Created
July 16, 2017 21:57
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| /home/ubuntu/envs/env-ga4gh-dream-bcbio/bin/cwltool 1.0.20170413194156 | |
| Resolved 'main-NA12878-platinum-chr20.cwl' to 'file:///home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/main-NA12878-platinum-chr20.cwl' | |
| [job alignment_to_rec] Output of job will be cached in /home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/fff9469d1a8ae685c1e99c2596513fb1 | |
| [job alignment_to_rec] /home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/fff9469d1a8ae685c1e99c2596513fb1$ docker \ | |
| run \ | |
| -i \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/collections/hg38/bwa-wf.tar.gz:/var/lib/cwl/stgea1545d6-7249-4453-bce3-d36d6bef00ae/bwa-wf.tar.gz:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/collections/hg38/seq/hg38.fa:/var/lib/cwl/stg807544db-f43d-4803-b59f-c63f2a957887/hg38.fa:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/giab/na12878/NA12878-platinum-chr20.bam:/var/lib/cwl/stg850be498-493c-4a0b-ab2f-63b567479c3c/NA12878-platinum-chr20.bam:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/collections/hg38/seq/hg38.fa.fai:/var/lib/cwl/stg807544db-f43d-4803-b59f-c63f2a957887/hg38.fa.fai:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/giab/na12878/NA12878-platinum-chr20.bam.bai:/var/lib/cwl/stg850be498-493c-4a0b-ab2f-63b567479c3c/NA12878-platinum-chr20.bam.bai:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/collections/hg38/seq/hg38.dict:/var/lib/cwl/stg807544db-f43d-4803-b59f-c63f2a957887/hg38.dict:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/fff9469d1a8ae685c1e99c2596513fb1:/var/spool/cwl:rw \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/tmp/Qh0eCI:/tmp:rw \ | |
| --workdir=/var/spool/cwl \ | |
| --read-only=true \ | |
| --user=1000 \ | |
| --rm \ | |
| --env=TMPDIR=/tmp \ | |
| --env=HOME=/var/spool/cwl \ | |
| --env=MPLCONFIGDIR=. \ | |
| quay.io/bcbio/bcbio-base \ | |
| bcbio_nextgen.py \ | |
| runfn \ | |
| alignment_to_rec \ | |
| cwl \ | |
| sentinel_runtime=cores,1,ram,3072 \ | |
| sentinel_parallel=multi-combined \ | |
| 'sentinel_outputs=alignment_rec:description;config__algorithm__align_split_size;reference__fasta__base;rgnames__lb;rgnames__rg;rgnames__lane;reference__bwa__indexes;files;config__algorithm__aligner;rgnames__pl;config__algorithm__mark_duplicates;rgnames__pu;rgnames__sample' \ | |
| sentinel_inputs=files:var,config__algorithm__align_split_size:var,reference__fasta__base:var,rgnames__pl:var,rgnames__sample:var,rgnames__pu:var,rgnames__lane:var,rgnames__rg:var,rgnames__lb:var,reference__bwa__indexes:var,config__algorithm__aligner:var,config__algorithm__mark_duplicates:var,description:var | |
| [job alignment_to_rec] completed success | |
| [step alignment_to_rec] completed success | |
| [job prep_samples_to_rec] Output of job will be cached in /home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/a5cb782c5a69dcd3836c6f6aaad47e4e | |
| [job prep_samples_to_rec] /home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/a5cb782c5a69dcd3836c6f6aaad47e4e$ docker \ | |
| run \ | |
| -i \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/collections/hg38/seq/hg38.fa.fai:/var/lib/cwl/stg5d8f219e-f71c-4be6-abe1-bd29fa50a0ee/hg38.fa.fai:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/collections/hg38/seq/hg38.fa:/var/lib/cwl/stg5d8f219e-f71c-4be6-abe1-bd29fa50a0ee/hg38.fa:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/collections/hg38/seq/hg38.dict:/var/lib/cwl/stg5d8f219e-f71c-4be6-abe1-bd29fa50a0ee/hg38.dict:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/a5cb782c5a69dcd3836c6f6aaad47e4e:/var/spool/cwl:rw \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/tmp/a89ee3:/tmp:rw \ | |
