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Updating anvil-production README for prod-24-09-01-00-39-1
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7 changes: 7 additions & 0 deletions
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reports/anvil-production/tool-tests/prod-24-09-01-00-39-1/chunk.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,7 @@ | ||
| { | ||
| "12": { | ||
| "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-09-01-00-39-1/results.html", | ||
| "date1": "Sun Sep 01 00:54:13 2024", | ||
| "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-09-01-00-39-1/tools.yml" | ||
| } | ||
| } |
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reports/anvil-production/tool-tests/prod-24-09-01-00-39-1/chunk.txt
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,15 @@ | ||
| -t regex_find_replace --tool-version ae8c4b2488e7 | ||
| -t datamash_ops --tool-version 562f3c677828 | ||
| -t pileup_interval --tool-version 9c1c0b947e46 | ||
| -t samtools_depth --tool-version 44de678a44c4 | ||
| -t samtools_rmdup --tool-version 586f9e1cdb2b | ||
| -t bcftools_mpileup --tool-version 0dbff46d5a1b | ||
| -t bcftools_filter --tool-version 6ca7c55a27e8 | ||
| -t vcfcombine --tool-version 1f0ba67cc85a | ||
| -t vcffilter --tool-version fa24bf0598f4 | ||
| -t poretools_squiggle --tool-version 34553d0caa5e | ||
| -t deeptools_bam_pe_fragmentsize --tool-version 62eb6d63f582 | ||
| -t minimap2 --tool-version f54f5baedfdd | ||
| -t freebayes --tool-version ef2c525bd8cd | ||
| -t kallisto_quant --tool-version 60f888039fb2 | ||
| -t mummer_dnadiff --tool-version 60698466facd |
44 changes: 44 additions & 0 deletions
44
reports/anvil-production/tool-tests/prod-24-09-01-00-39-1/errors/06b99ccac916a1d3.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,44 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "06b99ccac916a1d3", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "update_time": "2024-09-01T01:02:34.455697", | ||
| "create_time": "2024-09-01T01:02:24.455074", | ||
| "galaxy_version": "23.1", | ||
| "command_version": null, | ||
| "copied_from_job_id": null, | ||
| "tool_id": "upload1", | ||
| "history_id": "2a13282dc391f200", | ||
| "external_id": "gxy-746h9", | ||
| "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/36/registry.xml' '/galaxy/server/database/jobs_directory/000/36/upload_params.json' '36:/galaxy/server/database/objects/e/3/4/dataset_e34e35f6-9089-4e83-a6f5-f97e95a3fc43_files:/galaxy/server/database/objects/e/3/4/dataset_e34e35f6-9089-4e83-a6f5-f97e95a3fc43.dat'", | ||
| "traceback": null, | ||
| "params": { | ||
| "paramfile": "\"/galaxy/server/database/tmp/upload_params__p6nj2ji\"", | ||
| "files_metadata": "{\"__current_case__\": 36, \"file_type\": \"bam\"}", | ||
| "dbkey": "\"?\"", | ||
| "force_composite": "\"false\"", | ||
| "files": "[{\"NAME\": \"mpileup.3.bam\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_4n4rl724\", \"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": "06b99ccac916a1d3", | ||
| "src": "hda", | ||
| "uuid": "e34e35f6-9089-4e83-a6f5-f97e95a3fc43" | ||
| } | ||
| }, | ||
| "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-24-09-01-00-39-1/errors/0a41db2ecb033302.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,44 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "0a41db2ecb033302", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "update_time": "2024-09-01T01:13:23.391975", | ||
| "create_time": "2024-09-01T01:13:13.661983", | ||
| "galaxy_version": "23.1", | ||
| "command_version": null, | ||
| "copied_from_job_id": null, | ||
| "tool_id": "upload1", | ||
| "history_id": "2a13282dc391f200", | ||
| "external_id": "gxy-pfdfw", | ||
| "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' '99:/galaxy/server/database/objects/0/a/e/dataset_0aed5cce-80c2-4e9c-a9dd-4b9abdab2a45_files:/galaxy/server/database/objects/0/a/e/dataset_0aed5cce-80c2-4e9c-a9dd-4b9abdab2a45.dat'", | ||
| "traceback": null, | ||
| "params": { | ||
| "paramfile": "\"/galaxy/server/database/tmp/upload_params_19jym23m\"", | ||
| "files_metadata": "{\"__current_case__\": 82, \"file_type\": \"fastqsanger.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_begi13bh\", \"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": "f9abaff036530197", | ||
| "src": "hda", | ||
| "uuid": "0aed5cce-80c2-4e9c-a9dd-4b9abdab2a45" | ||
| } | ||
| }, | ||
| "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": [] | ||
| } |
49 changes: 49 additions & 0 deletions
49
