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Updating anvil-production README for prod-24-08-30-12-32-1
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7 changes: 7 additions & 0 deletions
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reports/anvil-production/tool-tests/prod-24-08-30-12-32-1/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-production/tool-tests/prod-24-08-30-12-32-1/results.html", | ||
| "date1": "Fri Aug 30 12:48:09 2024", | ||
| "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-08-30-12-32-1/tools.yml" | ||
| } | ||
| } |
15 changes: 15 additions & 0 deletions
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reports/anvil-production/tool-tests/prod-24-08-30-12-32-1/chunk.txt
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,15 @@ | ||
| -t sqlite_to_tabular --tool-version bce29ec10b78 | ||
| -t replace_column_by_key_value_file --tool-version d533e4b75800 | ||
| -t fastqc --tool-version e7b2202befea | ||
| -t samtools_markdup --tool-version 83b8e36e9cbe | ||
| -t bamtools_filter --tool-version cb20f99fd45b | ||
| -t bcftools_cnv --tool-version 01d6b7d6365e | ||
| -t bcftools_roh --tool-version b76adb2f1c51 | ||
| -t vcfbedintersect --tool-version aea8e90ad788 | ||
| -t vcfvcfintersect --tool-version 166c4f50525f | ||
| -t poretools_hist --tool-version 5a82eb9e1b89 | ||
| -t deeptools_compute_matrix --tool-version 514fa53b5efb | ||
| -t deeptools_bam_coverage --tool-version bb1e4f63e0e6 | ||
| -t lofreq_indelqual --tool-version 426d707dfc47 | ||
| -t snpsift --tool-version 2e497a770bca | ||
| -t mummer_nucmer --tool-version 636b049e6141 |
50 changes: 50 additions & 0 deletions
50
reports/anvil-production/tool-tests/prod-24-08-30-12-32-1/errors/6cded8ba9046fcf8.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,50 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "6cded8ba9046fcf8", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "update_time": "2024-08-30T12:55:13.131201", | ||
| "create_time": "2024-08-30T12:55:08.534034", | ||
| "galaxy_version": "23.1", | ||
| "command_version": null, | ||
| "copied_from_job_id": null, | ||
| "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2", | ||
| "history_id": "156c4392fa643bca", | ||
| "external_id": "gxy-f6mb4", | ||
| "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && samtools sort -@ $addthreads -m ${GALAXY_MEMORY_MB:-768}M -T \"${TMPDIR:-.}\" -O sam -o coordsort.sam '/galaxy/server/database/objects/9/8/8/dataset_988d51bd-daba-4ed9-a392-1ed7724aba4d.dat' && samtools markdup -@ $addthreads -r coordsort.sam '/galaxy/server/database/objects/a/6/6/dataset_a667be73-c02a-41a2-89f1-4bda7a51270c.dat'", | ||
| "traceback": null, | ||
| "params": { | ||
| "__input_ext": "\"sam\"", | ||
| "dbkey": "\"?\"", | ||
| "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", | ||
| "supp": "false", | ||
| "stats": "false", | ||
| "maxlen": "\"\"", | ||
| "remove": "true" | ||
| }, | ||
| "inputs": { | ||
| "bamfile": { | ||
| "id": "0f3b0b88fd8d3bd3", | ||
| "src": "hda", | ||
| "uuid": "988d51bd-daba-4ed9-a392-1ed7724aba4d" | ||
| } | ||
| }, | ||
| "outputs": { | ||
| "output": { | ||
| "id": "0a2d17a5e5658f2e", | ||
| "src": "hda", | ||
| "uuid": "a667be73-c02a-41a2-89f1-4bda7a51270c" | ||
| } | ||
| }, | ||
| "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": [] | ||
| } |
51 changes: 51 additions & 0 deletions
51
reports/anvil-production/tool-tests/prod-24-08-30-12-32-1/errors/95658726ede0b433.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,51 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "95658726ede0b433", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "update_time": "2024-08-30T13:03:30.926638", | ||
| "create_time": "2024-08-30T13:03:24.700290", | ||
| "galaxy_version": "23.1", | ||
| "command_version": null, | ||
| "copied_from_job_id": null, | ||
