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Updating anvil-production README for prod-25-01-14-12-34-1
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reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/chunk.json
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{ | ||
"3": { | ||
"run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/results.html", | ||
"date1": "Tue Jan 14 12:50:36 2025", | ||
"tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/tools.yml" | ||
} | ||
} |
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reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/chunk.txt
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-t split_file_to_collection --tool-version 6cbe2f30c2d7 | ||
-t reshape2_melt --tool-version 317ed0ee8bf2 | ||
-t fasta_compute_length --tool-version 7d37cfda8e00 | ||
-t bamtools --tool-version 4d343c1f606b | ||
-t samtools_idxstats --tool-version 7a6034296ae9 | ||
-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 flye --tool-version 3ee0ef312022 | ||
-t poretools_tabular --tool-version 2cb2feb94f0e | ||
-t deeptools_multi_bigwig_summary --tool-version 3c9f0c486cca | ||
-t unicycler --tool-version 9e3e80cc4ad4 | ||
-t ivar_removereads --tool-version ee2beb764a7b | ||
-t hisat2 --tool-version 26371a1df031 |
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reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/errors/251c84d7eaadebc5.json
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{ | ||
"model_class": "Job", | ||
"id": "251c84d7eaadebc5", | ||
"state": "error", | ||
"exit_code": null, | ||
"update_time": "2025-01-14T13:22:44.158163", | ||
"create_time": "2025-01-14T13:22:35.353297", | ||
"galaxy_version": "23.1", | ||
"command_version": null, | ||
"copied_from_job_id": null, | ||
"tool_id": "upload1", | ||
"history_id": "ddd7b7f231ac291f", | ||
"external_id": "gxy-s4pnc", | ||
"command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/129/registry.xml' '/galaxy/server/database/jobs_directory/000/129/upload_params.json' '155:/galaxy/server/database/objects/8/2/b/dataset_82ba407c-627e-47f2-b937-724058ea8f0e_files:/galaxy/server/database/objects/8/2/b/dataset_82ba407c-627e-47f2-b937-724058ea8f0e.dat'", | ||
"traceback": null, | ||
"params": { | ||
"paramfile": "\"/galaxy/server/database/tmp/upload_params_ndgduiyv\"", | ||
"files_metadata": "{\"__current_case__\": 75, \"file_type\": \"fasta\"}", | ||
"dbkey": "\"?\"", | ||
"force_composite": "\"false\"", | ||
"files": "[{\"NAME\": \"only_long.fasta\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_1i15hykn\", \"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": "6bec59745fc6b7fe", | ||
"src": "hda", | ||
"uuid": "82ba407c-627e-47f2-b937-724058ea8f0e" | ||
} | ||
}, | ||
"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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reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/errors/2fe056efb5e142a4.json
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{ | ||
"model_class": "Job", | ||
"id": "2fe056efb5e142a4", | ||
"state": "error", | ||
"exit_code": null, | ||
"update_time": "2025-01-14T13:36:23.294083", | ||
"create_time": "2025-01-14T13:36:13.547074", | ||
"galaxy_version": "23.1", | ||
"command_version": null, | ||
"copied_from_job_id": null, | ||
"tool_id": "upload1", | ||
"history_id": "ddd7b7f231ac291f", | ||
"external_id": "gxy-lhjx4", | ||
