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Updating anvil-edge README for edge-23-10-24-06-08-1
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7 changes: 7 additions & 0 deletions
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reports/anvil-edge/tool-tests/edge-23-10-24-06-08-1/chunk.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,7 @@ | ||
| { | ||
| "2": { | ||
| "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-23-10-24-06-08-1/results.html", | ||
| "date1": "Tue Oct 24 06:23:29 2023", | ||
| "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-23-10-24-06-08-1/tools.yml" | ||
| } | ||
| } |
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reports/anvil-edge/tool-tests/edge-23-10-24-06-08-1/chunk.txt
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,20 @@ | ||
| -t miniasm --tool-version 8dee0218ac7d | ||
| -t deeptools_bigwig_compare --tool-version 26e7304d6737 | ||
| -t fastq_groomer --tool-version 47e5dbc3e790 | ||
| -t sra_tools --tool-version 83c7d564b128 | ||
| -t mummer_mummerplot --tool-version ebe3b0f84de9 | ||
| -t poretools_qualpos --tool-version 4fe6b96aff72 | ||
| -t kallisto_pseudo --tool-version 5ae5c312d718 | ||
| -t sam_pileup --tool-version a3b4ad6858ff | ||
| -t samtools_calmd --tool-version 06dc50b7b711 | ||
| -t music_manipulate_eset --tool-version 22232092be53 | ||
| -t droplet_barcode_plot --tool-version 8f605643ccfd | ||
| -t scater_plot_exprs_freq --tool-version 058b40656107 | ||
| -t scanpy_parameter_iterator --tool-version 0387a2179f88 | ||
| -t query_tabular --tool-version cf34c344508d | ||
| -t column_remove_by_header --tool-version 372967836e98 | ||
| -t snpsift --tool-version 2e497a770bca | ||
| -t bcftools_plugin_mendelian --tool-version bf235558f2cf | ||
| -t bcftools_csq --tool-version fdd127bd4a32 | ||
| -t vcfcommonsamples --tool-version f1852ecef841 | ||
| -t vcfdistance --tool-version c506b8275b1a |
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100
reports/anvil-edge/tool-tests/edge-23-10-24-06-08-1/errors/1b14fde99d7533f4.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,100 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "1b14fde99d7533f4", | ||
| "state": "error", | ||
| "exit_code": 127, | ||
| "update_time": "2023-10-24T06:52:19.846117", | ||
| "create_time": "2023-10-24T06:52:05.518898", | ||
| "galaxy_version": "23.1", | ||
| "command_version": "", | ||
| "copied_from_job_id": null, | ||
| "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.3", | ||
| "history_id": "b8e3c9423bdc89f6", | ||
| "external_id": "gxy-97tz8", | ||
| "command_line": "ln -s '/galaxy/server/database/objects/1/5/b/dataset_15b2290e-dd2b-41d0-b5e4-3af2f3bae9b2.dat' input1.bam && ln -s '/galaxy/server/database/objects/_metadata_files/2/f/f/metadata_2ffd98a9-7424-4f3c-bcd0-a652ef3aa4f1.dat' 'input1.bam.bai' && ln -s '/galaxy/server/database/objects/1/8/5/dataset_18585bf8-66ce-43d3-a8e5-643d1a838a77.dat' reference.fasta && samtools faidx reference.fasta && samtools pileup -M 60 -f reference.fasta input1.bam > '/galaxy/server/database/objects/8/1/1/dataset_811d3f5c-0004-45af-a361-17b8d7e6c31e.dat'", | ||
| "traceback": null, | ||
| "params": { | ||
| "__input_ext": "\"input\"", | ||
| "dbkey": "\"equCab2\"", | ||
| "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/equCab2.len\"", | ||
| "c": "{\"__current_case__\": 0, \"consensus\": \"no\"}", | ||
