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Updating anvil-production README for prod-24-09-23-12-35-1
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7 changes: 7 additions & 0 deletions
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reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/chunk.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,7 @@ | ||
| { | ||
| "1": { | ||
| "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/results.html", | ||
| "date1": "Mon Sep 23 12:51:18 2024", | ||
| "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/tools.yml" | ||
| } | ||
| } |
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reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/chunk.txt
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,15 @@ | ||
| -t ncbi_acc_download --tool-version 1c58de56d587 | ||
| -t add_input_name_as_column --tool-version 3284b72eef56 | ||
| -t fastq_groomer --tool-version 47e5dbc3e790 | ||
| -t samtools_reheader --tool-version 30388d878f81 | ||
| -t samtools_bedcov --tool-version 9149ad20699a | ||
| -t bedtools --tool-version ce3c7f062223 | ||
| -t bcftools_convert_from_vcf --tool-version b8e9da766b0f | ||
| -t bcftools_plugin_dosage --tool-version 5c232a738c74 | ||
| -t vcfflatten --tool-version f285aa6bdcfb | ||
| -t vcftools_slice --tool-version 1363e5d4a8b8 | ||
| -t poretools_winner --tool-version 79c1ac92f31b | ||
| -t deeptools_correct_gc_bias --tool-version 2c37ce318bc3 | ||
| -t bwameth --tool-version 29bdbc353f20 | ||
| -t snpeff --tool-version 74aebe30fb52 | ||
| -t edger --tool-version 334ce9b1bac5 |
44 changes: 44 additions & 0 deletions
44
reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/errors/0cad9bac291447c2.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,44 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "0cad9bac291447c2", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "update_time": "2024-09-23T13:18:57.146452", | ||
| "create_time": "2024-09-23T13:18:46.237518", | ||
| "galaxy_version": "23.1", | ||
| "command_version": null, | ||
| "copied_from_job_id": null, | ||
| "tool_id": "upload1", | ||
| "history_id": "947bb6702479ed20", | ||
| "external_id": "gxy-87ggd", | ||
| "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/99/registry.xml' '/galaxy/server/database/jobs_directory/000/99/upload_params.json' '118:/galaxy/server/database/objects/e/0/2/dataset_e0255e89-7a41-413a-bd53-ce83af0bc52d_files:/galaxy/server/database/objects/e/0/2/dataset_e0255e89-7a41-413a-bd53-ce83af0bc52d.dat'", | ||
| "traceback": null, | ||
| "params": { | ||
| "paramfile": "\"/galaxy/server/database/tmp/upload_params_14usucg5\"", | ||
| "files_metadata": "{\"__current_case__\": 36, \"file_type\": \"bam\"}", | ||
| "dbkey": "\"?\"", | ||
| "force_composite": "\"false\"", | ||
| "files": "[{\"NAME\": \"eboVir3.bam\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_9diqqwps\", \"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": "c8764741bbb887fd", | ||
| "src": "hda", | ||
| "uuid": "e0255e89-7a41-413a-bd53-ce83af0bc52d" | ||
| } | ||
| }, | ||
| "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": [] | ||
| } |
48 changes: 48 additions & 0 deletions
48
reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/errors/2e416ed01d13ae5f.json
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,48 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "2e416ed01d13ae5f", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "update_time": "2024-09-23T13:16:08.450429", | ||
| "create_time": "2024-09-23T13:16:03.315857", | ||
| "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": "947bb6702479ed20", | ||
| "external_id": "gxy-tmrhs", | ||
| "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/d/e/b/dataset_deb69f7d-fb95-4061-b65c-ff8c62fb783e.dat' cssanger.bz2 '/galaxy/server/database/objects/e/0/4/dataset_e043c9fc-efe8-4f74-a4af-b09713ad6881.dat' cssanger ascii summarize_input", | ||
