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Updating anvil-edge README for edge-24-09-23-06-12-1
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reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/chunk.json
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{ | ||
"0": { | ||
"run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/results.html", | ||
"date1": "Mon Sep 23 06:26:44 2024", | ||
"tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/tools.yml" | ||
} | ||
} |
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reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/chunk.txt
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-t unicycler --tool-version 9e3e80cc4ad4 | ||
-t deeptools_bam_compare --tool-version e821645ef8fc | ||
-t cutadapt --tool-version 093678460093 | ||
-t cutadapt --tool-version 135b80fb1ac2 | ||
-t fastqc --tool-version 3d0c7bdf12f5 | ||
-t fastqc --tool-version e7b2202befea | ||
-t rna_starsolo --tool-version eec9494fdafa | ||
-t rna_starsolo --tool-version 79b885ce78d7 | ||
-t poretools_hist --tool-version 5a82eb9e1b89 | ||
-t picard --tool-version b502c227b5e6 | ||
-t samtools_view --tool-version b72793637686 | ||
-t samtools_split --tool-version 135c85f4cfaf | ||
-t sam_merge --tool-version 1977f1637890 | ||
-t dropletutils_read_10x --tool-version ca62f52e0d7f | ||
-t scater_normalize --tool-version 946179ef029c | ||
-t anndata_ops --tool-version 54f1212d26ac | ||
-t anndata_ops --tool-version 6aa025ea64d3 | ||
-t scanpy_plot_embed --tool-version 99dd7baf9e23 | ||
-t scanpy_plot_embed --tool-version a8ef4bc35839 | ||
-t jq --tool-version 5ff75eb1a893 | ||
-t snpsift_dbnsfp --tool-version 4e21e4f2bc48 | ||
-t bcftools_plugin_counts --tool-version 4813f99d81b7 | ||
-t bcftools_view --tool-version 23680a42e149 | ||
-t vcfcheck --tool-version 2968c6916579 | ||
-t vcfdistance --tool-version 5822b40f3037 |
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reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/012ff491024a103d.json
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{ | ||
"model_class": "Job", | ||
"id": "012ff491024a103d", | ||
"history_id": "abbc0a781ea0cf97", | ||
"tool_id": "upload1", | ||
"state": "error", | ||
"exit_code": null, | ||
"create_time": "2024-09-23T06:41:22.713459", | ||
"update_time": "2024-09-23T06:41:33.505423", | ||
"galaxy_version": "24.1", | ||
"external_id": "gxy-grx9c", | ||
"handler": null, | ||
"job_runner_name": null, | ||
"command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/54/registry.xml' '/galaxy/server/database/jobs_directory/000/54/upload_params.json' '68:/galaxy/server/database/objects/b/c/4/dataset_bc491a7e-04ba-4d27-bcfe-54610f49ac97_files:/galaxy/server/database/objects/b/c/4/dataset_bc491a7e-04ba-4d27-bcfe-54610f49ac97.dat'", | ||
"user_email": "tests@fake.org", | ||
"command_version": null, | ||
"params": { | ||
"paramfile": "\"/galaxy/server/database/tmp/upload_params_rn6k7235\"", | ||
"files_metadata": "{\"__current_case__\": 79, \"file_type\": \"fastq.gz\"}", | ||
"dbkey": "\"?\"", | ||
"force_composite": "\"false\"", | ||
"files": "[{\"NAME\": \"bwa-mem-fastq2_assimetric.fq.gz\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_9p8htxjc\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", | ||
"file_count": "\"auto\"", | ||
"file_type": "\"fastq.gz\"" | ||
}, | ||
"inputs": {}, | ||
"outputs": { | ||
"output0": { | ||
"id": "29192b1e2b9e7b20", | ||
"src": "hda", | ||
"uuid": "bc491a7e-04ba-4d27-bcfe-54610f49ac97" | ||
} | ||
}, | ||
"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": [] | ||
} |
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reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/242180e9e118d62b.json