| "mapCap": "\"60\"", | ||
| "indels": "\"no\"", | ||
| "lastCol": "\"no\"", | ||
| "refOrHistory": "{\"__current_case__\": 1, \"input1\": {\"values\": [{\"id\": 126, \"src\": \"hda\"}]}, \"ownFile\": {\"values\": [{\"id\": 127, \"src\": \"hda\"}]}, \"reference\": \"history\"}" | ||
| }, | ||
| "inputs": { | ||
| "refOrHistory|input1": { | ||
| "id": "0b46f4832cf85eda", | ||
| "src": "hda", | ||
| "uuid": "15b2290e-dd2b-41d0-b5e4-3af2f3bae9b2" | ||
| }, | ||
| "refOrHistory|ownFile": { | ||
| "id": "606f27db86776ff6", | ||
| "src": "hda", | ||
| "uuid": "18585bf8-66ce-43d3-a8e5-643d1a838a77" | ||
| } | ||
| }, | ||
| "outputs": { | ||
| "output1": { | ||
| "id": "26f3b5ab5b8463e6", | ||
| "src": "hda", | ||
| "uuid": "811d3f5c-0004-45af-a361-17b8d7e6c31e" | ||
| } | ||
| }, | ||
| "output_collections": {}, | ||
| "tool_stdout": "", | ||
| "tool_stderr": "samtools: error while loading shared libraries: libncurses.so.5: cannot open shared object file: No such file or directory\n", | ||
| "job_stdout": "", | ||
| "job_stderr": "", | ||
| "stderr": "samtools: error while loading shared libraries: libncurses.so.5: cannot open shared object file: No such file or directory\n", | ||
| "stdout": "", | ||
| "job_messages": [ | ||
| { | ||
| "code_desc": "", | ||
| "desc": "Fatal error: Exit code 127 ()", | ||
| "error_level": 3, | ||
| "exit_code": 127, | ||
| "type": "exit_code" | ||
| } | ||
| ], | ||
| "dependencies": [], | ||
| "user_email": "tests@fake.org", | ||
| "job_metrics": [ | ||
| { | ||
| "title": "Job Runtime (Wall Clock)", | ||
| "value": "0 seconds", | ||
| "plugin": "core", | ||
| "name": "runtime_seconds", | ||
| "raw_value": "0E-7" | ||
| }, | ||
| { | ||
| "title": "Job End Time", | ||
| "value": "2023-10-24 06:52:09", | ||
| "plugin": "core", | ||
| "name": "end_epoch", | ||
| "raw_value": "1698130329.0000000" | ||
| }, | ||
| { | ||
| "title": "Job Start Time", | ||
| "value": "2023-10-24 06:52:09", | ||
| "plugin": "core", | ||
| "name": "start_epoch", | ||
| "raw_value": "1698130329.0000000" | ||
| }, | ||
| { | ||
| "title": "Memory Allocated (MB)", | ||
| "value": "4080", | ||
| "plugin": "core", | ||
| "name": "galaxy_memory_mb", | ||
| "raw_value": "4080.0000000" | ||
| }, | ||
| { | ||
| "title": "Cores Allocated", | ||
| "value": "1", | ||
| "plugin": "core", | ||
| "name": "galaxy_slots", | ||
| "raw_value": "1.0000000" | ||
| } | ||
| ] | ||
| } |
48 changes: 48 additions & 0 deletions
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reports/anvil-edge/tool-tests/edge-23-10-24-06-08-1/errors/23b59d329824db73.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,48 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "23b59d329824db73", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "update_time": "2023-10-24T06:36:11.064450", | ||
| "create_time": "2023-10-24T06:36:04.414746", | ||
| "galaxy_version": "23.1", | ||
| "command_version": null, | ||
| "copied_from_job_id": null, | ||
| "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", | ||
| "history_id": "b8e3c9423bdc89f6", | ||
| "external_id": "gxy-s6hm5", | ||
| "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/e/b/1/dataset_eb1df349-5bf4-4311-ba16-4822ccbbf3dd.dat' sanger '/galaxy/server/database/objects/e/4/5/dataset_e45c9788-b2de-4733-a695-bac9b2cef89f.dat' cssanger None summarize_input --fix-id", | ||
| "traceback": null, | ||
| "params": { | ||
