9c95-48d8b211558b"}, "__new_primary_file_list_output_tab|batch_tab_000000.tabular__": {"id": "eb32687926f00cfa", "src": "hda", "uuid": "3c7f664a-5165-4dea-b1c3-39edfcd10b05"}}, "copied_from_job_id": null, "output_collections": {"list_output_tab": {"src": "hdca", "id": "fa19a58c7eaf71b5"}}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2025-01-02 06:30:24", "plugin": "core", "name": "end_epoch", "raw_value": "1735799424.0000000"}, {"title": "Job Start Time", "value": "2025-01-02 06:30:24", "plugin": "core", "name": "start_epoch", "raw_value": "1735799424.0000000"}, {"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": "split_file_to_collection/0.5.2-3", "has_data": true, "data": {"tool_id": "split_file_to_collection", "tool_version": "0.5.2", "test_index": 3, "time_seconds": 33.772274017333984, "inputs": {"split_parms|input": {"src": "hda", "id": "816fa2444522560a"}, "split_parms|top": "2", "split_parms|split_by|select_mode|chunksize": "2", "split_parms|split_by|select_mode|mode": "chunk", "split_parms|split_by|newfilenames": "batch_tab", "split_parms|split_by|select_allocate|allocate": "batch", "split_parms|split_by|select_split_by": "row", "split_parms|select_ftype": "tabular"}, "job": {"model_class": "Job", "id": "816fa2444522560a", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2", "state": "ok", "exit_code": 0, "create_time": "2025-01-02T06:30:55.859511", "update_time": "2025-01-02T06:31:09.792795", "galaxy_version": "24.1", "external_id": "gxy-47glk", "handler": null, "job_runner_name": null, "command_line": "mkdir ./out && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/2dae863c8f42/split_file_to_collection/split_file_to_collection.py' --out ./out --in '/galaxy/server/database/objects/0/5/8/dataset_058b46e5-6816-4e20-9f30-bb01f66236c6.dat' --ftype 'tabular' --top '2' --by 'row' --chunksize 2 --batch --file_names 'batch_tab' --file_ext 'tabular'", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "split_parms": "{\"__current_case__\": 0, \"input\": {\"values\": [{\"id\": 8, \"src\": \"hda\"}]}, \"select_ftype\": \"tabular\", \"split_by\": {\"__current_case__\": 1, \"newfilenames\": \"batch_tab\", \"select_allocate\": {\"__current_case__\": 1, \"allocate\": \"batch\"}, \"select_mode\": {\"__current_case__\": 0, \"chunksize\": \"2\", \"mode\": \"chunk\"}, \"select_split_by\": \"row\"}, \"top\": \"2\"}"}, "inputs": {"split_parms|input": {"id": "816fa2444522560a", "src": "hda", "uuid": "058b46e5-6816-4e20-9f30-bb01f66236c6"}}, "outputs": {"__new_primary_file_list_output_tab|batch_tab_000001.tabular__": {"id": "2da80dd8d646d9cd", "src": "hda", "uuid": "84863b15-6c83-44c5-8c4b-27028e97f21d"}, "__new_primary_file_list_output_tab|batch_tab_000000.tabular__": {"id": "4bb5a07230ffcb62", "src": "hda", "uuid": "3f70aca8-8e2f-4c95-8b4c-04726a425474"}}, "copied_from_job_id": null, "output_collections": {"list_output_tab": {"src": "hdca", "id": "7ffebc1e07d84419"}}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2025-01-02 06:30:58", "plugin": "core", "name": "end_epoch", "raw_value": "1735799458.0000000"}, {"title": "Job Start Time", "value": "2025-01-02 06:30:58", "plugin": "core", "name": "start_epoch", "raw_value": "1735799458.0000000"}, {"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": "split_file_to_collection/0.5.2-4", "has_data": true, "data": {"tool_id": "split_file_to_collection", "tool_version": "0.5.2", "test_index": 4, "time_seconds": 36.79792237281799, "inputs": {"split_parms|input": {"src": "hda", "id": "345f6aa96f8fc5bc"}, "split_parms|select_mode|numnew": "24", "split_parms|select_mode|mode": "numnew", "split_parms|newfilenames": "chr", "split_parms|select_allocate|allocate": "batch", "split_parms|select_ftype": "txt"}, "job": {"model_class": "Job", "id": "2da80dd8d646d9cd", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2", "state": "ok", "exit_code": 