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{ | ||
"model_class": "Job", | ||
"id": "242180e9e118d62b", | ||
"history_id": "abbc0a781ea0cf97", | ||
"tool_id": "upload1", | ||
"state": "error", | ||
"exit_code": null, | ||
"create_time": "2024-09-23T07:12:51.835349", | ||
"update_time": "2024-09-23T07:13:02.395004", | ||
"galaxy_version": "24.1", | ||
"external_id": "gxy-5zfnd", | ||
"handler": null, | ||
"job_runner_name": null, | ||
"command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/185/registry.xml' '/galaxy/server/database/jobs_directory/000/185/upload_params.json' '229:/galaxy/server/database/objects/9/1/4/dataset_9140b870-5465-4a80-bfe5-ce4bd8c09c09_files:/galaxy/server/database/objects/9/1/4/dataset_9140b870-5465-4a80-bfe5-ce4bd8c09c09.dat'", | ||
"user_email": "tests@fake.org", | ||
"command_version": null, | ||
"params": { | ||
"paramfile": "\"/galaxy/server/database/tmp/upload_params_2zrsc793\"", | ||
"files_metadata": "{\"__current_case__\": 79, \"file_type\": \"fastq.gz\"}", | ||
"dbkey": "\"?\"", | ||
"force_composite": "\"false\"", | ||
"files": "[{\"NAME\": \"bwa-mem-fastq1.fq.gz\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_z6i5pmcl\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", | ||
"file_count": "\"auto\"", | ||
"file_type": "\"fastq.gz\"" | ||
}, | ||
"inputs": {}, | ||
"outputs": { | ||
"output0": { | ||
"id": "121d75de73994175", | ||
"src": "hda", | ||
"uuid": "9140b870-5465-4a80-bfe5-ce4bd8c09c09" | ||
} | ||
}, | ||
"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": [] | ||
} |
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reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/33349d9168d83366.json
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{ | ||
"model_class": "Job", | ||
"id": "33349d9168d83366", | ||
"history_id": "abbc0a781ea0cf97", | ||
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.15.1+galaxy4", | ||
"state": "error", | ||
"exit_code": null, | ||
"create_time": "2024-09-23T08:13:56.431831", | ||
"update_time": "2024-09-23T08:14:01.873314", | ||
"galaxy_version": "24.1", | ||
"external_id": "gxy-xp65v", | ||
"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/2/a/d/dataset_2ad787a9-2083-4145-8593-16b90dd28f85.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools view --samples 'NA00002' --min-ac 1 --max-ac 1 --types \"snps\" --regions-overlap 1 --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/0/c/8/dataset_0c86100c-0640-493b-9cc3-1b2080b9b4cc.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_output": "{\"compression_level\": \"\", \"drop_genotypes\": false, \"header\": null, \"invert_targets_file\": false}", | ||
"sec_filter": "{\"exclude_types\": null, \"known_or_novel\": null, \"max_ac\": \"1\", \"max_af\": \"\", \"max_alleles\": \"\", \"min_ac\": \"1\", \"min_af\": \"\", \"min_alleles\": \"\", \"phased\": null, \"private\": null, \"select_genotype\": null, \"types\": \"snps\", \"uncalled\": null}", | ||
"sec_subset": "{\"force_samples\": false, \"invert_samples\": false, \"invert_samples_file\": false, \"no_update\": false, \"samples\": \"NA00002\", \"samples_file\": null, \"trim_alt_alleles\": false}", | ||
"sec_restrict": "{\"apply_filters\": \"\", \"exclude\": null, \"include\": null, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": \"1\", \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}" | ||
}, | ||
"inputs": { | ||
"input_file": { | ||
"id": "0aff707637dcc57b", | ||
"src": "hda", | ||
"uuid": "2ad787a9-2083-4145-8593-16b90dd28f85" | ||
} | ||
}, | ||
"outputs": { | ||
"output_file": { | ||
"id": "10723048ea900c78", | ||
"src": "hda", | ||
"uuid": "0c86100c-0640-493b-9cc3-1b2080b9b4cc" | ||
} | ||
}, | ||
