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Updating anvil-production README for prod-24-09-13-00-32-1
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7 changes: 7 additions & 0 deletions
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reports/anvil-production/tool-tests/prod-24-09-13-00-32-1/chunk.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,7 @@ | ||
| { | ||
| "8": { | ||
| "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-09-13-00-32-1/results.html", | ||
| "date1": "Fri Sep 13 00:47:48 2024", | ||
| "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-09-13-00-32-1/tools.yml" | ||
| } | ||
| } |
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reports/anvil-production/tool-tests/prod-24-09-13-00-32-1/chunk.txt
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,15 @@ | ||
| -t column_maker --tool-version 02026300aa45 | ||
| -t column_order_header_sort --tool-version 6ae9724caf4d | ||
| -t fastp --tool-version dbf9c561ef29 | ||
| -t samtools_merge --tool-version 740ce0a18f0d | ||
| -t bam_to_sam --tool-version 88eedb4abea0 | ||
| -t bcftools_plugin_missing2ref --tool-version dfef7a353ed0 | ||
| -t bcftools_merge --tool-version e03f2f3ac3a9 | ||
| -t vcfannotategenotypes --tool-version 84959112d9a6 | ||
| -t vcfsort --tool-version f0580efedada | ||
| -t poretools_events --tool-version 28d7819c312f | ||
| -t picard --tool-version a1f0b3f4b781 | ||
| -t deeptools_plot_pca --tool-version 69264da0ce77 | ||
| -t lofreq_viterbi --tool-version aa35ee7f3ab2 | ||
| -t ivar_variants --tool-version f95f403841ad | ||
| -t volcanoplot --tool-version 73b8cb5bddcd |
44 changes: 44 additions & 0 deletions
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reports/anvil-production/tool-tests/prod-24-09-13-00-32-1/errors/0d2116abed03c367.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,44 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "0d2116abed03c367", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "update_time": "2024-09-13T00:54:55.247692", | ||
| "create_time": "2024-09-13T00:54:43.361701", | ||
| "galaxy_version": "23.1", | ||
| "command_version": null, | ||
| "copied_from_job_id": null, | ||
| "tool_id": "upload1", | ||
| "history_id": "f7d34f62d1b23699", | ||
| "external_id": "gxy-dg8dp", | ||
| "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/33/registry.xml' '/galaxy/server/database/jobs_directory/000/33/upload_params.json' '49:/galaxy/server/database/objects/5/9/2/dataset_592a5d03-afbe-4982-a4fd-a93346e13430_files:/galaxy/server/database/objects/5/9/2/dataset_592a5d03-afbe-4982-a4fd-a93346e13430.dat'", | ||
| "traceback": null, | ||
| "params": { | ||
| "paramfile": "\"/galaxy/server/database/tmp/upload_params_wuo5miz3\"", | ||
| "files_metadata": "{\"__current_case__\": 677, \"file_type\": \"auto\"}", | ||
| "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__0emuqm9\", \"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": "5d8536f92b8ccace", | ||
| "src": "hda", | ||
| "uuid": "592a5d03-afbe-4982-a4fd-a93346e13430" | ||
| } | ||
| }, | ||
| "output_collections": {}, | ||
| "tool_stdout": "", | ||
| "tool_stderr": "", | ||
| "job_stdout": null, | ||
| "job_stderr": null, | ||
| "stderr": "", | ||
| "stdout": "", | ||
| "job_messages": null, | ||
| "dependencies": [], | ||
| "user_email": "tests@fake.org", | ||
| "job_metrics": [] | ||
| } |
44 changes: 44 additions & 0 deletions
44
reports/anvil-production/tool-tests/prod-24-09-13-00-32-1/errors/17256f0142ebeae7.json