| "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/poretools_hist/poretools_hist/0.6.1a1.1", | ||
| "history_id": "156c4392fa643bca", | ||
| "external_id": "gxy-qbhxr", | ||
| "command_line": "export MPLBACKEND=\"agg\" && poretools hist '/galaxy/server/database/objects/c/e/a/dataset_cea96354-2672-45e7-a710-006d866d1524.dat' --saveas histogram.svg --min-length 0 --max-length 1000000000 --num-bins 50 && mv histogram.svg '/galaxy/server/database/objects/8/3/6/dataset_836c00e8-a52e-41ff-9aed-169c2737422e.dat'", | ||
| "traceback": null, | ||
| "params": { | ||
| "__input_ext": "\"fast5.tar\"", | ||
| "dbkey": "\"?\"", | ||
| "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", | ||
| "num_bins": "\"50\"", | ||
| "max_length": "\"1000000000\"", | ||
| "min_length": "\"0\"", | ||
| "theme_bw": "false", | ||
| "extension": "\"svg\"" | ||
| }, | ||
| "inputs": { | ||
| "input": { | ||
| "id": "2d284e114fa37175", | ||
| "src": "hda", | ||
| "uuid": "cea96354-2672-45e7-a710-006d866d1524" | ||
| } | ||
| }, | ||
| "outputs": { | ||
| "output": { | ||
| "id": "f4f3e423337ae3b0", | ||
| "src": "hda", | ||
| "uuid": "836c00e8-a52e-41ff-9aed-169c2737422e" | ||
| } | ||
| }, | ||
| "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-24-08-30-12-32-1/errors/ee864d120e6ad4da.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,57 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "ee864d120e6ad4da", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "update_time": "2024-08-30T12:53:14.827157", | ||
| "create_time": "2024-08-30T12:53:06.972295", | ||
| "galaxy_version": "23.1", | ||
| "command_version": null, | ||
| "copied_from_job_id": null, | ||
| "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0", | ||
| "history_id": "156c4392fa643bca", | ||
| "external_id": "gxy-lj7sk", | ||
| "command_line": "ln -s '/galaxy/server/database/objects/c/7/7/dataset_c779310f-6c04-4ec2-a7b8-ed0679e21e17.dat' '1000trimmed_fastq' && mkdir -p '/galaxy/server/database/objects/e/f/f/dataset_eff11dba-52dc-40a6-acb2-426075fb0264_files' && fastqc --outdir '/galaxy/server/database/objects/e/f/f/dataset_eff11dba-52dc-40a6-acb2-426075fb0264_files' --threads ${GALAXY_SLOTS:-2} --quiet --extract --min_length 108 --kmers 7 -f 'fastq' '1000trimmed_fastq' && cp '/galaxy/server/database/objects/e/f/f/dataset_eff11dba-52dc-40a6-acb2-426075fb0264_files'/*/fastqc_data.txt output.txt && cp '/galaxy/server/database/objects/e/f/f/dataset_eff11dba-52dc-40a6-acb2-426075fb0264_files'/*\\.html output.html", | ||
| "traceback": null, | ||
| "params": { | ||
| "__input_ext": "\"fastqsanger\"", | ||
| "dbkey": "\"?\"", | ||
| "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", | ||
| "kmers": "\"7\"", | ||
| "min_length": "\"108\"", | ||
| "nogroup": "false", | ||
| "limits": null, | ||
| "adapters": null, | ||
| "contaminants": null | ||
| }, | ||
| "inputs": { | ||
| "input_file": { | ||
| "id": "8484cc763161da97", | ||
| "src": "hda", | ||
| "uuid": "c779310f-6c04-4ec2-a7b8-ed0679e21e17" | ||
| } | ||
| }, | ||
| "outputs": { | ||
| "html_file": { | ||
| "id": "3ca01b6fa3c2aaf5", | ||
| "src": "hda", | ||
| "uuid": "eff11dba-52dc-40a6-acb2-426075fb0264" | ||
| }, | ||
| "text_file": { | ||
| "id": "633d64f77bff13b3", | ||
| "src": "hda", | ||
| "uuid": "366f2433-d768-44fa-bae1-205e2035b74c" | ||
| } | ||
| }, | ||
| "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": [] | ||
| } |
95 changes: 95 additions & 0 deletions
95
reports/anvil-production/tool-tests/prod-24-08-30-12-32-1/job-metrics.csv
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,95 @@ | ||
| id,history_id,history_name,state,tool_id,invocation_id,workflow_id,cpuacct.usage,galaxy_memory_mb,galaxy_slots,memory.limit_in_bytes,memory.peak,memory.soft_limit_in_bytes,memtotal,processor_count,runtime_seconds | ||
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