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Updating anvil-edge README for edge-24-11-08-18-17-1
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7 changes: 7 additions & 0 deletions
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reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/chunk.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,7 @@ | ||
| { | ||
| "9": { | ||
| "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/results.html", | ||
| "date1": "Fri Nov 08 18:33:31 2024", | ||
| "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/tools.yml" | ||
| } | ||
| } |
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reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/chunk.txt
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,26 @@ | ||
| -t datamash_reverse --tool-version f198773344e4 | ||
| -t deeptools_plot_enrichment --tool-version e65d16fb2724 | ||
| -t umi_tools_count --tool-version 8250ea3a1501 | ||
| -t umi_tools_count --tool-version b557acca0b56 | ||
| -t umi_tools_count --tool-version a535cf1e5da4 | ||
| -t bowtie2 --tool-version 09b2cdb7ace5 | ||
| -t medaka_consensus_pipeline --tool-version a7228a7ea146 | ||
| -t poretools_stats --tool-version 4b17acf9b6ab | ||
| -t stringtie --tool-version 1ebd14235b92 | ||
| -t samtools_markdup --tool-version 83b8e36e9cbe | ||
| -t samtools_markdup --tool-version b5527cc104ab | ||
| -t bamtools_filter --tool-version cb20f99fd45b | ||
| -t bamtools_filter --tool-version bd735cae4ce6 | ||
| -t anndata_manipulate --tool-version 9bd945a03d7b | ||
| -t anndata_manipulate --tool-version 3d748954434b | ||
| -t salmonquantmerge --tool-version 88c07fc4024c | ||
| -t scanpy_remove_confounders --tool-version bf2017df9837 | ||
| -t scanpy_compute_graph --tool-version 2401808e20e8 | ||
| -t scanpy_compute_graph --tool-version a58d4166805b | ||
| -t split_file_on_column --tool-version 37a53100b67e | ||
| -t lofreq_indelqual --tool-version 426d707dfc47 | ||
| -t bcftools_norm --tool-version c077f71d351f | ||
| -t bcftools_plugin_fill_tags --tool-version bf7d6acd9884 | ||
| -t vcfallelicprimitives --tool-version 57a16b310fe8 | ||
| -t vcfprimers --tool-version 17096387c0e6 | ||
| -t ivar_filtervariants --tool-version 7fe36019c073 |
45 changes: 45 additions & 0 deletions
45
reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/errors/28ca52757f505a15.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,45 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "28ca52757f505a15", | ||
| "history_id": "da7414b0e37eac28", | ||
| "tool_id": "upload1", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "create_time": "2024-11-08T19:08:26.807587", | ||
| "update_time": "2024-11-08T19:08:39.496430", | ||
| "galaxy_version": "24.1", | ||
| "external_id": "gxy-jr97t", | ||
| "handler": null, | ||
| "job_runner_name": null, | ||
| "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/122/registry.xml' '/galaxy/server/database/jobs_directory/000/122/upload_params.json' '141:/galaxy/server/database/objects/e/7/b/dataset_e7b7875c-20ad-4b39-a910-cf352f7cdc0e_files:/galaxy/server/database/objects/e/7/b/dataset_e7b7875c-20ad-4b39-a910-cf352f7cdc0e.dat'", | ||
| "user_email": "tests@fake.org", | ||
| "command_version": null, | ||
| "params": { | ||
| "paramfile": "\"/galaxy/server/database/tmp/upload_params_irhxrn7r\"", | ||
| "files_metadata": "{\"__current_case__\": 36, \"file_type\": \"bam\"}", | ||
| "dbkey": "\"?\"", | ||
| "force_composite": "\"false\"", | ||
| "files": "[{\"NAME\": \"long_reads.bam\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_sp4_tis8\", \"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": "e9cb4075989abeb8", | ||