0, "create_time": "2025-01-02T06:31:29.410695", "update_time": "2025-01-02T06:31:42.526064", "galaxy_version": "24.1", "external_id": "gxy-nq29c", "handler": null, "job_runner_name": null, "command_line": "mkdir ./out && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/2dae863c8f42/split_file_to_collection/split_file_to_collection.py' --out ./out --in '/galaxy/server/database/objects/8/e/0/dataset_8e0e0bb2-eefa-4db1-978b-393055fd6e6d.dat' --ftype 'txt' --numnew '24' --batch --file_names 'chr' --file_ext 'txt'", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"txt\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "split_parms": "{\"__current_case__\": 5, \"input\": {\"values\": [{\"id\": 11, \"src\": \"hda\"}]}, \"newfilenames\": \"chr\", \"select_allocate\": {\"__current_case__\": 1, \"allocate\": \"batch\"}, \"select_ftype\": \"txt\", \"select_mode\": {\"__current_case__\": 1, \"mode\": \"numnew\", \"numnew\": \"24\"}}"}, "inputs": {"split_parms|input": {"id": "345f6aa96f8fc5bc", "src": "hda", "uuid": "8e0e0bb2-eefa-4db1-978b-393055fd6e6d"}}, "outputs": {"__new_primary_file_list_output_txt|chr_000023.txt__": {"id": "391e5b1591bc17af", "src": "hda", "uuid": "7b266076-7322-4ddc-ae64-de8cc44e18ee"}, "__new_primary_file_list_output_txt|chr_000022.txt__": {"id": "52803ce717ec40bb", "src": "hda", "uuid": "b11edc06-6342-4217-b175-aa931424f0d8"}, "__new_primary_file_list_output_txt|chr_000021.txt__": {"id": "14b55797034a16ee", "src": "hda", "uuid": "5d163f14-f233-49b1-8015-75c80e9b9232"}, "__new_primary_file_list_output_txt|chr_000020.txt__": {"id": "b05369fb76ed1035", "src": "hda", "uuid": "6bd283f3-4fab-46d4-a372-ad999e36d96b"}, "__new_primary_file_list_output_txt|chr_000019.txt__": {"id": "00fed3ded302320f", "src": "hda", "uuid": "6244d923-bbd9-4d67-bcc7-6e14b7eeaf44"}, "__new_primary_file_list_output_txt|chr_000018.txt__": {"id": "3225cbe6af27668b", "src": "hda", "uuid": "7d16ebf0-f988-4638-a45c-93460b1df6c3"}, "__new_primary_file_list_output_txt|chr_000017.txt__": {"id": "c2c9997c29a1ad4a", "src": "hda", "uuid": "8afaa51d-ed17-4028-b869-3e3408700daa"}, "__new_primary_file_list_output_txt|chr_000016.txt__": {"id": "5c3d35f5b5f60693", "src": "hda", "uuid": "0c944137-330e-4787-8b37-7e5f5167ce95"}, "__new_primary_file_list_output_txt|chr_000015.txt__": {"id": "8c6a9a635ccb6b1c", "src": "hda", "uuid": "340bf375-cee1-4f2d-85b1-b19e8446810f"}, "__new_primary_file_list_output_txt|chr_000014.txt__": {"id": "5a07dcc0f79b3c50", "src": "hda", "uuid": "a7695b81-4588-4d92-80ad-288cc74ae9e4"}, "__new_primary_file_list_output_txt|chr_000013.txt__": {"id": "2dca843539d91a0d", "src": "hda", "uuid": "95bd4f80-e661-4f1c-9ca6-ac11fe60a633"}, "__new_primary_file_list_output_txt|chr_000012.txt__": {"id": "deecf5987acb48d2", "src": "hda", "uuid": "555f4802-50b1-4c53-b183-c3e88b489f10"}, "__new_primary_file_list_output_txt|chr_000011.txt__": {"id": "1b77217c2414c23e", "src": "hda", "uuid": "29be613c-ff6a-4835-b846-6c9a7c208a9b"}, "__new_primary_file_list_output_txt|chr_000010.txt__": {"id": "1b86423d2d9923d4", "src": "hda", "uuid": "36786f5c-5c50-4e8d-be2a-481b3e3d208a"}, "__new_primary_file_list_output_txt|chr_000009.txt__": {"id": "b691c7254e38a402", "src": "hda", "uuid": "6adc74ab-d4d8-47c9-af61-319c1fecd2ef"}, "__new_primary_file_list_output_txt|chr_000008.txt__": {"id": "f479df8956fff6f2", "src": "hda", "uuid": "037d79cd-2f98-4fe2-a9fa-82ef90f8fd02"}, "__new_primary_file_list_output_txt|chr_000007.txt__": {"id": "c4520508ec6517a8", "src": "hda", "uuid": "91c13d0e-43c8-4f3a-8a64-e6e2645ac9d6"}, "__new_primary_file_list_output_txt|chr_000006.txt__": {"id": "4f527a71b6c9dd50", "src": "hda", "uuid