| --workdir=/var/spool/cwl \ | |
| --read-only=true \ | |
| --user=1000 \ | |
| --rm \ | |
| --env=TMPDIR=/tmp \ | |
| --env=HOME=/var/spool/cwl \ | |
| --env=MPLCONFIGDIR=. \ | |
| quay.io/bcbio/bcbio-base \ | |
| bcbio_nextgen.py \ | |
| runfn \ | |
| prep_samples_to_rec \ | |
| cwl \ | |
| sentinel_runtime=cores,1,ram,3072 \ | |
| sentinel_parallel=multi-combined \ | |
| 'sentinel_outputs=prep_samples_rec:description;reference__fasta__base;config__algorithm__variant_regions' \ | |
| sentinel_inputs=config__algorithm__variant_regions:var,reference__fasta__base:var,description:var | |
| [job prep_samples_to_rec] completed success | |
| [step prep_samples_to_rec] completed success | |
| [job prep_align_inputs] Output of job will be cached in /home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/c49bfc76e3b35586f1622e2cacb0abc4 | |
| [job prep_align_inputs] /home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/c49bfc76e3b35586f1622e2cacb0abc4$ docker \ | |
| run \ | |
| -i \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/giab/na12878/NA12878-platinum-chr20.bam.bai:/var/lib/cwl/stg82bb13ff-2527-4ad5-a635-584e3b88e98a/NA12878-platinum-chr20.bam.bai:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/collections/hg38/seq/hg38.fa:/var/lib/cwl/stgb5ff14d1-2422-459b-aa3a-88d7261c837c/hg38.fa:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/giab/na12878/NA12878-platinum-chr20.bam:/var/lib/cwl/stg82bb13ff-2527-4ad5-a635-584e3b88e98a/NA12878-platinum-chr20.bam:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/collections/hg38/seq/hg38.dict:/var/lib/cwl/stgb5ff14d1-2422-459b-aa3a-88d7261c837c/hg38.dict:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/collections/hg38/bwa-wf.tar.gz:/var/lib/cwl/stg08459faa-b95b-46b4-ab2e-5fc51b363aca/bwa-wf.tar.gz:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/collections/hg38/seq/hg38.fa.fai:/var/lib/cwl/stgb5ff14d1-2422-459b-aa3a-88d7261c837c/hg38.fa.fai:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/c49bfc76e3b35586f1622e2cacb0abc4:/var/spool/cwl:rw \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/tmp/HCbv2u:/tmp:rw \ | |
| --workdir=/var/spool/cwl \ | |
| --read-only=true \ | |
| --user=1000 \ | |
| --rm \ | |
| --env=TMPDIR=/tmp \ | |
| --env=HOME=/var/spool/cwl \ | |
| --env=MPLCONFIGDIR=. \ | |
| quay.io/bcbio/bcbio-align \ | |
| bcbio_nextgen.py \ | |
| runfn \ | |
| prep_align_inputs \ | |
| cwl \ | |
| sentinel_runtime=cores,1,ram,3072 \ | |
| sentinel_parallel=single-split \ | |
| 'sentinel_outputs=process_alignment_rec:files;config__algorithm__quality_format;align_split' \ | |
| sentinel_inputs=alignment_rec:record | |
| [job prep_align_inputs] completed success | |
| [step prep_align_inputs] completed success | |
| [job process_alignment] Output of job will be cached in /home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/941268b19921972cb4ba9201bef6dcb3 | |
| [job process_alignment] /home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/941268b19921972cb4ba9201bef6dcb3$ docker \ | |
| run \ | |