| "src": "hda", | ||
| "uuid": "e7b7875c-20ad-4b39-a910-cf352f7cdc0e" | ||
| } | ||
| }, | ||
| "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
45
reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/errors/2cd95566f4d04a2a.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,45 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "2cd95566f4d04a2a", | ||
| "history_id": "da7414b0e37eac28", | ||
| "tool_id": "upload1", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "create_time": "2024-11-08T19:02:05.761737", | ||
| "update_time": "2024-11-08T19:02:18.074024", | ||
| "galaxy_version": "24.1", | ||
| "external_id": "gxy-4wscw", | ||
| "handler": null, | ||
| "job_runner_name": null, | ||
| "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/96/registry.xml' '/galaxy/server/database/jobs_directory/000/96/upload_params.json' '104:/galaxy/server/database/objects/3/1/c/dataset_31cba7c9-425a-4ca4-a36a-e1b95f8ae94d_files:/galaxy/server/database/objects/3/1/c/dataset_31cba7c9-425a-4ca4-a36a-e1b95f8ae94d.dat'", | ||
| "user_email": "tests@fake.org", | ||
| "command_version": null, | ||
| "params": { | ||
| "paramfile": "\"/galaxy/server/database/tmp/upload_params_b37384th\"", | ||
| "files_metadata": "{\"__current_case__\": 248, \"file_type\": \"fast5.tar\"}", | ||
| "dbkey": "\"?\"", | ||
| "force_composite": "\"false\"", | ||
| "files": "[{\"NAME\": \"poretools-in1.tar.bz2\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_ao_cevnx\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", | ||
| "file_count": "\"auto\"", | ||
| "file_type": "\"fast5.tar\"" | ||
| }, | ||
| "inputs": {}, | ||
| "outputs": { | ||
| "output0": { | ||
| "id": "1ca8330398e88230", | ||
| "src": "hda", | ||
| "uuid": "31cba7c9-425a-4ca4-a36a-e1b95f8ae94d" | ||
| } | ||
| }, | ||
| "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": [] | ||
| } |
62 changes: 62 additions & 0 deletions
62
reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/errors/38e2156fd7401822.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,62 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "38e2156fd7401822", | ||
| "history_id": "da7414b0e37eac28", | ||
| "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.15.1+galaxy4", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "create_time": "2024-11-08T19:37:00.489978", | ||
| "update_time": "2024-11-08T19:37:06.053487", | ||
| "galaxy_version": "24.1", | ||
| "external_id": "gxy-xfpsb", | ||
| "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/7/a/a/dataset_7aaae6d9-5b8e-4c4a-ac0b-c92aad2008a6.dat' > input.vcf.gz && bcftools index input.vcf.gz && ln -s '/galaxy/server/database/objects/5/7/3/dataset_573fcc22-f2c2-4d81-be0d-19d8e9001df9.dat' ref.fa && samtools faidx ref.fa && awk '{ if ($0 !~ />/) {print toupper($0)} else {print $0} }' 'ref.fa' > ref_upper.fa && bcftools norm --fasta-ref ref_upper.fa --check-ref w --do-not-normalize --multiallelics '+both' --strict-filter --site-win 1000 --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/2/c/8/dataset_2c83b419-25a1-4495-a502-bcb398c76eba.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_default": "{\"site_win\": \"1000\"}", | ||
| "sec_restrict": "{\"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}", | ||
| "multiallelics": "{\"__current_case__\": 2, \"mode\": \"+\", \"multiallelic_types\": \"both\", \"strict_filter\": true}", | ||
| "rm_dup": "\"\"", | ||
| "old_rec_tag": "\"\"", | ||
| "normalize_indels": "false", | ||
| "atomize": "false", | ||
| "check_ref": "\"w\"", | ||