": "01f479cf-93b7-45c0-afaf-735978f05ea2"}, "__new_primary_file_list_output_txt|chr_000005.txt__": {"id": "81ab1de02ece1727", "src": "hda", "uuid": "03cfa805-d69a-42b3-9d02-035ec7f6feb9"}, "__new_primary_file_list_output_txt|chr_000004.txt__": {"id": "dcbf6c083c690e6e", "src": "hda", "uuid": "364dab8d-128c-482d-98ec-60feed05ce20"}, "__new_primary_file_list_output_txt|chr_000003.txt__": {"id": "307e56616f72abf0", "src": "hda", "uuid": "0d258133-ad6d-4d62-a9d8-7f09acb651af"}, "__new_primary_file_list_output_txt|chr_000002.txt__": {"id": "b6825f59da9f7281", "src": "hda", "uuid": "b21cbf20-fd3f-40ce-b84d-26eacaef552b"}, "__new_primary_file_list_output_txt|chr_000001.txt__": {"id": "9de504bc018e2949", "src": "hda", "uuid": "a1ccdc6c-8f91-4d99-b8c4-37e76eeb963c"}, "__new_primary_file_list_output_txt|chr_000000.txt__": {"id": "ecd04b30e568d759", "src": "hda", "uuid": "fea6eae0-2923-4d3d-b51e-8a976643597b"}}, "copied_from_job_id": null, "output_collections": {"list_output_txt": {"src": "hdca", "id": "af6ecdbda415fbdd"}}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2025-01-02 06:31:30", "plugin": "core", "name": "end_epoch", "raw_value": "1735799490.0000000"}, {"title": "Job Start Time", "value": "2025-01-02 06:31:30", "plugin": "core", "name": "start_epoch", "raw_value": "1735799490.0000000"}, {"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": "split_file_to_collection/0.5.2-5", "has_data": true, "data": {"tool_id": "split_file_to_collection", "tool_version": "0.5.2", "test_index": 5, "time_seconds": 33.03203225135803, "inputs": {"split_parms|input": {"src": "hda", "id": "b5109b578da9c816"}, "split_parms|top": "1", "split_parms|split_by|id_col": "10", "split_parms|split_by|match_regex": "(.*)\\.mgf", "split_parms|split_by|sub_regex": "\\1.tab", "split_parms|split_by|select_split_by": "col", "split_parms|select_ftype": "tabular"}, "job": {"model_class": "Job", "id": "ecd04b30e568d759", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2", "state": "ok", "exit_code": 0, "create_time": "2025-01-02T06:32:05.720716", "update_time": "2025-01-02T06:32:19.558931", "galaxy_version": "24.1", "external_id": "gxy-vx7zw", "handler": null, "job_runner_name": null, "command_line": "mkdir ./out && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/2dae863c8f42/split_file_to_collection/split_file_to_collection.py' --out ./out --in '/galaxy/server/database/objects/9/0/2/dataset_902e6410-553b-4658-8943-9239568c4124.dat' --ftype 'tabular' --top '1' --by 'col' --id_column '10' --match '(.*)__backslash__.mgf' --sub '__backslash__1.tab'", "user_email": "tests@fake.org", "command_version": null, "params": {"split_parms": "{\"__current_case__\": 0, \"input\": {\"values\": [{\"id\": 36, \"src\": \"hda\"}]}, \"select_ftype\": \"tabular\", \"split_by\": {\"__current_case__\": 0, \"id_col\": \"10\", \"match_regex\": \"(.*)\\\\.mgf\", \"select_split_by\": \"col\", \"sub_regex\": \"\\\\1.tab\"}, \"top\": \"1\"}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"tabular\""}, "inputs": {"split_parms|input": {"id": "b5109b578da9c816", "src": "hda", "uuid": "902e6410-553b-4658-8943-9239568c4124"}}, "outputs": {"__new_primary_file_list_output_tab|file1.tab__": {"id": "2e865966e3c3766e", "src": "hda", "uuid": "509cf6bb-4267-46ec-9e8e-8af9fe5b9d3f"}, "__new_primary_file_list_output_tab|file2.tab__": {"id": "8414badffa71b2a6", "src": "hda", "uuid": "2246dc52-8c0b-4086-a3d3-33e86651b9d8"}, "__new_primary_file_list_output_tab|file3.tab__": {"id": "d90ec30be9b29d47", "src": "hda", "uuid": "96de7d5c-04bf-4cff-b7b2-b6c551d30d26"}, "__new_primary_file_list_output_tab|file4.tab__": {"id": "a7333bc2f91bf09b", "src": "hda", "uuid": "c7a8f8ba-083d-4919-8269-c3cbc7ca4bb9"}}, "copied_from_job_id": null, "output_collections": {"list_output_tab": {"src": "hdca", "id": "eb32687926f00cfa"}}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2025-01-02 