| -i \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/giab/na12878/NA12878-platinum-chr20.bam.bai:/var/lib/cwl/stgac78e8d6-094f-45c6-8f08-20af24203b6f/NA12878-platinum-chr20.bam.bai:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/c49bfc76e3b35586f1622e2cacb0abc4/align_prep/NA12878-platinum-chr20-1.fq.gz.gbi:/var/lib/cwl/stga61bc9e4-fdc8-4acc-9d01-f0111fc93853/NA12878-platinum-chr20-1.fq.gz.gbi:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/collections/hg38/seq/hg38.fa:/var/lib/cwl/stgd25d7cd6-35c8-431d-8c02-624846fbc7b2/hg38.fa:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/giab/na12878/NA12878-platinum-chr20.bam:/var/lib/cwl/stgac78e8d6-094f-45c6-8f08-20af24203b6f/NA12878-platinum-chr20.bam:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/collections/hg38/seq/hg38.dict:/var/lib/cwl/stgd25d7cd6-35c8-431d-8c02-624846fbc7b2/hg38.dict:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/collections/hg38/bwa-wf.tar.gz:/var/lib/cwl/stg47c008ac-bbac-4843-9e0a-93c5a96b3f4d/bwa-wf.tar.gz:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/collections/hg38/seq/hg38.fa.fai:/var/lib/cwl/stgd25d7cd6-35c8-431d-8c02-624846fbc7b2/hg38.fa.fai:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/c49bfc76e3b35586f1622e2cacb0abc4/align_prep/NA12878-platinum-chr20-2.fq.gz.gbi:/var/lib/cwl/stgab8fa093-a43a-4c6e-ab59-bdd0ba37b9a2/NA12878-platinum-chr20-2.fq.gz.gbi:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/c49bfc76e3b35586f1622e2cacb0abc4/align_prep/NA12878-platinum-chr20-2.fq.gz:/var/lib/cwl/stgab8fa093-a43a-4c6e-ab59-bdd0ba37b9a2/NA12878-platinum-chr20-2.fq.gz:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/c49bfc76e3b35586f1622e2cacb0abc4/align_prep/NA12878-platinum-chr20-1.fq.gz:/var/lib/cwl/stga61bc9e4-fdc8-4acc-9d01-f0111fc93853/NA12878-platinum-chr20-1.fq.gz:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/941268b19921972cb4ba9201bef6dcb3:/var/spool/cwl:rw \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/tmp/pz8sbD:/tmp:rw \ | |
| --workdir=/var/spool/cwl \ | |
| --read-only=true \ | |
| --user=1000 \ | |
| --rm \ | |
| --env=TMPDIR=/tmp \ | |
| --env=HOME=/var/spool/cwl \ | |
| --env=MPLCONFIGDIR=. \ | |
| quay.io/bcbio/bcbio-align \ | |
| bcbio_nextgen.py \ | |
| runfn \ | |
| process_alignment \ | |
| cwl \ | |
| sentinel_runtime=cores,8,ram,24576 \ | |
| sentinel_parallel=single-parallel \ | |
| sentinel_outputs=work_bam,align_bam,hla__fastq,work_bam_plus__disc,work_bam_plus__sr \ | |
| sentinel_inputs=alignment_rec:record,process_alignment_rec:record | |
| [job process_alignment] completed success | |
| [step process_alignment] completed success | |
| [job merge_split_alignments] Output of job will be cached in /home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/d3d1bf8df7088fcbd617ba0b72e96a52 | |
| [job merge_split_alignments] /home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/d3d1bf8df7088fcbd617ba0b72e96a52$ docker \ | |
| run \ | |
| -i \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/941268b19921972cb4ba9201bef6dcb3/align/NA12878-chr20/hla/NA12878-chr20-sort.bam.hla.HLA-DQA1.fq:/var/lib/cwl/stga6c5f4ef-9207-491c-9421-7e03dacd303b/NA12878-chr20-sort.bam.hla.HLA-DQA1.fq:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/giab/na12878/NA12878-platinum-chr20.bam.bai:/var/lib/cwl/stgab627262-77c7-4c2e-943b-f2acbf121d1c/NA12878-platinum-chr20.bam.bai:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/941268b19921972cb4ba9201bef6dcb3/align/NA12878-chr20/hla/NA12878-chr20-sort.bam.hla.HLA-A.fq:/var/lib/cwl/stg7326a84f-d8b4-4a89-8796-a346ae0fca65/NA12878-chr20-sort.bam.hla.HLA-A.fq:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/941268b19921972cb4ba9201bef6dcb3/align/NA12878-chr20/hla/NA12878-chr20-sort.bam.hla