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,44 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "17256f0142ebeae7", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "update_time": "2024-09-13T01:05:02.397214", | ||
| "create_time": "2024-09-13T01:04:52.487322", | ||
| "galaxy_version": "23.1", | ||
| "command_version": null, | ||
| "copied_from_job_id": null, | ||
| "tool_id": "upload1", | ||
| "history_id": "f7d34f62d1b23699", | ||
| "external_id": "gxy-pv77x", | ||
| "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/87/registry.xml' '/galaxy/server/database/jobs_directory/000/87/upload_params.json' '104:/galaxy/server/database/objects/a/1/d/dataset_a1dc8eec-5843-4e89-a199-eab5a83ac658_files:/galaxy/server/database/objects/a/1/d/dataset_a1dc8eec-5843-4e89-a199-eab5a83ac658.dat'", | ||
| "traceback": null, | ||
| "params": { | ||
| "paramfile": "\"/galaxy/server/database/tmp/upload_params_6vskoa9y\"", | ||
| "files_metadata": "{\"__current_case__\": 75, \"file_type\": \"fasta\"}", | ||
| "dbkey": "\"?\"", | ||
| "force_composite": "\"false\"", | ||
| "files": "[{\"NAME\": \"pBR322.fa\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_q54x1obh\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", | ||
| "file_count": "\"auto\"", | ||
| "file_type": "\"fasta\"" | ||
| }, | ||
| "inputs": {}, | ||
| "outputs": { | ||
| "output0": { | ||
| "id": "318bf3846fb301ff", | ||
| "src": "hda", | ||
| "uuid": "a1dc8eec-5843-4e89-a199-eab5a83ac658" | ||
| } | ||
| }, | ||
| "output_collections": {}, | ||
| "tool_stdout": "", | ||
| "tool_stderr": "", | ||
| "job_stdout": null, | ||
| "job_stderr": null, | ||
| "stderr": "", | ||
| "stdout": "", | ||
| "job_messages": null, | ||
| "dependencies": [], | ||
| "user_email": "tests@fake.org", | ||
| "job_metrics": [] | ||
| } |
56 changes: 56 additions & 0 deletions
56
reports/anvil-production/tool-tests/prod-24-09-13-00-32-1/errors/22a7048063a9ba1f.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,56 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "22a7048063a9ba1f", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "update_time": "2024-09-13T00:51:13.620948", | ||
| "create_time": "2024-09-13T00:51:07.648214", | ||
| "galaxy_version": "23.1", | ||
| "command_version": null, | ||
| "copied_from_job_id": null, | ||
| "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1", | ||
| "history_id": "f7d34f62d1b23699", | ||
| "external_id": "gxy-7vfmx", | ||
| "command_line": "ln -sf '/galaxy/server/database/objects/3/9/5/dataset_3950c75f-9a18-4833-b853-fe942e887c01.dat' 'R1_fq.fastq' && fastp --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for R1_fq.fastq' -i 'R1_fq.fastq' -o first.fastq -U --umi_loc 'read1' --umi_len 12 && mv first.fastq '/galaxy/server/database/objects/7/0/b/dataset_70b7cebb-9dcc-4584-9556-e32a12512b20.dat'", | ||
| "traceback": null, | ||
| "params": { | ||
| "__input_ext": "\"input\"", | ||
| "dbkey": "\"?\"", | ||
| "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", | ||
| "output_options": "{\"report_html\": true, \"report_json\": false}", | ||
| "read_mod_options": "{\"base_correction_options\": {\"correction\": false}, \"cutting_by_quality_options\": {\"cut_by_quality3\": false, \"cut_by_quality5\": false, \"cut_mean_quality\": \"\", \"cut_window_size\": \"\"}, \"polyg_tail_trimming\": {\"__current_case__\": 1, \"poly_g_min_len\": \"\", \"trimming_select\": \"\"}, \"polyx_tail_trimming\": {\"__current_case__\": 1, \"polyx_trimming_select\": \"\"}, \"umi_processing\": {\"umi\": true, \"umi_len\": \"12\", \"umi_loc\": \"read1\", \"umi_prefix\": null}}", | ||