| "reference_source": "{\"__current_case__\": 1, \"fasta_ref\": {\"values\": [{\"id\": 240, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}" | ||
| }, | ||
| "inputs": { | ||
| "input_file": { | ||
| "id": "dc82172fda263ec8", | ||
| "src": "hda", | ||
| "uuid": "7aaae6d9-5b8e-4c4a-ac0b-c92aad2008a6" | ||
| }, | ||
| "reference_source|fasta_ref": { | ||
| "id": "82ce24234cd1d762", | ||
| "src": "hda", | ||
| "uuid": "573fcc22-f2c2-4d81-be0d-19d8e9001df9" | ||
| } | ||
| }, | ||
| "outputs": { | ||
| "output_file": { | ||
| "id": "8edb363bd0a3069a", | ||
| "src": "hda", | ||
| "uuid": "2c83b419-25a1-4495-a502-bcb398c76eba" | ||
| } | ||
| }, | ||
| "copied_from_job_id": null, | ||
| "output_collections": {}, | ||
| "tool_stdout": "", | ||
| "tool_stderr": "Lines total/split/realigned/skipped:\t26/0/0/0\n", | ||
| "job_stdout": null, | ||
| "job_stderr": null, | ||
| "stdout": "", | ||
| "stderr": "Lines total/split/realigned/skipped:\t26/0/0/0\n", | ||
| "job_messages": null, | ||
| "dependencies": [], | ||
| "job_metrics": [] | ||
| } |
45 changes: 45 additions & 0 deletions
45
reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/errors/45abc3d0f8b42070.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,45 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "45abc3d0f8b42070", | ||
| "history_id": "da7414b0e37eac28", | ||
| "tool_id": "upload1", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "create_time": "2024-11-08T18:55:57.249760", | ||
| "update_time": "2024-11-08T18:56:09.556380", | ||
| "galaxy_version": "24.1", | ||
| "external_id": "gxy-j8jd7", | ||
| "handler": null, | ||
| "job_runner_name": null, | ||
| "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/82/registry.xml' '/galaxy/server/database/jobs_directory/000/82/upload_params.json' '84:/galaxy/server/database/objects/8/8/b/dataset_88b2d692-3432-4763-8775-7d213402ad14_files:/galaxy/server/database/objects/8/8/b/dataset_88b2d692-3432-4763-8775-7d213402ad14.dat'", | ||
| "user_email": "tests@fake.org", | ||
| "command_version": null, | ||
| "params": { | ||
| "paramfile": "\"/galaxy/server/database/tmp/upload_params_3znrpibx\"", | ||
| "files_metadata": "{\"__current_case__\": 75, \"file_type\": \"fasta\"}", | ||
| "dbkey": "\"?\"", | ||
| "force_composite": "\"false\"", | ||
| "files": "[{\"NAME\": \"bowtie2-fq2.fa\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_fwtxel0e\", \"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": "30453ec4f199ee7d", | ||
| "src": "hda", | ||
| "uuid": "88b2d692-3432-4763-8775-7d213402ad14" | ||
| } | ||
| }, | ||
| "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
45
reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/errors/75b0d11877e26dbe.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,45 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "75b0d11877e26dbe", | ||
| "history_id": "da7414b0e37eac28", | ||
| "tool_id": "upload1", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "create_time": "2024-11-08T18:50:33.496526", | ||
| "update_time": "2024-11-08T18:50:45.672994", | ||
| "galaxy_version": "24.1", | ||
| "external_id": "gxy-kxcrf", | ||
| "handler": null, | ||
| "job_runner_name": null, | ||
| "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/52/registry.xml' '/galaxy/server/database/jobs_directory/000/52/upload_params.json' '53:/galaxy/server/database/objects/e/9/6/dataset_e9694852-f518-41a0-98f9-d50d8a670a57_files:/galaxy/server/database/objects/e/9/6/dataset_e9694852-f518-41a0-98f9-d50d8a670a57.dat'", | ||
| "user_email": "tests@fake.org", | ||
| "command_version": null, | ||
| "params": { | ||