"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": [] | ||
} |
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reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/363809241d2e2d64.json
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{ | ||
"model_class": "Job", | ||
"id": "363809241d2e2d64", | ||
"history_id": "abbc0a781ea0cf97", | ||
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3", | ||
"state": "error", | ||
"exit_code": null, | ||
"create_time": "2024-09-23T07:59:50.616480", | ||
"update_time": "2024-09-23T07:59:55.788130", | ||
"galaxy_version": "24.1", | ||
"external_id": "gxy-bvgp9", | ||
"handler": null, | ||
"job_runner_name": null, | ||
"command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/4/d/2/dataset_4d2d6f9a-a69a-442d-922d-4a8a589f2557.dat' infile && sample_fragment=`samtools view -c infile | awk '{s=$1} END {frac=s/20; print(frac > 1 ? 6776+1/frac : \".0\")}'` && samtools view -@ $addthreads -h -s ${sample_fragment} -o outfile infile", | ||
"user_email": "tests@fake.org", | ||
"command_version": null, | ||
"params": { | ||
"__input_ext": "\"sam\"", | ||
"dbkey": "\"?\"", | ||
"chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", | ||
"addref_cond": "{\"__current_case__\": 0, \"addref_select\": \"no\"}", | ||
"mode": "{\"__current_case__\": 1, \"filter_config\": {\"cigarcons\": \"\", \"cond_region\": {\"__current_case__\": 0, \"select_region\": \"no\"}, \"cond_rg\": {\"__current_case__\": 0, \"select_rg\": \"no\"}, \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"inclusive_filter\": null, \"library\": null, \"quality\": \"\"}, \"output_options\": {\"__current_case__\": 0, \"adv_output\": {\"collapsecigar\": false, \"readtags\": []}, \"complementary_output\": false, \"output_format\": {\"__current_case__\": 0, \"oformat\": \"input\"}, \"reads_report_type\": \"retained\"}, \"outtype\": \"selected_reads\", \"subsample_config\": {\"subsampling_mode\": {\"__current_case__\": 1, \"seed\": \"\", \"select_subsample\": \"target\", \"target\": \"20\"}}}" | ||
}, | ||
"inputs": { | ||
"input": { | ||
"id": "9ba29b32212e9193", | ||
"src": "hda", | ||
"uuid": "4d2d6f9a-a69a-442d-922d-4a8a589f2557" | ||
} | ||
}, | ||
"outputs": { | ||
"outputsam": { | ||
"id": "8e06e5b36898b515", | ||
"src": "hda", | ||
"uuid": "64ee866e-0707-46e5-bd5b-73a833baf83c" | ||
} | ||
}, | ||
"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": [] | ||
} |
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reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/49adb5f856bc6730.json
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{ | ||
"model_class": "Job", | ||
"id": "49adb5f856bc6730", | ||
"history_id": "abbc0a781ea0cf97", | ||
"tool_id": "upload1", | ||
"state": "error", | ||
"exit_code": null, | ||
"create_time": "2024-09-23T07:21:39.458280", | ||
"update_time": "2024-09-23T07:21:50.363149", | ||
"galaxy_version": "24.1", | ||
"external_id": "gxy-dcw7t", | ||
"handler": null, | ||
"job_runner_name": null, | ||
"command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/221/registry.xml' '/galaxy/server/database/jobs_directory/000/221/upload_params.json' '273:/galaxy/server/database/objects/4/6/f/dataset_46fbbabd-90ea-4e08-b61a-98b91c9795be_files:/galaxy/server/database/objects/4/6/f/dataset_46fbbabd-90ea-4e08-b61a-98b91c9795be.dat'", | ||
"user_email": "tests@fake.org", | ||
"command_version": null, | ||
"params": { | ||
"paramfile": "\"/galaxy/server/database/tmp/upload_params_a1fmm3f4\"", | ||
"files_metadata": "{\"__current_case__\": 78, \"file_type\": \"fastq\"}", | ||
"dbkey": "\"?\"", | ||
"force_composite": "\"false\"", | ||
"files": "[{\"NAME\": \"1000trimmed.fastq\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_rghzxhre\", \"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": "7ab67487331b1c1a", | ||