| "filter_options": "{\"length_filtering_options\": {\"disable_length_filtering\": false, \"length_limit\": \"\", \"length_required\": \"\"}, \"low_complexity_filter\": {\"complexity_threshold\": \"\", \"enable_low_complexity_filter\": false}, \"quality_filtering_options\": {\"disable_quality_filtering\": false, \"n_base_limit\": \"\", \"qualified_quality_phred\": \"\", \"unqualified_percent_limit\": \"\"}}", | ||
| "overrepresented_sequence_analysis": "{\"overrepresentation_analysis\": false, \"overrepresentation_sampling\": \"\"}", | ||
| "single_paired": "{\"__current_case__\": 0, \"adapter_trimming_options\": {\"adapter_sequence1\": null, \"disable_adapter_trimming\": false}, \"global_trimming_options\": {\"trim_front1\": \"\", \"trim_tail1\": \"\"}, \"in1\": {\"values\": [{\"id\": 15, \"src\": \"hda\"}]}, \"single_paired_selector\": \"single\"}" | ||
| }, | ||
| "inputs": { | ||
| "single_paired|in1": { | ||
| "id": "045b657df5499133", | ||
| "src": "hda", | ||
| "uuid": "3950c75f-9a18-4833-b853-fe942e887c01" | ||
| } | ||
| }, | ||
| "outputs": { | ||
| "out1": { | ||
| "id": "1748fbed85e0fe76", | ||
| "src": "hda", | ||
| "uuid": "70b7cebb-9dcc-4584-9556-e32a12512b20" | ||
| }, | ||
| "report_html": { | ||
| "id": "96f828630427b2d5", | ||
| "src": "hda", | ||
| "uuid": "4cb7415e-1bb0-454a-ba00-be0202c230b1" | ||
| } | ||
| }, | ||
| "output_collections": {}, | ||
| "tool_stdout": "", | ||
| "tool_stderr": "", | ||
| "job_stdout": null, | ||
| "job_stderr": null, | ||
| "stderr": "", | ||
| "stdout": "", | ||
| "job_messages": null, | ||
| "dependencies": [], | ||
| "user_email": "tests@fake.org", | ||
| "job_metrics": [] | ||
| } |
44 changes: 44 additions & 0 deletions
44
reports/anvil-production/tool-tests/prod-24-09-13-00-32-1/errors/882d69a10c225441.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,44 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "882d69a10c225441", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "update_time": "2024-09-13T00:52:52.789411", | ||
| "create_time": "2024-09-13T00:52:43.311998", | ||
| "galaxy_version": "23.1", | ||
| "command_version": null, | ||
| "copied_from_job_id": null, | ||
| "tool_id": "upload1", | ||
| "history_id": "f7d34f62d1b23699", | ||
| "external_id": "gxy-dm6lq", | ||
| "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/21/registry.xml' '/galaxy/server/database/jobs_directory/000/21/upload_params.json' '33:/galaxy/server/database/objects/0/3/7/dataset_037c9fdb-3ae4-428b-9312-e4547e71ece5_files:/galaxy/server/database/objects/0/3/7/dataset_037c9fdb-3ae4-428b-9312-e4547e71ece5.dat'", | ||
| "traceback": null, | ||
| "params": { | ||
| "paramfile": "\"/galaxy/server/database/tmp/upload_params_o3gs5dmx\"", | ||
| "files_metadata": "{\"__current_case__\": 81, \"file_type\": \"fastqsanger\"}", | ||
| "dbkey": "\"?\"", | ||
| "force_composite": "\"false\"", | ||
| "files": "[{\"NAME\": \"R1.fq\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_tafw3zt5\", \"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": "0d2116abed03c367", | ||
| "src": "hda", | ||
| "uuid": "037c9fdb-3ae4-428b-9312-e4547e71ece5" | ||
| } | ||
| }, | ||
| "output_collections": {}, | ||
| "tool_stdout": "", | ||
| "tool_stderr": "", | ||