"command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/167/registry.xml' '/galaxy/server/database/jobs_directory/000/167/upload_params.json' '211:/galaxy/server/database/objects/5/4/b/dataset_54b83834-efd8-4036-af4f-16b4567d3f70_files:/galaxy/server/database/objects/5/4/b/dataset_54b83834-efd8-4036-af4f-16b4567d3f70.dat'", | ||
"traceback": null, | ||
"params": { | ||
"paramfile": "\"/galaxy/server/database/tmp/upload_params_16zigu_m\"", | ||
"files_metadata": "{\"__current_case__\": 81, \"file_type\": \"fastqsanger\"}", | ||
"dbkey": "\"?\"", | ||
"force_composite": "\"false\"", | ||
"files": "[{\"NAME\": \"hisat_input_2_forward.fastq\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_66s3o4nf\", \"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": "afbccd33a8adf6bf", | ||
"src": "hda", | ||
"uuid": "54b83834-efd8-4036-af4f-16b4567d3f70" | ||
} | ||
}, | ||
"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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reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/errors/59c78cc5c60b5503.json
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{ | ||
"model_class": "Job", | ||
"id": "59c78cc5c60b5503", | ||
"state": "error", | ||
"exit_code": null, | ||
"update_time": "2025-01-14T13:03:29.073933", | ||
"create_time": "2025-01-14T13:03:19.117406", | ||
"galaxy_version": "23.1", | ||
"command_version": null, | ||
"copied_from_job_id": null, | ||
"tool_id": "upload1", | ||
"history_id": "ddd7b7f231ac291f", | ||
"external_id": "gxy-c6pj4", | ||
"command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/45/registry.xml' '/galaxy/server/database/jobs_directory/000/45/upload_params.json' '52:/galaxy/server/database/objects/a/4/a/dataset_a4a10885-52e8-4312-aef7-b326a3776b75_files:/galaxy/server/database/objects/a/4/a/dataset_a4a10885-52e8-4312-aef7-b326a3776b75.dat'", | ||
"traceback": null, | ||
"params": { | ||
"paramfile": "\"/galaxy/server/database/tmp/upload_params__msl4usc\"", | ||
"files_metadata": "{\"__current_case__\": 79, \"file_type\": \"fastq.gz\"}", | ||
"dbkey": "\"?\"", | ||
"force_composite": "\"false\"", | ||
"files": "[{\"NAME\": \"ecoli_hifi_02.fastq.gz\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_zm7j4fxk\", \"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": "b949d99cf2477ca1", | ||
"src": "hda", | ||
"uuid": "a4a10885-52e8-4312-aef7-b326a3776b75" | ||
} | ||
}, | ||
"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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reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/errors/81dc4f6d51ba7b35.json
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{ | ||
"model_class": "Job", | ||
"id": "81dc4f6d51ba7b35", | ||
"state": "error", | ||
"exit_code": null, | ||
"update_time": "2025-01-14T13:08:25.278955", | ||
"create_time": "2025-01-14T13:08:09.756425", | ||
"galaxy_version": "23.1", | ||
"command_version": null, | ||
"copied_from_job_id": null, | ||
"tool_id": "upload1", | ||
"history_id": "ddd7b7f231ac291f", | ||
"external_id": "gxy-xlvwz", | ||
"command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/86/registry.xml' '/galaxy/server/database/jobs_directory/000/86/upload_params.json' '102:/galaxy/server/database/objects/6/b/7/dataset_6b73af94-8448-419b-b56b-59e492d0ac04_files:/galaxy/server/database/objects/6/b/7/dataset_6b73af94-8448-419b-b56b-59e492d0ac04.dat'", | ||
"traceback": null, | ||
"params": { | ||
"paramfile": "\"/galaxy/server/database/tmp/upload_params_zgxydc0j\"", | ||
"files_metadata": "{\"__current_case__\": 79, \"file_type\": \"fastq.gz\"}", | ||