.HLA-DQB1.fq:/var/lib/cwl/stgbe818dea-897a-4001-b458-811daf02b5ac/NA12878-chr20-sort.bam.hla.HLA-DQB1.fq:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/collections/hg38/seq/hg38.fa:/var/lib/cwl/stge3653c79-4c9b-49ad-9484-b9723ca5dafd/hg38.fa:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/giab/na12878/NA12878-platinum-chr20.bam:/var/lib/cwl/stgab627262-77c7-4c2e-943b-f2acbf121d1c/NA12878-platinum-chr20.bam:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/collections/hg38/seq/hg38.dict:/var/lib/cwl/stge3653c79-4c9b-49ad-9484-b9723ca5dafd/hg38.dict:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/941268b19921972cb4ba9201bef6dcb3/align/NA12878-chr20/hla/NA12878-chr20-sort.bam.hla.HLA-B.fq:/var/lib/cwl/stg4b628730-c91d-4c82-b53a-27ee4884f3db/NA12878-chr20-sort.bam.hla.HLA-B.fq:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/collections/hg38/bwa-wf.tar.gz:/var/lib/cwl/stg92259708-a49d-4f05-b8bf-21d1e1628283/bwa-wf.tar.gz:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/collections/hg38/seq/hg38.fa.fai:/var/lib/cwl/stge3653c79-4c9b-49ad-9484-b9723ca5dafd/hg38.fa.fai:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/941268b19921972cb4ba9201bef6dcb3/align/NA12878-chr20/hla/NA12878-chr20-sort.bam.hla.HLA-DRB1.fq:/var/lib/cwl/stg50459ba7-10bf-4563-90db-84f1cc761b81/NA12878-chr20-sort.bam.hla.HLA-DRB1.fq:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/941268b19921972cb4ba9201bef6dcb3/align/NA12878-chr20/NA12878-chr20-sort.bam.bai:/var/lib/cwl/stg1e352097-1a33-4e10-8edd-5468575d178a/NA12878-chr20-sort.bam.bai:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/941268b19921972cb4ba9201bef6dcb3/align/NA12878-chr20/NA12878-chr20-sort.bam:/var/lib/cwl/stg1e352097-1a33-4e10-8edd-5468575d178a/NA12878-chr20-sort.bam:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/941268b19921972cb4ba9201bef6dcb3/align/NA12878-chr20/hla/NA12878-chr20-sort.bam.hla.HLA-C.fq:/var/lib/cwl/stg185113bc-65d1-46b9-ba11-9d4546b02432/NA12878-chr20-sort.bam.hla.HLA-C.fq:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/d3d1bf8df7088fcbd617ba0b72e96a52:/var/spool/cwl:rw \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/tmp/CEePCT:/tmp:rw \ | |
| --workdir=/var/spool/cwl \ | |
| --read-only=true \ | |
| --user=1000 \ | |
| --rm \ | |
| --env=TMPDIR=/tmp \ | |
| --env=HOME=/var/spool/cwl \ | |
| --env=MPLCONFIGDIR=. \ | |
| quay.io/bcbio/bcbio-align \ | |
| bcbio_nextgen.py \ | |
| runfn \ | |
| merge_split_alignments \ | |
| cwl \ | |
| sentinel_runtime=cores,8,ram,24576 \ | |
| sentinel_parallel=single-merge \ | |
| sentinel_outputs=align_bam,work_bam_plus__disc,work_bam_plus__sr,hla__fastq \ | |
| sentinel_inputs=alignment_rec:record,work_bam:var,align_bam:var,work_bam_plus__disc:var,work_bam_plus__sr:var,hla__fastq:var | |
| [job merge_split_alignments] completed success | |
| [step merge_split_alignments] completed success | |
| [workflow alignment] outdir is /home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/67jLWw | |
| [step alignment] completed success | |
| [job prep_samples] Output of job will be cached in /home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/e46ca5cb310cae6ef76a206ecfadb759 | |
| [job prep_samples] /home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/e46ca5cb310cae6ef76a206ecfadb759$ docker \ | |
| run \ | |