| "__input_ext": "\"fastq\"", | ||
| "dbkey": "\"?\"", | ||
| "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", | ||
| "options_type": "{\"__current_case__\": 1, \"fix_id\": true, \"force_quality_encoding\": \"None\", \"options_type_selector\": \"advanced\", \"output_type\": \"cssanger\", \"summarize_input\": \"summarize_input\"}", | ||
| "input_type": "\"sanger\"" | ||
| }, | ||
| "inputs": { | ||
| "input_file": { | ||
| "id": "f8591243569e9382", | ||
| "src": "hda", | ||
| "uuid": "eb1df349-5bf4-4311-ba16-4822ccbbf3dd" | ||
| } | ||
| }, | ||
| "outputs": { | ||
| "output_file": { | ||
| "id": "23b59d329824db73", | ||
| "src": "hda", | ||
| "uuid": "e45c9788-b2de-4733-a695-bac9b2cef89f" | ||
| } | ||
| }, | ||
| "output_collections": {}, | ||
| "tool_stdout": "", | ||
| "tool_stderr": "", | ||
| "job_stdout": null, | ||
| "job_stderr": null, | ||
| "stderr": "", | ||
| "stdout": "", | ||
| "job_messages": null, | ||
| "dependencies": [], | ||
| "user_email": "tests@fake.org", | ||
| "job_metrics": [] | ||
| } |
44 changes: 44 additions & 0 deletions
44
reports/anvil-edge/tool-tests/edge-23-10-24-06-08-1/errors/31728c841d35499b.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,44 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "31728c841d35499b", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "update_time": "2023-10-24T06:41:39.517836", | ||
| "create_time": "2023-10-24T06:41:28.279780", | ||
| "galaxy_version": "23.1", | ||
| "command_version": null, | ||
| "copied_from_job_id": null, | ||
| "tool_id": "upload1", | ||
| "history_id": "b8e3c9423bdc89f6", | ||
| "external_id": "gxy-vbnlp", | ||
| "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/62/registry.xml' '/galaxy/server/database/jobs_directory/000/62/upload_params.json' '62:/galaxy/server/database/objects/5/d/9/dataset_5d989378-4020-4184-a09d-5cb092a89ccf_files:/galaxy/server/database/objects/5/d/9/dataset_5d989378-4020-4184-a09d-5cb092a89ccf.dat'", | ||
| "traceback": null, | ||
| "params": { | ||
| "paramfile": "\"/galaxy/server/database/tmp/upload_params_8krk2pul\"", | ||
| "files_metadata": "{\"__current_case__\": 78, \"file_type\": \"fastq\"}", | ||
| "dbkey": "\"?\"", | ||
| "force_composite": "\"false\"", | ||
| "files": "[{\"NAME\": \"wrapping_original_sanger.fastqsanger\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_fzyx79c6\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", | ||
| "file_count": "\"auto\"", | ||
| "file_type": "\"fastq\"" | ||
| }, | ||
| "inputs": {}, | ||
| "outputs": { | ||
| "output0": { | ||
| "id": "31728c841d35499b", | ||
| "src": "hda", | ||
| "uuid": "5d989378-4020-4184-a09d-5cb092a89ccf" | ||
| } | ||
| }, | ||
| "output_collections": {}, | ||
| "tool_stdout": "", | ||
| "tool_stderr": "", | ||
| "job_stdout": null, | ||
| "job_stderr": null, | ||
| "stderr": "", | ||
| "stdout": "", | ||
| "job_messages": null, | ||
| "dependencies": [], | ||
| "user_email": "tests@fake.org", | ||
| "job_metrics": [] | ||
| } |
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44
reports/anvil-edge/tool-tests/edge-23-10-24-06-08-1/errors/7052fe37f5fb71c3.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,44 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "7052fe37f5fb71c3", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "update_time": "2023-10-24T06:27:54.324527", | ||
| "create_time": "2023-10-24T06:27:43.860003", | ||