"dbkey": "\"?\"", | ||
"force_composite": "\"false\"", | ||
"files": "[{\"NAME\": \"ecoli_hifi_06.fastq.gz\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_wv1_luv7\", \"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": "1bd8cb2f8194097a", | ||
"src": "hda", | ||
"uuid": "6b73af94-8448-419b-b56b-59e492d0ac04" | ||
} | ||
}, | ||
"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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reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/errors/8b01e92d9d187e3b.json
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{ | ||
"model_class": "Job", | ||
"id": "8b01e92d9d187e3b", | ||
"state": "error", | ||
"exit_code": null, | ||
"update_time": "2025-01-14T12:55:33.007037", | ||
"create_time": "2025-01-14T12:55:24.556132", | ||
"galaxy_version": "23.1", | ||
"command_version": null, | ||
"copied_from_job_id": null, | ||
"tool_id": "upload1", | ||
"history_id": "ddd7b7f231ac291f", | ||
"external_id": "gxy-8tdjg", | ||
"command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/16/registry.xml' '/galaxy/server/database/jobs_directory/000/16/upload_params.json' '16:/galaxy/server/database/objects/b/c/4/dataset_bc4b82cb-55fe-4cbd-aa11-f33a21f8d455_files:/galaxy/server/database/objects/b/c/4/dataset_bc4b82cb-55fe-4cbd-aa11-f33a21f8d455.dat'", | ||
"traceback": null, | ||
"params": { | ||
"paramfile": "\"/galaxy/server/database/tmp/upload_params_beck4v4r\"", | ||
"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_n3rx3hr0\", \"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": "8b01e92d9d187e3b", | ||
"src": "hda", | ||
"uuid": "bc4b82cb-55fe-4cbd-aa11-f33a21f8d455" | ||
} | ||
}, | ||
"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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reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/errors/e693ca82ce43d2f8.json
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{ | ||
"model_class": "Job", | ||
"id": "e693ca82ce43d2f8", | ||
"state": "error", | ||
"exit_code": null, | ||
"update_time": "2025-01-14T13:28:48.505416", | ||
"create_time": "2025-01-14T13:26:15.700977", | ||
"galaxy_version": "23.1", | ||
"command_version": null, | ||
"copied_from_job_id": null, | ||
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.1+galaxy0", | ||
"history_id": "ddd7b7f231ac291f", | ||
"external_id": "gxy-hkmrb", | ||
"command_line": "ln -s '/galaxy/server/database/objects/a/8/e/dataset_a8e7667e-3e06-4941-833a-173c42cb310d.dat' fq1.fastq && ln -s '/galaxy/server/database/objects/7/3/8/dataset_738fb138-e581-4661-98b6-3d90bc357e56.dat' fq2.fastq && ln -s '/galaxy/server/database/objects/6/6/4/dataset_664606f8-030b-409a-8205-6ded7a8045fd.dat' 'lr.fasta' && unicycler -t \"${GALAXY_SLOTS:-4}\" -o ./ --verbosity 3 -1 'fq1.fastq' -2 'fq2.fastq' -l lr.fasta --mode 'normal' --min_fasta_length '100' --linear_seqs '0' --min_kmer_frac '0.2' --max_kmer_frac '0.95' --kmer_count '10' --depth_filter '0.25' --start_gene_id '90.0' --start_gene_cov '95.0' --min_component_size '1000' --min_dead_end_size '1000' --scores '3,-6,-5,-2' --keep 2 && mkdir 'spades_graphs' && mv 00*gfa './spades_graphs/' && samtools view -@ \"${GALAXY_SLOTS:-4}\" -u 'read_alignment/long_read_alignments.sam' | samtools sort -@ \"${GALAXY_SLOTS:-4}\" -o 'read_alignment/long_read_alignments.bam'", | ||
"traceback": null, | ||
"params": { | ||
"__input_ext": "\"input\"", | ||
"dbkey": "\"?\"", | ||
"chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", | ||
"reuse": "[]", | ||