reports/anvil-production/tool-tests/prod-24-09-01-00-39-1/errors/1e2aa7a9ce5331b1.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,49 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "1e2aa7a9ce5331b1", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "update_time": "2024-09-01T01:06:00.501324", | ||
| "create_time": "2024-09-01T01:05:55.097987", | ||
| "galaxy_version": "23.1", | ||
| "command_version": null, | ||
| "copied_from_job_id": null, | ||
| "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/bcftools_filter/1.10", | ||
| "history_id": "2a13282dc391f200", | ||
| "external_id": "gxy-7qxct", | ||
| "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/4/9/c/dataset_49c04be8-54c2-47dd-81f9-ec3f56bb662f.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools filter --mode '+' --soft-filter \"XX\" --exclude 'INFO/DP=19' --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/9/b/6/dataset_9b63bc40-ad9b-476e-bb58-58b91d06038f.dat'", | ||
| "traceback": null, | ||
| "params": { | ||
| "__input_ext": "\"vcf\"", | ||
| "dbkey": "\"?\"", | ||
| "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", | ||
| "output_type": "\"v\"", | ||
| "sec_filter": "{\"IndelGap\": \"\", \"SnpGap\": \"\", \"mode\": \"+\", \"select_set_GTs\": null, \"soft_filter\": \"XX\"}", | ||
| "sec_restrict": "{\"exclude\": \"INFO/DP=19\", \"include\": null, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}}" | ||
| }, | ||
| "inputs": { | ||
| "input_file": { | ||
| "id": "f07cc9a70cc49836", | ||
| "src": "hda", | ||
| "uuid": "49c04be8-54c2-47dd-81f9-ec3f56bb662f" | ||
| } | ||
| }, | ||
| "outputs": { | ||
| "output_file": { | ||
| "id": "1e2aa7a9ce5331b1", | ||
| "src": "hda", | ||
| "uuid": "9b63bc40-ad9b-476e-bb58-58b91d06038f" | ||
| } | ||
| }, | ||
| "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-24-09-01-00-39-1/errors/2a0faa0d697f07f9.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,44 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "2a0faa0d697f07f9", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "update_time": "2024-09-01T01:02:56.068978", | ||
| "create_time": "2024-09-01T01:02:45.165906", | ||
| "galaxy_version": "23.1", | ||
| "command_version": null, | ||
| "copied_from_job_id": null, | ||
| "tool_id": "upload1", | ||
| "history_id": "2a13282dc391f200", | ||
| "external_id": "gxy-2xmxf", | ||
| "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/39/registry.xml' '/galaxy/server/database/jobs_directory/000/39/upload_params.json' '39:/galaxy/server/database/objects/2/9/f/dataset_29f4d179-7623-48b0-a389-45c98ee38d07_files:/galaxy/server/database/objects/2/9/f/dataset_29f4d179-7623-48b0-a389-45c98ee38d07.dat'", | ||
| "traceback": null, | ||
| "params": { | ||
| "paramfile": "\"/galaxy/server/database/tmp/upload_params_vr_pwyey\"", | ||
| "files_metadata": "{\"__current_case__\": 36, \"file_type\": \"bam\"}", | ||
| "dbkey": "\"?\"", | ||
| "force_composite": "\"false\"", | ||
| "files": "[{\"NAME\": \"mpileup.2.bam\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_o1_2ib_i\", \"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": "2a0faa0d697f07f9", | ||
| "src": "hda", | ||
| "uuid": "29f4d179-7623-48b0-a389-45c98ee38d07" | ||
| } | ||
| }, | ||
| "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-24-09-01-00-39-1/errors/455a36967d4728b8.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,44 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "455a36967d4728b8", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "update_time": "2024-09-01T01:18:20.441751", | ||
| "create_time": "2024-09-01T01:18:10.608249", | ||
| "galaxy_version": "23.1", | ||
| "command_version": null, | ||
| "copied_from_job_id": null, | ||
| "tool_id": "upload1", | ||
| "history_id": "2a13282dc391f200", | ||
| "external_id": "gxy-92xwm", | ||
| "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/115/registry.xml' '/galaxy/server/database/jobs_directory/000/115/upload_params.json' '128:/galaxy/server/database/objects/8/e/0/dataset_8e0bf91f-ae3b-4e03-b91e-087c94cc810a_files:/galaxy/server/database/objects/8/e/0/dataset_8e0bf91f-ae3b-4e03-b91e-087c94cc810a.dat'", | ||
| "traceback": null, | ||
| "params": { | ||
| "paramfile": "\"/galaxy/server/database/tmp/upload_params_bcsa0umm\"", | ||
| "files_metadata": "{\"__current_case__\": 42, \"file_type\": \"cram\"}", | ||
| "dbkey": "\"?\"", | ||
| "force_composite": "\"false\"", | ||
| "files": "[{\"NAME\": \"freebayes-phix174.cram\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_lxpn4qcx\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", | ||
| "file_count": "\"auto\"", | ||
| "file_type": "\"cram\"" | ||
| }, | ||
| "inputs": {}, | ||
| "outputs": { | ||
| "output0": { | ||
