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Updating anvil-production README for prod-24-10-13-12-32-1
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actions-user committed Oct 13, 2024
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2 changes: 1 addition & 1 deletion reports/anvil-production/README.md
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10 changes: 5 additions & 5 deletions reports/anvil-production/tool-tests/chunks.json
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"date2": "Fri Oct 04 12:50:37 2024"
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"date2": "Sun Sep 29 12:48:22 2024"
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7 changes: 7 additions & 0 deletions reports/anvil-production/tool-tests/prod-24-10-13-12-32-1/chunk.json
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15 changes: 15 additions & 0 deletions reports/anvil-production/tool-tests/prod-24-10-13-12-32-1/chunk.txt
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-t table_compute --tool-version 60ff16842fcd
-t cutadapt --tool-version 093678460093
-t qualimap_bamqc --tool-version 19ece8afbaab
-t samtools_stats --tool-version 145f6d74ff5e
-t filter_on_md --tool-version ac70bfaf1224
-t bcftools_plugin_mendelian --tool-version bf235558f2cf
-t bcftools_csq --tool-version fdd127bd4a32
-t vcfcommonsamples --tool-version f1852ecef841
-t vcfdistance --tool-version c506b8275b1a
-t poretools_yield_plot --tool-version ca22d8497db5
-t deeptools_bigwig_compare --tool-version 26e7304d6737
-t bowtie2 --tool-version 09b2cdb7ace5
-t snpsift_genesets --tool-version d12a810c837e
-t deseq2 --tool-version 6a3a025714d3
-t mummer_mummer --tool-version 48823c9635a4
62 changes: 62 additions & 0 deletions reports/anvil-production/tool-tests/prod-24-10-13-12-32-1/errors/01444879b993b150.json
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51 changes: 51 additions & 0 deletions reports/anvil-production/tool-tests/prod-24-10-13-12-32-1/errors/0f445745229cda9d.json
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106 changes: 106 additions & 0 deletions reports/anvil-production/tool-tests/prod-24-10-13-12-32-1/errors/13b73356e89c7f0d.json
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{
"model_class": "Job",
"id": "13b73356e89c7f0d",
"state": "error",
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"update_time": "2024-10-13T13:25:34.827996",
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"tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1",
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"command_line": "ln -f -s '/galaxy/server/database/objects/b/a/7/dataset_ba78ae77-10ca-4f9e-bbe1-21328559cef0.dat' 'bwa-mem-fastq1_fq_gz.fq.gz' && ln -f -s '/galaxy/server/database/objects/5/9/2/dataset_59275da4-d301-46cb-9501-aac29d88579d.dat' 'bwa-mem-fastq_mispaired2_fq_gz.fq.gz' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'AGATCGGAAGAGC' -A 'AGATCGGAAGAGC' --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o 'out1.fq.gz' -p 'out2.fq.gz' 'bwa-mem-fastq1_fq_gz.fq.gz' 'bwa-mem-fastq_mispaired2_fq_gz.fq.gz'",
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"adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}",
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},
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"src": "hda",
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"src": "hda",
"uuid": "46837ae1-d4da-4fa8-9280-c62a45316020"
},
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"src": "hda",
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"tool_stdout": "This is cutadapt 4.9 with Python 3.12.7\nCommand line parameters: -j=5 -a AGATCGGAAGAGC -A AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o out1.fq.gz -p out2.fq.gz bwa-mem-fastq1_fq_gz.fq.gz bwa-mem-fastq_mispaired2_fq_gz.fq.gz\nProcessing paired-end reads on 5 cores ...\n",
"tool_stderr": "Error in sequence file at unknown line: Reads are improperly paired. Read name 'M01368:8:000000000-A3GHV:1:1101:6911:8255/1' in file 1 does not match 'M01368:8:000000000-A3GHV:1:1101:14518:9998/2' in file 2.\n",
"job_stdout": "",
"job_stderr": "",
"stderr": "Error in sequence file at unknown line: Reads are improperly paired. Read name 'M01368:8:000000000-A3GHV:1:1101:6911:8255/1' in file 1 does not match 'M01368:8:000000000-A3GHV:1:1101:14518:9998/2' in file 2.\n",
"stdout": "This is cutadapt 4.9 with Python 3.12.7\nCommand line parameters: -j=5 -a AGATCGGAAGAGC -A AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o out1.fq.gz -p out2.fq.gz bwa-mem-fastq1_fq_gz.fq.gz bwa-mem-fastq_mispaired2_fq_gz.fq.gz\nProcessing paired-end reads on 5 cores ...\n",
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{
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"desc": "Fatal error: Exit code 1 ()",
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{
"title": "Cores Allocated",
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]
}
66 changes: 66 additions & 0 deletions reports/anvil-production/tool-tests/prod-24-10-13-12-32-1/errors/3d549b4fe1b83cb9.json
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{
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49 changes: 49 additions & 0 deletions reports/anvil-production/tool-tests/prod-24-10-13-12-32-1/errors/42d78e024f24bc12.json
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@@ -0,0 +1,49 @@
{
"model_class": "Job",
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"job_messages": null,
"dependencies": [],
"user_email": "tests@fake.org",
"job_metrics": []
}
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