| "paramfile": "\"/galaxy/server/database/tmp/upload_params_678yu6q2\"", | ||
| "files_metadata": "{\"__current_case__\": 81, \"file_type\": \"fastqsanger\"}", | ||
| "dbkey": "\"?\"", | ||
| "force_composite": "\"false\"", | ||
| "files": "[{\"NAME\": \"bowtie2-fq2.fq\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_nlo5cv8v\", \"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": "e5b1b68f6c1b4f43", | ||
| "src": "hda", | ||
| "uuid": "e9694852-f518-41a0-98f9-d50d8a670a57" | ||
| } | ||
| }, | ||
| "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": [] | ||
| } |
61 changes: 61 additions & 0 deletions
61
reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/errors/87afed66c00a7675.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,61 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "87afed66c00a7675", | ||
| "history_id": "da7414b0e37eac28", | ||
| "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "create_time": "2024-11-08T19:07:23.730144", | ||
| "update_time": "2024-11-08T19:07:29.338183", | ||
| "galaxy_version": "24.1", | ||
| "external_id": "gxy-jvrng", | ||
| "handler": null, | ||
| "job_runner_name": null, | ||
| "command_line": "mkdir -p ./special_de_output/sample1/ && ln -s '/galaxy/server/database/objects/b/5/9/dataset_b5948e20-50b6-4e9f-bf48-07845a8d3710.dat' guide.gff && stringtie '/galaxy/server/database/objects/e/f/1/dataset_ef1e9415-0b70-45ee-844d-a778ac4ee621.dat' -o '/galaxy/server/database/objects/d/d/9/dataset_dd909ae8-ad9e-450d-89e3-30605e6a5aff.dat' -p \"${GALAXY_SLOTS:-1}\" -G guide.gff -b ./special_de_output/sample1/ -f '0.17' -m '200' -a '10' -j '1' -c '1' -g '50' -M '1.0' -A '/galaxy/server/database/objects/b/4/6/dataset_b46627df-7520-449d-85d7-60f9a4e3540c.dat'", | ||
| "user_email": "tests@fake.org", | ||
| "command_version": null, | ||
| "params": { | ||
| "__input_ext": "\"input\"", | ||
| "dbkey": "\"?\"", | ||
| "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", | ||
| "adv": "{\"abundance_estimation\": true, \"bdist\": \"50\", \"bundle_fraction\": \"1.0\", \"disable_trimming\": false, \"fraction\": \"0.17\", \"min_anchor_cov\": \"1\", \"min_anchor_len\": \"10\", \"min_bundle_cov\": \"1\", \"min_tlen\": \"200\", \"multi_mapping\": false, \"name_prefix\": null, \"omit_sequences\": \"\", \"point_features\": null}", | ||
| "guide": "{\"__current_case__\": 1, \"coverage_file\": false, \"guide_source\": {\"__current_case__\": 1, \"guide_gff_select\": \"history\", \"ref_hist\": {\"values\": [{\"id\": 134, \"src\": \"hda\"}]}}, \"input_estimation\": false, \"special_outputs\": {\"__current_case__\": 2, \"special_outputs_select\": \"no\"}, \"use_guide\": \"yes\"}", | ||
| "rna_strandness": "\"\"", | ||
| "input_options": "{\"__current_case__\": 0, \"input_bam\": {\"values\": [{\"id\": 133, \"src\": \"hda\"}]}, \"input_mode\": \"short_reads\"}" | ||
| }, | ||
| "inputs": { | ||
| "input_options|input_bam": { | ||
| "id": "0875c422d93fe122", | ||
| "src": "hda", | ||
| "uuid": "ef1e9415-0b70-45ee-844d-a778ac4ee621" | ||
| }, | ||
| "guide|guide_source|ref_hist": { | ||
| "id": "d4aba126f7fdc3f6", | ||
| "src": "hda", | ||
| "uuid": "b5948e20-50b6-4e9f-bf48-07845a8d3710" | ||
| } | ||
| }, | ||
| "outputs": { | ||
| "output_gtf": { | ||
| "id": "7807a571f0107626", | ||
| "src": "hda", | ||
| "uuid": "dd909ae8-ad9e-450d-89e3-30605e6a5aff" | ||
| }, | ||
| "gene_abundance_estimation": { | ||
| "id": "d29a7e08587fb6be", | ||
| "src": "hda", | ||
| "uuid": "b46627df-7520-449d-85d7-60f9a4e3540c" | ||
| } | ||
| }, | ||
| "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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