06:32:08", "plugin": "core", "name": "end_epoch", "raw_value": "1735799528.0000000"}, {"title": "Job Start Time", "value": "2025-01-02 06:32:07", "plugin": "core", "name": "start_epoch", "raw_value": "1735799527.0000000"}, {"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": "split_file_to_collection/0.5.2-6", "has_data": true, "data": {"tool_id": "split_file_to_collection", "tool_version": "0.5.2", "test_index": 6, "time_seconds": 32.12832045555115, "inputs": {"split_parms|input": {"src": "hda", "id": "81359fa1d48d9bab"}, "split_parms|select_mode|numnew": "3", "split_parms|select_mode|mode": "numnew", "split_parms|newfilenames": "demo", "split_parms|select_ftype": "mgf"}, "job": {"model_class": "Job", "id": "b6825f59da9f7281", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2", "state": "ok", "exit_code": 0, "create_time": "2025-01-02T06:32:39.428827", "update_time": "2025-01-02T06:32:51.836152", "galaxy_version": "24.1", "external_id": "gxy-d4b67", "handler": null, "job_runner_name": null, "command_line": "mkdir ./out && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/2dae863c8f42/split_file_to_collection/split_file_to_collection.py' --out ./out --in '/galaxy/server/database/objects/5/4/8/dataset_54876c92-1a4d-4a2a-945d-0803e45f2b15.dat' --ftype 'mgf' --numnew '3' --file_names 'demo' --file_ext 'mgf'", "user_email": "tests@fake.org", "command_version": null, "params": {"split_parms": "{\"__current_case__\": 1, \"input\": {\"values\": [{\"id\": 41, \"src\": \"hda\"}]}, \"newfilenames\": \"demo\", \"select_allocate\": {\"__current_case__\": 2, \"allocate\": \"byrow\"}, \"select_ftype\": \"mgf\", \"select_mode\": {\"__current_case__\": 1, \"mode\": \"numnew\", \"numnew\": \"3\"}}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"mgf\""}, "inputs": {"split_parms|input": {"id": "81359fa1d48d9bab", "src": "hda", "uuid": "54876c92-1a4d-4a2a-945d-0803e45f2b15"}}, "outputs": {"__new_primary_file_list_output_mgf|demo_000000.mgf__": {"id": "be431f3fd6e35768", "src": "hda", "uuid": "b934cffa-5287-47ba-9599-79ea5959746a"}, "__new_primary_file_list_output_mgf|demo_000001.mgf__": {"id": "e7ac640723d4ad6f", "src": "hda", "uuid": "9f4faff2-c8b1-43ed-945b-dc42d560a098"}, "__new_primary_file_list_output_mgf|demo_000002.mgf__": {"id": "bb15c2d946ad8a9e", "src": "hda", "uuid": "e86a0486-3e82-4311-8b5a-68120acf490b"}}, "copied_from_job_id": null, "output_collections": {"list_output_mgf": {"src": "hdca", "id": "86525e5b18646427"}}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2025-01-02 06:32:41", "plugin": "core", "name": "end_epoch", "raw_value": "1735799561.0000000"}, {"title": "Job Start Time", "value": "2025-01-02 06:32:41", "plugin": "core", "name": "start_epoch", "raw_value": "1735799561.0000000"}, {"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": "split_file_to_collection/0.5.2-7", "has_data": true, "data": {"tool_id": "split_file_to_collection", "tool_version": "0.5.2", "test_index": 7, "time_seconds": 32.13507795333862, "inputs": {"split_parms|input": {"src": "hda", "id": "c68db52f6074a879"}, "split_parms|select_mode|numnew": "2", "split_parms|select_mode|mode": "numnew", "split_parms|newfilenames": "test", "split_parms|select_ftype": "fasta"}, "job": {"model_class": "Job", "id": "dcbf6c083c690e6e", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2", "state": "ok", "exit_code": 0, "create_time": "2025-01-02T06:33:11.212835", "update_time": "2025-01-02T06:33:24.168426", "galaxy_version": "24.1", "external_id": "gxy-jqh6s", "handler": null, "job_runner_name": null, "command_line": "mkdir ./out && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/2dae863c8f42/split_file_to_collection/split_file_to_collection.py' --out ./out --in '/galaxy/server/database/objects/6/c/5/dataset_6c5a55eb-0f2f-49e8-b7a7-a8a71cfe34a7.dat' --ftype 'fasta' --numnew '2' --file_names 'test' --file_ext 'fasta'", "user_email": "tests@fake.org", "command_version": null, "params": {"split_parms": "{\"__current_case__\": 3, \"input\": {\"values\": [{\"id\": 45, \"src\": \"hda\"}]}, \"newfilenames\": \"test\", \"select_allocate\": {\"__current_case__\": 2, \"allocate\": \"byrow\"}, \"select_ftype\": \"fasta\", \"select_mode\": {\"__current_case__\": 1, \"mode\": \"numnew\", \"numnew\": \"2\"}}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"fasta\""}, "inputs": {"split_parms|input": {"id": "c68db52f6074a879", "src": "hda", "uuid": "6c5a55eb-0f2f-49e8-b7a7-a8a71cfe34a7"}}, "outputs": {"__new_primary_file_list_output_fasta|test_000000.fasta__": {"id": "9cbe38f6b92875dd", "src": "hda", "uuid": "66ea32dc-26a5-45ea-a2d2-a89b82198ee6"}, "__new_primary_file_list_output_fasta|test_000001.fasta__": {"id": "da152380dd2f9bf1", "src": "hda", "uuid": "821e01d6-534b-4378-88d3-b07740e600ae"}}, "copied_from_job_id": null, "output_collections": {"list_output_fasta": {"src": "hdca", "id": "816fa2444522560a"}}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Job Start Time", "value": "2025-01-02 06:33:13", "plugin": "core", "name": "start_epoch", "raw_value": "1735799593.0000000"}, {"title": "Job End Time", "value": "2025-01-02 06:33:13", "plugin": "core", "name": "end_epoch", "raw_value": "1735799593.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "split_file_to_collection/0.5.2-8", "has_data": true, "data": {"tool_id": "split_file_to_collection", "tool_version": "0.5.2", "test_index": 8, "time_seconds": 32.3090660572052, "inputs": {"split_parms|input": {"src": "hda", "id": "d612dfbfd1130b42"}, "split_parms|select_mode|chunksize": "3", "split_parms|select_mode|mode": "chunk", "split_parms|newfilenames": "test", "split_parms|select_ftype": "fasta"}, "job": {"model_class": "Job", "id": "4f527a71b6c9dd50", "history_id": "417947348fdacb2d", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2", "state": "ok", "exit_code": 0, "create_time": "2025-01-02T06:33:43.642518", "update_time": "2025-01-02T06:33:56.608111", "galaxy_version": "24.1", "external_id": "gxy-njc8t", "handler": null, "job_runner_name": null, "command_line": "mkdir ./out && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/2dae863c8f42/split_file_to_collection/split_file_to_collection.py' --out ./out --in '/galaxy/server/database/objects/e/9/4/dataset_e94f5926-a481-461f-9ef1-ae0c71556aaa.dat' --ftype 'fasta' --chunksize 3 --file_names 'test' --file_ext 'fasta'", "user_email": "tests@fake.org", "command_version": null, "params": {"split_parms": "{\"__current_case__\": 3, \"input\": {\"values\": [{\"id\": 48, \"src\": \"hda\"}]}, \"newfilenames\": \"test\", \"select_allocate\": {\"__current_case__\": 2, \"allocate\": \"byrow\"}, \"select_ftype\": \"fasta\", \"select_mode\": {\"__current_case__\": 0, \"chunksize\": \"3\", \"mode\": \"chunk\"}}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"fasta\""}, "inputs": {"split_parms|input": {"id": "d612dfbfd1130b42", "src": "hda", "uuid": "e94f5926-a481-461f-9ef1-ae0c71556aaa"}}, "outputs": {"__new_primary_file_list_output_fasta|test_000000.fasta__": {"id": "c096ce05add57702", "src": "hda", "uuid": "8a9d531f-d910-4def-a512-86eee291a778"}, "__new_primary_file_list_output_fasta|test_000001.fasta__": {"id": "294c47ae7ea33e75", "src": "hda", "uuid": "8e21712f-9ff0-451e-9b51-4bbb9a7bdbcc"}}, "copied_from_job_id": null, "output_collections": {"list_output_fasta": {"src": "hdca", 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tool_panel_section_label: Virology