| "traceback": null, | ||
| "params": { | ||
| "__input_ext": "\"fastq.bz2\"", | ||
| "dbkey": "\"?\"", | ||
| "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", | ||
| "options_type": "{\"__current_case__\": 0, \"options_type_selector\": \"basic\"}", | ||
| "input_type": "\"cssanger\"" | ||
| }, | ||
| "inputs": { | ||
| "input_file": { | ||
| "id": "00ceb129d5865519", | ||
| "src": "hda", | ||
| "uuid": "deb69f7d-fb95-4061-b65c-ff8c62fb783e" | ||
| } | ||
| }, | ||
| "outputs": { | ||
| "output_file": { | ||
| "id": "c7371e849dcb6dbd", | ||
| "src": "hda", | ||
| "uuid": "e043c9fc-efe8-4f74-a4af-b09713ad6881" | ||
| } | ||
| }, | ||
| "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": [] | ||
| } |
87 changes: 87 additions & 0 deletions
87
reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/errors/6cdd2d16f3c221fc.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,87 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "6cdd2d16f3c221fc", | ||
| "state": "error", | ||
| "exit_code": 0, | ||
| "update_time": "2024-09-23T13:26:40.642801", | ||
| "create_time": "2024-09-23T13:26:24.004271", | ||
| "galaxy_version": "23.1", | ||
| "command_version": "", | ||
| "copied_from_job_id": null, | ||
| "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/vcftools_slice/vcftools_slice/0.1", | ||
| "history_id": "947bb6702479ed20", | ||
| "external_id": "gxy-ttmdk", | ||
| "command_line": "vcf-sort /galaxy/server/database/objects/e/7/2/dataset_e7207a25-878e-4480-940f-1479ba6dba90.dat > sorted.vcf ; echo '#dummy header' | cat - /galaxy/server/database/objects/f/9/a/dataset_f9a1fea0-a327-45fc-91c4-4cf8a6eb5057.dat > regions.bed ; vcftools --vcf sorted.vcf --out output --bed regions.bed --recode", | ||
| "traceback": null, | ||
| "params": { | ||
| "__input_ext": "\"vcf\"", | ||
| "dbkey": "\"?\"", | ||
| "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"" | ||
| }, | ||
| "inputs": { | ||
| "input": { | ||
| "id": "c16d38066b90b3b3", | ||
| "src": "hda", | ||
| "uuid": "e7207a25-878e-4480-940f-1479ba6dba90" | ||
| }, | ||
| "regions": { | ||
| "id": "d2c1b52b78bc35bb", | ||
| "src": "hda", | ||
| "uuid": "f9a1fea0-a327-45fc-91c4-4cf8a6eb5057" | ||
| } | ||
| }, | ||
| "outputs": { | ||
| "output": { | ||
| "id": "79679f468efbca13", | ||
| "src": "hda", | ||
| "uuid": "1fb6c01a-b1b9-487e-aaf9-25b611ba218e" | ||
| } | ||
| }, | ||
| "output_collections": {}, | ||
| "tool_stdout": "\nVCFtools - v0.1.11\n(C) Adam Auton 2009\n\nParameters as interpreted:\n\t--vcf sorted.vcf\n\t--out output\n\t--recode\n\t--bed regions.bed\n\nIndex file is older than variant file. Will regenerate.\nBuilding new index file.\nError:No header or meta information. Invalid file: sorted.vcf\n", | ||
| "tool_stderr": "/galaxy/server/database/jobs_directory/000/131/tool_script.sh: line 22: vcf-sort: command not found\n", | ||
| "job_stdout": "", | ||
| "job_stderr": "", | ||
| "stderr": "/galaxy/server/database/jobs_directory/000/131/tool_script.sh: line 22: vcf-sort: command not found\n", | ||
| "stdout": "\nVCFtools - v0.1.11\n(C) Adam Auton 2009\n\nParameters as interpreted:\n\t--vcf sorted.vcf\n\t--out output\n\t--recode\n\t--bed regions.bed\n\nIndex file is older than variant file. Will regenerate.\nBuilding new index file.\nError:No header or meta information. Invalid file: sorted.vcf\n", | ||
| "job_messages": [], | ||
| "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": "2024-09-23 13:26:29", | ||
| "plugin": "core", | ||
| "name": "end_epoch", | ||
| "raw_value": "1727097989.0000000" | ||
| }, | ||
| { | ||
| "title": "Job Start Time", | ||
| "value": "2024-09-23 13:26:29", | ||
| "plugin": "core", | ||
| "name": "start_epoch", | ||
| "raw_value": "1727097989.0000000" | ||
| }, | ||
| { | ||
| "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" | ||
| } | ||
| ] | ||
| } |
47 changes: 47 additions & 0 deletions