| -i \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/collections/hg38/seq/hg38.dict:/var/lib/cwl/stg064e90b7-84c5-48b2-ad3b-b74e23bf06e4/hg38.dict:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/collections/hg38/seq/hg38.fa:/var/lib/cwl/stg064e90b7-84c5-48b2-ad3b-b74e23bf06e4/hg38.fa:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/collections/hg38/seq/hg38.fa.fai:/var/lib/cwl/stg064e90b7-84c5-48b2-ad3b-b74e23bf06e4/hg38.fa.fai:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/e46ca5cb310cae6ef76a206ecfadb759:/var/spool/cwl:rw \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/tmp/iJV9hw:/tmp:rw \ | |
| --workdir=/var/spool/cwl \ | |
| --read-only=true \ | |
| --user=1000 \ | |
| --rm \ | |
| --env=TMPDIR=/tmp \ | |
| --env=HOME=/var/spool/cwl \ | |
| --env=MPLCONFIGDIR=. \ | |
| quay.io/bcbio/bcbio-align \ | |
| bcbio_nextgen.py \ | |
| runfn \ | |
| prep_samples \ | |
| cwl \ | |
| sentinel_runtime=cores,1,ram,3072 \ | |
| sentinel_parallel=multi-parallel \ | |
| sentinel_outputs=config__algorithm__variant_regions,config__algorithm__variant_regions_merged,config__algorithm__variant_regions_orig,config__algorithm__coverage,config__algorithm__coverage_merged,config__algorithm__coverage_orig,config__algorithm__seq2c_bed_ready \ | |
| sentinel_inputs=prep_samples_rec:record | |
| [job prep_samples] completed success | |
| [step prep_samples] completed success | |
| [job postprocess_alignment_to_rec] Output of job will be cached in /home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/7422aae9ae5e6917d74f825ea1e44b9f | |
| [job postprocess_alignment_to_rec] /home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/7422aae9ae5e6917d74f825ea1e44b9f$ docker \ | |
| run \ | |
| -i \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/collections/hg38/seq/hg38.fa.fai:/var/lib/cwl/stg340ebc27-e9e8-4e4f-af6a-386e2952610e/hg38.fa.fai:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/d3d1bf8df7088fcbd617ba0b72e96a52/align/NA12878-chr20/NA12878-chr20-sort.bam:/var/lib/cwl/stg2a1c7693-e41f-4545-a94c-4e26168f4340/NA12878-chr20-sort.bam:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/collections/hg38/seq/hg38.fa:/var/lib/cwl/stg340ebc27-e9e8-4e4f-af6a-386e2952610e/hg38.fa:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/collections/hg38/seq/hg38.dict:/var/lib/cwl/stg340ebc27-e9e8-4e4f-af6a-386e2952610e/hg38.dict:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/d3d1bf8df7088fcbd617ba0b72e96a52/align/NA12878-chr20/NA12878-chr20-sort.bam.bai:/var/lib/cwl/stg2a1c7693-e41f-4545-a94c-4e26168f4340/NA12878-chr20-sort.bam.bai:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/7422aae9ae5e6917d74f825ea1e44b9f:/var/spool/cwl:rw \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/tmp/Y2IbLK:/tmp:rw \ | |
| --workdir=/var/spool/cwl \ | |
| --read-only=true \ | |
| --user=1000 \ | |
| --rm \ | |
| --env=TMPDIR=/tmp \ | |
| --env=HOME=/var/spool/cwl \ | |
| --env=MPLCONFIGDIR=. \ | |
| quay.io/bcbio/bcbio-base \ | |
| bcbio_nextgen.py \ | |
| runfn \ | |
| postprocess_alignment_to_rec \ | |
| cwl \ | |
| sentinel_runtime=cores,1,ram,3072 \ | |
| sentinel_parallel=multi-combined \ | |
| 'sentinel_outputs=postprocess_alignment_rec:description;reference__fasta__base;config__algorithm__coverage_interval;config__algorithm__recalibrate;config__algorithm__variant_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__variant_regions_orig;config__algorithm__coverage;config__algorithm__coverage_merged;config__algorithm__coverage_orig;config__algorithm__seq2c_bed_ready' \ | |