| "job_stdout": null, | ||
| "job_stderr": null, | ||
| "stderr": "", | ||
| "stdout": "", | ||
| "job_messages": null, | ||
| "dependencies": [], | ||
| "user_email": "tests@fake.org", | ||
| "job_metrics": [] | ||
| } |
47 changes: 47 additions & 0 deletions
47
reports/anvil-production/tool-tests/prod-24-09-13-00-32-1/errors/909d90d7c19e046d.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,47 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "909d90d7c19e046d", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "update_time": "2024-09-13T01:03:32.139781", | ||
| "create_time": "2024-09-13T01:03:26.314410", | ||
| "galaxy_version": "23.1", | ||
| "command_version": null, | ||
| "copied_from_job_id": null, | ||
| "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/poretools_events/poretools_events/0.6.1a1.1", | ||
| "history_id": "f7d34f62d1b23699", | ||
| "external_id": "gxy-hqp2x", | ||
| "command_line": "poretools events --pre-basecalled '/galaxy/server/database/objects/7/5/c/dataset_75cf25f8-de37-4c29-8f9a-5456d3e2fc00.dat' > '/galaxy/server/database/objects/6/5/5/dataset_65508595-9138-4390-bbef-0dfacae4baaa.dat'", | ||
| "traceback": null, | ||
| "params": { | ||
| "__input_ext": "\"fast5.tar\"", | ||
| "dbkey": "\"?\"", | ||
| "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", | ||
| "precalled": "true" | ||
| }, | ||
| "inputs": { | ||
| "input": { | ||
| "id": "015474589d37b41b", | ||
| "src": "hda", | ||
| "uuid": "75cf25f8-de37-4c29-8f9a-5456d3e2fc00" | ||
| } | ||
| }, | ||
| "outputs": { | ||
| "output": { | ||
| "id": "a2adb3ff90e6fb1c", | ||
| "src": "hda", | ||
| "uuid": "65508595-9138-4390-bbef-0dfacae4baaa" | ||
| } | ||
| }, | ||
| "output_collections": {}, | ||
| "tool_stdout": "", | ||
| "tool_stderr": "", | ||
| "job_stdout": null, | ||
| "job_stderr": null, | ||
| "stderr": "", | ||
| "stdout": "", | ||
| "job_messages": null, | ||
| "dependencies": [], | ||
| "user_email": "tests@fake.org", | ||
| "job_metrics": [] | ||
| } |
99 changes: 99 additions & 0 deletions
99
reports/anvil-production/tool-tests/prod-24-09-13-00-32-1/errors/90eb30300ad01ede.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,99 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "90eb30300ad01ede", | ||
| "state": "error", | ||
| "exit_code": 1, | ||
| "update_time": "2024-09-13T01:03:09.365641", | ||
| "create_time": "2024-09-13T01:02:38.268656", | ||
| "galaxy_version": "23.1", | ||
| "command_version": "", | ||
| "copied_from_job_id": null, | ||
| "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/poretools_events/poretools_events/0.6.1a1.1", | ||
| "history_id": "f7d34f62d1b23699", | ||
| "external_id": "gxy-hhzhd", | ||
| "command_line": "poretools events '/galaxy/server/database/objects/8/7/b/dataset_87bba3c6-55f0-4bac-ac84-745355eb19ed.dat' > '/galaxy/server/database/objects/7/d/8/dataset_7d8b686f-4e44-48b9-ad5f-2776390e9e11.dat'", | ||
| "traceback": null, | ||
| "params": { | ||
| "__input_ext": "\"fast5.tar\"", | ||
| "dbkey": "\"?\"", | ||
| "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", | ||
| "precalled": "false" | ||
| }, | ||
| "inputs": { | ||
| "input": { | ||
| "id": "338c64700aaf5de1", | ||
| "src": "hda", | ||
| "uuid": "87bba3c6-55f0-4bac-ac84-745355eb19ed" | ||
| } | ||
| }, | ||
| "outputs": { | ||
| "output": { | ||
| "id": "debf6fbf5b12a3f3", | ||
| "src": "hda", | ||
| "uuid": "7d8b686f-4e44-48b9-ad5f-2776390e9e11" | ||
| } | ||
| }, | ||