"src": "hda", | ||
"uuid": "46fbbabd-90ea-4e08-b61a-98b91c9795be" | ||
} | ||
}, | ||
"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": [] | ||
} |
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reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/56d12ec3242f54cb.json
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{ | ||
"model_class": "Job", | ||
"id": "56d12ec3242f54cb", | ||
"history_id": "abbc0a781ea0cf97", | ||
"tool_id": "upload1", | ||
"state": "error", | ||
"exit_code": null, | ||
"create_time": "2024-09-23T07:12:05.082288", | ||
"update_time": "2024-09-23T07:12:16.197787", | ||
"galaxy_version": "24.1", | ||
"external_id": "gxy-q7vl6", | ||
"handler": null, | ||
"job_runner_name": null, | ||
"command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/180/registry.xml' '/galaxy/server/database/jobs_directory/000/180/upload_params.json' '223:/galaxy/server/database/objects/5/1/1/dataset_5114b8d1-d54c-4111-b7be-20805fd54b4d_files:/galaxy/server/database/objects/5/1/1/dataset_5114b8d1-d54c-4111-b7be-20805fd54b4d.dat'", | ||
"user_email": "tests@fake.org", | ||
"command_version": null, | ||
"params": { | ||
"paramfile": "\"/galaxy/server/database/tmp/upload_params_awrq_0q9\"", | ||
"files_metadata": "{\"__current_case__\": 79, \"file_type\": \"fastq.gz\"}", | ||
"dbkey": "\"?\"", | ||
"force_composite": "\"false\"", | ||
"files": "[{\"NAME\": \"bwa-mem-fastq1_assimetric.fq.gz\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_57rcuy04\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", | ||
"file_count": "\"auto\"", | ||
"file_type": "\"fastq.gz\"" | ||
}, | ||
"inputs": {}, | ||
"outputs": { | ||
"output0": { | ||
"id": "2f502f8caf6f5267", | ||
"src": "hda", | ||
"uuid": "5114b8d1-d54c-4111-b7be-20805fd54b4d" | ||
} | ||
}, | ||
"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": [] | ||
} |
45 changes: 45 additions & 0 deletions
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reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/5b2bf096077bd243.json
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{ | ||
"model_class": "Job", | ||
"id": "5b2bf096077bd243", | ||
"history_id": "abbc0a781ea0cf97", | ||
"tool_id": "upload1", | ||
"state": "error", | ||
"exit_code": null, | ||
"create_time": "2024-09-23T07:36:07.425685", | ||
"update_time": "2024-09-23T07:37:30.027172", | ||
"galaxy_version": "24.1", | ||
"external_id": "gxy-jdnfp", | ||
"handler": null, | ||
"job_runner_name": null, | ||
"command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/300/registry.xml' '/galaxy/server/database/jobs_directory/000/300/upload_params.json' '385:/galaxy/server/database/objects/7/1/7/dataset_71722d05-4f44-4443-9471-d1210ff8a7ad_files:/galaxy/server/database/objects/7/1/7/dataset_71722d05-4f44-4443-9471-d1210ff8a7ad.dat'", | ||
"user_email": "tests@fake.org", | ||
"command_version": null, | ||
"params": { | ||
"paramfile": "\"/galaxy/server/database/tmp/upload_params_fo0n2ak8\"", | ||
"files_metadata": "{\"__current_case__\": 82, \"file_type\": \"fastqsanger.gz\"}", | ||
"dbkey": "\"?\"", | ||
"force_composite": "\"false\"", | ||
"files": "[{\"NAME\": \"smartseq4.R1.fastq.gz\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_tmvvsbrb\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", | ||
"file_count": "\"auto\"", | ||
"file_type": "\"fastqsanger.gz\"" | ||
}, | ||
"inputs": {}, | ||
"outputs": { | ||
"output0": { | ||
"id": "a2c05ef4a0017263", | ||
"src": "hda", | ||
"uuid": "71722d05-4f44-4443-9471-d1210ff8a7ad" | ||
} | ||
}, | ||
"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": [] | ||
} |
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