| sentinel_inputs=align_bam:var,config__algorithm__coverage_interval:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__variant_regions_orig:var,config__algorithm__coverage:var,config__algorithm__coverage_merged:var,config__algorithm__coverage_orig:var,config__algorithm__seq2c_bed_ready:var,config__algorithm__recalibrate:var,reference__fasta__base:var,description:var | |
| [job postprocess_alignment_to_rec] completed success | |
| [step postprocess_alignment_to_rec] completed success | |
| [job postprocess_alignment] Output of job will be cached in /home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/d6c7737674b5336e2aea262275667719 | |
| [job postprocess_alignment] /home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/d6c7737674b5336e2aea262275667719$ docker \ | |
| run \ | |
| -i \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/collections/hg38/seq/hg38.dict:/var/lib/cwl/stg57d97c17-c5db-46c8-b3ea-935b0f7bc2f5/hg38.dict:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/collections/hg38/seq/hg38.fa:/var/lib/cwl/stg57d97c17-c5db-46c8-b3ea-935b0f7bc2f5/hg38.fa:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/d3d1bf8df7088fcbd617ba0b72e96a52/align/NA12878-chr20/NA12878-chr20-sort.bam.bai:/var/lib/cwl/stg5760139e-1213-4bc5-a7aa-f8150d73edd3/NA12878-chr20-sort.bam.bai:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/collections/hg38/seq/hg38.fa.fai:/var/lib/cwl/stg57d97c17-c5db-46c8-b3ea-935b0f7bc2f5/hg38.fa.fai:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/d3d1bf8df7088fcbd617ba0b72e96a52/align/NA12878-chr20/NA12878-chr20-sort.bam:/var/lib/cwl/stg5760139e-1213-4bc5-a7aa-f8150d73edd3/NA12878-chr20-sort.bam:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/d6c7737674b5336e2aea262275667719:/var/spool/cwl:rw \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/tmp/4LPGgL:/tmp:rw \ | |
| --workdir=/var/spool/cwl \ | |
| --read-only=true \ | |
| --user=1000 \ | |
| --rm \ | |
| --env=TMPDIR=/tmp \ | |
| --env=HOME=/var/spool/cwl \ | |
| --env=MPLCONFIGDIR=. \ | |
| quay.io/bcbio/bcbio-align \ | |
| bcbio_nextgen.py \ | |
| runfn \ | |
| postprocess_alignment \ | |
| cwl \ | |
| sentinel_runtime=cores,8,ram,24576 \ | |
| sentinel_parallel=multi-parallel \ | |
| sentinel_outputs=config__algorithm__coverage_interval,config__algorithm__variant_regions,config__algorithm__variant_regions_merged,config__algorithm__variant_regions_orig,config__algorithm__coverage,config__algorithm__coverage_merged,config__algorithm__coverage_orig,config__algorithm__seq2c_bed_ready,regions__callable,regions__sample_callable,regions__nblock,regions__highdepth \ | |
| sentinel_inputs=postprocess_alignment_rec:record | |
| ***** WARNING: File /var/spool/cwl/align/NA12878-chr20/NA12878-chr20-coverage.callable.bed has inconsistent naming convention for record: | |
| HLA-A*01:01:01:01 0 3503 NO_COVERAGE | |
| ***** WARNING: File /var/spool/cwl/align/NA12878-chr20/NA12878-chr20-coverage.callable.bed has inconsistent naming convention for record: | |
| HLA-A*01:01:01:01 0 3503 NO_COVERAGE | |
| [job postprocess_alignment] completed success | |
| [step postprocess_alignment] completed success | |
| [job qc_to_rec] Output of job will be cached in /home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/2b0092b605b712c39f34724e5149f52f | |
| [job qc_to_rec] /home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/2b0092b605b712c39f34724e5149f52f$ docker \ | |
| run \ | |