| "galaxy_version": "23.1", | ||
| "command_version": null, | ||
| "copied_from_job_id": null, | ||
| "tool_id": "upload1", | ||
| "history_id": "b8e3c9423bdc89f6", | ||
| "external_id": "gxy-lm94v", | ||
| "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/9/registry.xml' '/galaxy/server/database/jobs_directory/000/9/upload_params.json' '9:/galaxy/server/database/objects/c/6/d/dataset_c6d3bf47-747a-4ff2-980c-4e0ce164af9a_files:/galaxy/server/database/objects/c/6/d/dataset_c6d3bf47-747a-4ff2-980c-4e0ce164af9a.dat'", | ||
| "traceback": null, | ||
| "params": { | ||
| "paramfile": "\"/galaxy/server/database/tmp/upload_params_o3xg_31o\"", | ||
| "files_metadata": "{\"__current_case__\": 56, \"file_type\": \"bigwig\"}", | ||
| "dbkey": "\"?\"", | ||
| "force_composite": "\"false\"", | ||
| "files": "[{\"NAME\": \"test.bw\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_z7z7aeuc\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", | ||
| "file_count": "\"auto\"", | ||
| "file_type": "\"bigwig\"" | ||
| }, | ||
| "inputs": {}, | ||
| "outputs": { | ||
| "output0": { | ||
| "id": "7052fe37f5fb71c3", | ||
| "src": "hda", | ||
| "uuid": "c6d3bf47-747a-4ff2-980c-4e0ce164af9a" | ||
| } | ||
| }, | ||
| "output_collections": {}, | ||
| "tool_stdout": "", | ||
| "tool_stderr": "", | ||
| "job_stdout": null, | ||
| "job_stderr": null, | ||
| "stderr": "", | ||
| "stdout": "", | ||
| "job_messages": null, | ||
| "dependencies": [], | ||
| "user_email": "tests@fake.org", | ||
| "job_metrics": [] | ||
| } |
44 changes: 44 additions & 0 deletions
44
reports/anvil-edge/tool-tests/edge-23-10-24-06-08-1/errors/911c99275447de60.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,44 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "911c99275447de60", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "update_time": "2023-10-24T06:58:29.896507", | ||
| "create_time": "2023-10-24T06:58:20.473923", | ||
| "galaxy_version": "23.1", | ||
| "command_version": null, | ||
| "copied_from_job_id": null, | ||
| "tool_id": "upload1", | ||
| "history_id": "b8e3c9423bdc89f6", | ||
| "external_id": "gxy-5tt8n", | ||
| "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/130/registry.xml' '/galaxy/server/database/jobs_directory/000/130/upload_params.json' '154:/galaxy/server/database/objects/6/a/1/dataset_6a15c4f5-800d-4dbe-9de0-3b9c99026370_files:/galaxy/server/database/objects/6/a/1/dataset_6a15c4f5-800d-4dbe-9de0-3b9c99026370.dat'", | ||
| "traceback": null, | ||
| "params": { | ||
| "paramfile": "\"/galaxy/server/database/tmp/upload_params_8prhi7k6\"", | ||
| "files_metadata": "{\"__current_case__\": 311, \"file_type\": \"tabular\"}", | ||
| "dbkey": "\"?\"", | ||
| "force_composite": "\"false\"", | ||
| "files": "[{\"NAME\": \"pets.tsv\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_dx4d1o57\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", | ||
| "file_count": "\"auto\"", | ||
| "file_type": "\"tabular\"" | ||
| }, | ||
| "inputs": {}, | ||
| "outputs": { | ||
| "output0": { | ||
| "id": "0170cd6e6911e97e", | ||
| "src": "hda", | ||
| "uuid": "6a15c4f5-800d-4dbe-9de0-3b9c99026370" | ||
| } | ||
| }, | ||
| "output_collections": {}, | ||
| "tool_stdout": "", | ||
| "tool_stderr": "", | ||
| "job_stdout": null, | ||
| "job_stderr": null, | ||
| "stderr": "", | ||
| "stdout": "", | ||
| "job_messages": null, | ||