47
reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/errors/6d06355ae4d880d1.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,47 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "6d06355ae4d880d1", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "update_time": "2024-09-23T13:28:06.312944", | ||
| "create_time": "2024-09-23T13:28:00.206460", | ||
| "galaxy_version": "23.1", | ||
| "command_version": null, | ||
| "copied_from_job_id": null, | ||
| "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/poretools_winner/poretools_winner/0.6.1a1.0", | ||
| "history_id": "947bb6702479ed20", | ||
| "external_id": "gxy-lts2x", | ||
| "command_line": "poretools winner --type all '/galaxy/server/database/objects/7/8/3/dataset_78345283-4682-41e9-9629-1805188c55a5.dat' > '/galaxy/server/database/objects/e/b/1/dataset_eb1b9008-bb7c-4b92-a15a-b93161671015.dat'", | ||
| "traceback": null, | ||
| "params": { | ||
| "__input_ext": "\"fast5.tar\"", | ||
| "dbkey": "\"?\"", | ||
| "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", | ||
| "type": "\"all\"" | ||
| }, | ||
| "inputs": { | ||
| "input": { | ||
| "id": "1ab519c4d5a3f600", | ||
| "src": "hda", | ||
| "uuid": "78345283-4682-41e9-9629-1805188c55a5" | ||
| } | ||
| }, | ||
| "outputs": { | ||
| "output": { | ||
| "id": "d0757380334e66c8", | ||
| "src": "hda", | ||
| "uuid": "eb1b9008-bb7c-4b92-a15a-b93161671015" | ||
| } | ||
| }, | ||
| "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": [] | ||
| } |
84 changes: 84 additions & 0 deletions
84
reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/errors/7956cb04120de21b.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,84 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "7956cb04120de21b", | ||
| "state": "error", | ||
| "exit_code": 1, | ||
| "update_time": "2024-09-23T12:59:22.336268", | ||
| "create_time": "2024-09-23T12:59:09.755571", | ||
| "galaxy_version": "23.1", | ||
| "command_version": "", | ||
| "copied_from_job_id": null, | ||
| "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", | ||
| "history_id": "947bb6702479ed20", | ||
| "external_id": "gxy-4p88j", | ||
| "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/4/3/5/dataset_43579847-a887-42e8-bcfb-82cb86308b1c.dat' sanger '/galaxy/server/database/objects/4/f/8/dataset_4f883c4c-4e0e-439c-8b76-fe9918f340a6.dat' sanger ascii summarize_input --no-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\": false, \"force_quality_encoding\": \"ascii\", \"options_type_selector\": \"advanced\", \"output_type\": \"sanger\", \"summarize_input\": \"summarize_input\"}", | ||
| "input_type": "\"sanger\"" | ||
| }, | ||
| "inputs": { | ||
| "input_file": { | ||
| "id": "b39635dd5af16c5f", | ||
| "src": "hda", | ||
| "uuid": "43579847-a887-42e8-bcfb-82cb86308b1c" | ||
| } | ||
| }, | ||
| "outputs": { | ||
| "output_file": { | ||
| "id": "254170a0185eab4b", | ||
| "src": "hda", | ||
| "uuid": "4f883c4c-4e0e-439c-8b76-fe9918f340a6" | ||
| } | ||
| }, | ||
| "output_collections": {}, | ||
| "tool_stdout": "There was an error reading your input file. Your input file is likely malformed.\nIt is suggested that you double-check your original input file for errors -- helpful information for this purpose has been provided below.\nHowever, if you think that you have encountered an actual error with this tool, please do tell us by using the bug reporting mechanism.\n\nThe reported error is: 'Invalid FASTQ file: quality score identifier (+invalid line) does not match sequence identifier (@FAKE-1).'.\nThe error occurred at the start of your file and no valid FASTQ reads were found.\nThe error in your file occurs between lines '1' and '3', which corresponds to byte-offsets '0' and '33', and contains the text (33 of 33 bytes shown):\n\n@FAKE-1\nACGTACGTAC\n+invalid line\n\n", | ||