| "output_collections": {}, | ||
| "tool_stdout": "", | ||
| "tool_stderr": "Traceback (most recent call last):\n File \"/usr/local/bin/poretools\", line 11, in <module>\n load_entry_point('poretools==0.6.0', 'console_scripts', 'poretools')()\n File \"/usr/local/lib/python2.7/site-packages/poretools/poretools_main.py\", line 543, in main\n args.func(parser, args)\n File \"/usr/local/lib/python2.7/site-packages/poretools/poretools_main.py\", line 55, in run_subtool\n submodule.run(parser, args)\n File \"/usr/local/lib/python2.7/site-packages/poretools/events.py\", line 17, in run\n for fast5 in Fast5File.Fast5FileSet(args.files):\n File \"/usr/local/lib/python2.7/site-packages/poretools/Fast5File.py\", line 110, in next\n shutil.rmtree(PORETOOLS_TMPDIR)\n File \"/usr/local/lib/python2.7/shutil.py\", line 261, in rmtree\n rmtree(fullname, ignore_errors, onerror)\n File \"/usr/local/lib/python2.7/shutil.py\", line 270, in rmtree\n onerror(os.rmdir, path, sys.exc_info())\n File \"/usr/local/lib/python2.7/shutil.py\", line 268, in rmtree\n os.rmdir(path)\nOSError: [Errno 39] Directory not empty: '.poretools_tmp/test-data'\n", | ||
| "job_stdout": "", | ||
| "job_stderr": "", | ||
| "stderr": "Traceback (most recent call last):\n File \"/usr/local/bin/poretools\", line 11, in <module>\n load_entry_point('poretools==0.6.0', 'console_scripts', 'poretools')()\n File \"/usr/local/lib/python2.7/site-packages/poretools/poretools_main.py\", line 543, in main\n args.func(parser, args)\n File \"/usr/local/lib/python2.7/site-packages/poretools/poretools_main.py\", line 55, in run_subtool\n submodule.run(parser, args)\n File \"/usr/local/lib/python2.7/site-packages/poretools/events.py\", line 17, in run\n for fast5 in Fast5File.Fast5FileSet(args.files):\n File \"/usr/local/lib/python2.7/site-packages/poretools/Fast5File.py\", line 110, in next\n shutil.rmtree(PORETOOLS_TMPDIR)\n File \"/usr/local/lib/python2.7/shutil.py\", line 261, in rmtree\n rmtree(fullname, ignore_errors, onerror)\n File \"/usr/local/lib/python2.7/shutil.py\", line 270, in rmtree\n onerror(os.rmdir, path, sys.exc_info())\n File \"/usr/local/lib/python2.7/shutil.py\", line 268, in rmtree\n os.rmdir(path)\nOSError: [Errno 39] Directory not empty: '.poretools_tmp/test-data'\n", | ||
| "stdout": "", | ||
| "job_messages": [ | ||
| { | ||
| "code_desc": "", | ||
| "desc": "Fatal error: Exit code 1 ()", | ||
| "error_level": 3, | ||
| "exit_code": 1, | ||
| "type": "exit_code" | ||
| }, | ||
| { | ||
| "code_desc": "", | ||
| "desc": "Fatal error: ", | ||
| "error_level": 3, | ||
| "match": "Error:", | ||
| "stream": "stderr", | ||
| "type": "regex" | ||
| } | ||
| ], | ||
| "dependencies": [], | ||
| "user_email": "tests@fake.org", | ||
| "job_metrics": [ | ||
| { | ||
| "title": "Job Runtime (Wall Clock)", | ||
| "value": "1 second", | ||
| "plugin": "core", | ||
| "name": "runtime_seconds", | ||
| "raw_value": "1.0000000" | ||
| }, | ||
| { | ||
| "title": "Job End Time", | ||
| "value": "2024-09-13 01:02:54", | ||
| "plugin": "core", | ||
| "name": "end_epoch", | ||
| "raw_value": "1726189374.0000000" | ||
| }, | ||
| { | ||
| "title": "Job Start Time", | ||
| "value": "2024-09-13 01:02:53", | ||
| "plugin": "core", | ||
| "name": "start_epoch", | ||
| "raw_value": "1726189373.0000000" | ||
| }, | ||
| { | ||
| "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" | ||
| } | ||
| ] | ||
| } |
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