| "dependencies": [], | ||
| "user_email": "tests@fake.org", | ||
| "job_metrics": [] | ||
| } |
59 changes: 59 additions & 0 deletions
59
reports/anvil-edge/tool-tests/edge-23-10-24-06-08-1/errors/9c5885c0875e8135.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,59 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "9c5885c0875e8135", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "update_time": "2023-10-24T06:59:57.255203", | ||
| "create_time": "2023-10-24T06:59:51.843701", | ||
| "galaxy_version": "23.1", | ||
| "command_version": null, | ||
| "copied_from_job_id": null, | ||
| "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0", | ||
| "history_id": "b8e3c9423bdc89f6", | ||
| "external_id": "gxy-qb9wr", | ||
| "command_line": "cat '/galaxy/server/database/jobs_directory/000/136/configs/tmpkgl6zl5q' && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/cf34c344508d/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/136/configs/tmp_mvqe1xq' -Q '/galaxy/server/database/jobs_directory/000/136/configs/tmpkgl6zl5q' --comment_char='#' -o '/galaxy/server/database/objects/9/d/9/dataset_9d97200a-860c-4cbf-b5d0-f148971d13cc.dat'", | ||
| "traceback": null, | ||
| "params": { | ||
| "__input_ext": "\"tabular\"", | ||
| "dbkey": "\"?\"", | ||
| "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", | ||
| "addqueries": "{\"queries\": [{\"__index__\": 0, \"query_result\": {\"__current_case__\": 0, \"header\": \"yes\", \"header_prefix\": \"\"}, \"sqlquery\": \"SELECT * FROM psms WHERE confidence > 97.0\"}]}", | ||
| "query_result": "{\"__current_case__\": 0, \"header\": \"yes\", \"header_prefix\": \"35\"}", | ||
| "sqlquery": "\"SELECT scan,\\\"m/z\\\", \\\"Precursor m/z Error [ppm]\\\", Sequence, \\\"Protein(s)\\\", confidence FROM PSMs WHERE NOT re_search(', ',\\\"Protein(s)\\\")\"", | ||
| "save_db": "false", | ||
| "modify_database": "{\"sql_stmts\": [{\"__index__\": 0, \"sqlstmt\": \"UPDATE psms SET confidence = 99.999 WHERE confidence = 100.0\"}]}", | ||
| "tables": "[{\"__index__\": 0, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"__current_case__\": 9, \"columns\": \"1,3,2,6,14,19,23\", \"filter_type\": \"select_columns\"}}]}, \"table\": {\"values\": [{\"id\": 159, \"src\": \"hda\"}]}, \"tbl_opts\": {\"col_names\": \"scan,,,,,,confidence\", \"column_names_from_first_line\": true, \"indexes\": [], \"load_named_columns\": false, \"pkey_autoincr\": \"\", \"table_name\": \"PSMs\"}}]", | ||
| "add_to_database": "{\"withdb\": null}", | ||
| "workdb": "\"workdb.sqlite\"" | ||
| }, | ||
| "inputs": { | ||
| "tables_0|table": { | ||
| "id": "11fb2a0834893de8", | ||
| "src": "hda", | ||
| "uuid": "4205196f-f5fe-4d09-a48d-0ad19b421c6d" | ||
| } | ||
| }, | ||
| "outputs": { | ||
| "output": { | ||
| "id": "544076db5bd97db8", | ||
| "src": "hda", | ||
| "uuid": "9d97200a-860c-4cbf-b5d0-f148971d13cc" | ||
| }, | ||
| "output1": { | ||
| "id": "61be5cba484a304d", | ||
| "src": "hda", | ||
| "uuid": "8f744d3d-98e2-4a61-ba4a-0a4d07b57705" | ||
| } | ||
| }, | ||
| "output_collections": {}, | ||
| "tool_stdout": "", | ||
| "tool_stderr": "", | ||
| "job_stdout": null, | ||
| "job_stderr": null, | ||
| "stderr": "", | ||
| "stdout": "", | ||
| "job_messages": null, | ||
| "dependencies": [], | ||
| "user_email": "tests@fake.org", | ||
| "job_metrics": [] | ||
| } |
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