| "tool_stderr": "Traceback (most recent call last):\n File \"/usr/local/bin/gx-fastq-groomer\", line 10, in <module>\n sys.exit(main())\n ^^^^^^\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/scripts/fastq_groomer.py\", line 99, in main\n Groomer().run()\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/scripts/fastq_groomer.py\", line 48, in run\n for read_count, fastq_read in enumerate(reader):\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py\", line 683, in __iter__\n yield next(self)\n ^^^^^^^^^^\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py\", line 742, in __next__\n raise e\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py\", line 724, in __next__\n block = super(fastqVerboseErrorReader, self).__next__()\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py\", line 621, in __next__\n self._read_fastq_sequence(rval, id_line)\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py\", line 666, in _read_fastq_sequence\n raise fastqFormatError(\ngalaxy_utils.sequence.fastq.fastqFormatError: Invalid FASTQ file: quality score identifier (+invalid line) does not match sequence identifier (@FAKE-1).\n", | ||
| "job_stdout": "", | ||
| "job_stderr": "", | ||
| "stderr": "Traceback (most recent call last):\n File \"/usr/local/bin/gx-fastq-groomer\", line 10, in <module>\n sys.exit(main())\n ^^^^^^\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/scripts/fastq_groomer.py\", line 99, in main\n Groomer().run()\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/scripts/fastq_groomer.py\", line 48, in run\n for read_count, fastq_read in enumerate(reader):\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py\", line 683, in __iter__\n yield next(self)\n ^^^^^^^^^^\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py\", line 742, in __next__\n raise e\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py\", line 724, in __next__\n block = super(fastqVerboseErrorReader, self).__next__()\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py\", line 621, in __next__\n self._read_fastq_sequence(rval, id_line)\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py\", line 666, in _read_fastq_sequence\n raise fastqFormatError(\ngalaxy_utils.sequence.fastq.fastqFormatError: Invalid FASTQ file: quality score identifier (+invalid line) does not match sequence identifier (@FAKE-1).\n", | ||
| "stdout": "There was an error reading your input file. Your input file is likely malformed.\nIt is suggested that you double-check your original input file for errors -- helpful information for this purpose has been provided below.\nHowever, if you think that you have encountered an actual error with this tool, please do tell us by using the bug reporting mechanism.\n\nThe reported error is: 'Invalid FASTQ file: quality score identifier (+invalid line) does not match sequence identifier (@FAKE-1).'.\nThe error occurred at the start of your file and no valid FASTQ reads were found.\nThe error in your file occurs between lines '1' and '3', which corresponds to byte-offsets '0' and '33', and contains the text (33 of 33 bytes shown):\n\n@FAKE-1\nACGTACGTAC\n+invalid line\n\n", | ||
| "job_messages": [], | ||
| "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": "2024-09-23 12:59:11", | ||
| "plugin": "core", | ||
| "name": "end_epoch", | ||
| "raw_value": "1727096351.0000000" | ||
| }, | ||
| { | ||
| "title": "Job Start Time", | ||
| "value": "2024-09-23 12:59:11", | ||
| "plugin": "core", | ||
| "name": "start_epoch", | ||
| "raw_value": "1727096351.0000000" | ||
| }, | ||
| { | ||
| "title": "Memory Allocated (MB)", | ||
| "value": "8160", | ||
| "plugin": "core", | ||
| "name": "galaxy_memory_mb", | ||
| "raw_value": "8160.0000000" | ||
| }, | ||
| { | ||
| "title": "Cores Allocated", | ||
| "value": "1", | ||
| "plugin": "core", | ||
| "name": "galaxy_slots", | ||
| "raw_value": "1.0000000" | ||
| } | ||
| ] | ||
| } |
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