| "id": "f3128c6a3b4a39a6", | ||
| "src": "hda", | ||
| "uuid": "8e0bf91f-ae3b-4e03-b91e-087c94cc810a" | ||
| } | ||
| }, | ||
| "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-24-09-01-00-39-1/errors/70fd6c6a0f088918.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,44 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "70fd6c6a0f088918", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "update_time": "2024-09-01T01:21:16.037811", | ||
| "create_time": "2024-09-01T01:21:06.938089", | ||
| "galaxy_version": "23.1", | ||
| "command_version": null, | ||
| "copied_from_job_id": null, | ||
| "tool_id": "upload1", | ||
| "history_id": "2a13282dc391f200", | ||
| "external_id": "gxy-gssz4", | ||
| "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/137/registry.xml' '/galaxy/server/database/jobs_directory/000/137/upload_params.json' '156:/galaxy/server/database/objects/8/f/b/dataset_8fb96364-35c9-4912-abb1-cadb112d027c_files:/galaxy/server/database/objects/8/f/b/dataset_8fb96364-35c9-4912-abb1-cadb112d027c.dat'", | ||
| "traceback": null, | ||
| "params": { | ||
| "paramfile": "\"/galaxy/server/database/tmp/upload_params_4dv1aetm\"", | ||
| "files_metadata": "{\"__current_case__\": 78, \"file_type\": \"fastq\"}", | ||
| "dbkey": "\"sacCer2\"", | ||
| "force_composite": "\"false\"", | ||
| "files": "[{\"NAME\": \"sacCer2_chrM_R.fq\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_k3rlfzd9\", \"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": "89bf0fd5324d48eb", | ||
| "src": "hda", | ||
| "uuid": "8fb96364-35c9-4912-abb1-cadb112d027c" | ||
| } | ||
| }, | ||
| "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": [] | ||
| } |
57 changes: 57 additions & 0 deletions
57
reports/anvil-production/tool-tests/prod-24-09-01-00-39-1/errors/89b76523334e7da9.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,57 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "89b76523334e7da9", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "update_time": "2024-09-01T01:12:11.005381", | ||
| "create_time": "2024-09-01T01:12:02.514848", | ||
| "galaxy_version": "23.1", | ||
| "command_version": null, | ||
| "copied_from_job_id": null, | ||
| "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy4", | ||
| "history_id": "2a13282dc391f200", | ||
| "external_id": "gxy-s65pz", | ||
| "command_line": "ln -f -s '/galaxy/server/database/objects/c/0/7/dataset_c072b9d4-6a1c-4fa5-b314-c12bf4738857.dat' reference.fa && minimap2 -x sr -t ${GALAXY_SLOTS:-4} reference.fa '/galaxy/server/database/objects/1/2/3/dataset_1238966b-4ed5-40a0-a7ed-f2c6cb8b314a.dat' -a | samtools sort -@${GALAXY_SLOTS:-2} -T \"${TMPDIR:-.}\" -O BAM -o '/galaxy/server/database/objects/3/9/7/dataset_39779258-e8e2-448e-84d9-77b2c9233af0.dat'", | ||
| "traceback": null, | ||
| "params": { | ||
| "__input_ext": "\"input\"", | ||
| "dbkey": "\"?\"", | ||
| "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", | ||
| "io_options": "{\"K\": \"\", \"L\": false, \"Q\": false, \"Y\": false, \"c\": false, \"cs\": null, \"eqx\": false, \"output_format\": \"BAM\"}", | ||
| "alignment_options": "{\"A\": \"\", \"B\": \"\", \"E\": \"\", \"E2\": \"\", \"O\": \"\", \"O2\": \"\", \"no_end_flt\": true, \"s\": \"\", \"splicing\": {\"__current_case__\": 0, \"splice_mode\": \"preset\"}, \"z\": \"\", \"z2\": \"\"}", | ||
| "mapping_options": "{\"F\": \"\", \"N\": \"\", \"X\": false, \"f\": \"\", \"g\": \"\", \"m\": \"\", \"max_chain_iter\": \"\", \"max_chain_skip\": \"\", \"min_occ_floor\": \"\", \"n\": \"\", \"p\": \"\", \"r\": \"\"}", | ||
| "indexing_options": "{\"H\": false, \"I\": \"\", \"k\": \"\", \"w\": \"\"}", | ||
| "fastq_input": "{\"__current_case__\": 0, \"analysis_type_selector\": \"sr\", \"fastq_input1\": {\"values\": [{\"id\": 89, \"src\": \"hda\"}]}, \"fastq_input_selector\": \"single\"}", | ||
| "reference_source": "{\"__current_case__\": 1, \"ref_file\": {\"values\": [{\"id\": 88, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}" | ||
| }, | ||
| "inputs": { | ||
| "reference_source|ref_file": { | ||
| "id": "f1f195604a987904", | ||
| "src": "hda", | ||
| "uuid": "c072b9d4-6a1c-4fa5-b314-c12bf4738857" | ||
| }, | ||
| "fastq_input|fastq_input1": { | ||
| "id": "279a67189ec2da21", | ||
| "src": "hda", | ||
| "uuid": "1238966b-4ed5-40a0-a7ed-f2c6cb8b314a" | ||
| } | ||
| }, | ||
| "outputs": { | ||
| "alignment_output": { | ||
| "id": "ff34dbc215c76d2e", | ||
| "src": "hda", | ||
| "uuid": "39779258-e8e2-448e-84d9-77b2c9233af0" | ||
| } | ||
| }, | ||
| "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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