"keep": "\"2\"", | ||
"lr_align": "{\"contamination\": null, \"low_score\": \"\", \"no_simple_bridges\": false, \"scores\": \"3,-6,-5,-2\"}", | ||
"graph_clean": "{\"min_component_size\": \"1000\", \"min_dead_end_size\": \"1000\"}", | ||
"rotation": "{\"no_rotate\": false, \"start_gene_cov\": \"95.0\", \"start_gene_id\": \"90.0\", \"start_genes\": null}", | ||
"spades": "{\"depth_filter\": \"0.25\", \"kmer_count\": \"10\", \"kmers\": \"\", \"largest_component\": false, \"max_kmer_frac\": \"0.95\", \"min_kmer_frac\": \"0.2\"}", | ||
"min_anchor_seg_len": "\"\"", | ||
"linear_seqs": "\"0\"", | ||
"min_fasta_length": "\"100\"", | ||
"mode": "\"normal\"", | ||
"paired_unpaired": "{\"__current_case__\": 0, \"fastq_input1\": {\"values\": [{\"id\": 175, \"src\": \"hda\"}]}, \"fastq_input2\": {\"values\": [{\"id\": 176, \"src\": \"hda\"}]}, \"fastq_input_selector\": \"paired\"}" | ||
}, | ||
"inputs": { | ||
"paired_unpaired|fastq_input1": { | ||
"id": "5b3e62e1ffa8c393", | ||
"src": "hda", | ||
"uuid": "a8e7667e-3e06-4941-833a-173c42cb310d" | ||
}, | ||
"paired_unpaired|fastq_input2": { | ||
"id": "bfcea19bfdadace0", | ||
"src": "hda", | ||
"uuid": "738fb138-e581-4661-98b6-3d90bc357e56" | ||
}, | ||
"long": { | ||
"id": "5aceb46017159497", | ||
"src": "hda", | ||
"uuid": "664606f8-030b-409a-8205-6ded7a8045fd" | ||
} | ||
}, | ||
"outputs": { | ||
"assembly_graph": { | ||
"id": "baaeb697833af929", | ||
"src": "hda", | ||
"uuid": "47cff645-4a58-4097-85ed-8615d0c178f3" | ||
}, | ||
"assembly": { | ||
"id": "ea258d7a926adca1", | ||
"src": "hda", | ||
"uuid": "ab428f4c-4d1c-4507-b764-a1f500f5ccde" | ||
}, | ||
"bam_file": { | ||
"id": "83cc9c9255d88d7e", | ||
"src": "hda", | ||
"uuid": "2f09dae1-4821-4429-84c6-df5b3b7d03ab" | ||
} | ||
}, | ||
"output_collections": { | ||
"spades_collection": { | ||
"id": "7dc5a28cdd92d68e", | ||
"src": "hdca" | ||
} | ||
}, | ||
"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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reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/errors/fcce236af6e81fef.json
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{ | ||
"model_class": "Job", | ||
"id": "fcce236af6e81fef", | ||
"state": "error", | ||
"exit_code": null, | ||
"update_time": "2025-01-14T13:22:03.034610", | ||
"create_time": "2025-01-14T13:21:46.542884", | ||
"galaxy_version": "23.1", | ||
"command_version": null, | ||
"copied_from_job_id": null, | ||
"tool_id": "upload1", | ||
"history_id": "ddd7b7f231ac291f", | ||
"external_id": "gxy-c286n", | ||
"command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/124/registry.xml' '/galaxy/server/database/jobs_directory/000/124/upload_params.json' '149:/galaxy/server/database/objects/b/1/b/dataset_b1bd11ce-26d7-49e4-b95a-ed0190c2ea4d_files:/galaxy/server/database/objects/b/1/b/dataset_b1bd11ce-26d7-49e4-b95a-ed0190c2ea4d.dat'", | ||
"traceback": null, | ||
"params": { | ||
"paramfile": "\"/galaxy/server/database/tmp/upload_params_58rfvkf1\"", | ||
"files_metadata": "{\"__current_case__\": 81, \"file_type\": \"fastqsanger\"}", | ||
"dbkey": "\"?\"", | ||
"force_composite": "\"false\"", | ||
"files": "[{\"NAME\": \"phix_r.fq.gz\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_0po_ljfp\", \"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": "0df423c058b39e96", | ||
"src": "hda", | ||
"uuid": "b1bd11ce-26d7-49e4-b95a-ed0190c2ea4d" | ||
} | ||
}, | ||
"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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