| -i \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/d6c7737674b5336e2aea262275667719/bedprep/NA12878-chr20-coverage.callable-vrsubset-callableblocks.bed:/var/lib/cwl/stgb6e3100b-7786-4359-bb75-6dbb50d8ca3f/NA12878-chr20-coverage.callable-vrsubset-callableblocks.bed:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/collections/hg38/seq/hg38.fa:/var/lib/cwl/stg13aee753-606a-4efe-aea4-aa5610011a64/hg38.fa:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/d6c7737674b5336e2aea262275667719/bedprep/NA12878-chr20-coverage.callable-vrsubset-callableblocks-merged.bed:/var/lib/cwl/stg46dbff4e-16f3-43d6-999f-677ebe71ae3e/NA12878-chr20-coverage.callable-vrsubset-callableblocks-merged.bed:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/collections/hg38/seq/hg38.fa.fai:/var/lib/cwl/stg13aee753-606a-4efe-aea4-aa5610011a64/hg38.fa.fai:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/d3d1bf8df7088fcbd617ba0b72e96a52/align/NA12878-chr20/NA12878-chr20-sort.bam:/var/lib/cwl/stge1c320fe-a801-4eff-b81d-c66151aa4211/NA12878-chr20-sort.bam:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/collections/hg38/seq/hg38.dict:/var/lib/cwl/stg13aee753-606a-4efe-aea4-aa5610011a64/hg38.dict:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/d3d1bf8df7088fcbd617ba0b72e96a52/align/NA12878-chr20/NA12878-chr20-sort.bam.bai:/var/lib/cwl/stge1c320fe-a801-4eff-b81d-c66151aa4211/NA12878-chr20-sort.bam.bai:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/2b0092b605b712c39f34724e5149f52f:/var/spool/cwl:rw \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/tmp/zBlzfu:/tmp:rw \ | |
| --workdir=/var/spool/cwl \ | |
| --read-only=true \ | |
| --user=1000 \ | |
| --rm \ | |
| --env=TMPDIR=/tmp \ | |
| --env=HOME=/var/spool/cwl \ | |
| --env=MPLCONFIGDIR=. \ | |
| quay.io/bcbio/bcbio-base \ | |
| bcbio_nextgen.py \ | |
| runfn \ | |
| qc_to_rec \ | |
| cwl \ | |
| sentinel_runtime=cores,1,ram,3072 \ | |
| sentinel_parallel=multi-combined \ | |
| 'sentinel_outputs=qc_rec:description;reference__fasta__base;config__algorithm__coverage_interval;genome_build;config__algorithm__tools_off;config__algorithm__qc;analysis;config__algorithm__tools_on;config__algorithm__variant_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__coverage;config__algorithm__coverage_merged' \ | |
| sentinel_inputs=align_bam:var,analysis:var,reference__fasta__base:var,genome_build:var,config__algorithm__coverage_interval:var,config__algorithm__tools_on:var,config__algorithm__tools_off:var,config__algorithm__qc:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__coverage:var,config__algorithm__coverage_merged:var,description:var | |
| [job qc_to_rec] completed success | |
| [step qc_to_rec] completed success | |
| [job combine_sample_regions] Output of job will be cached in /home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/11bce35340f7b5d1492f051cb82d9a75 | |
| [job combine_sample_regions] /home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/11bce35340f7b5d1492f051cb82d9a75$ docker \ | |
| run \ | |
| -i \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/collections/hg38/seq/hg38.fa.fai:/var/lib/cwl/stg648a9f51-4e0b-4886-b391-7f1b2442a0ea/hg38.fa.fai:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/d6c7737674b5336e2aea262275667719/align/NA12878-chr20/NA12878-chr20-coverage.callable-vrsubset-nblocks.bed:/var/lib/cwl/stg128aa02b-44b6-4519-b19e-1fbde0f8d49c/NA12878-chr20-coverage.callable-vrsubset-nblocks.bed:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/collections/hg38/seq/hg38.fa:/var/lib/cwl/stg648a9f51-4e0b-4886-b391-7f1b2442a0ea/hg38.fa:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/collections/hg38/seq/hg38.dict:/var/lib/cwl/stg648a9f51-4e0b-4886-b391-7f1b2442a0ea/hg38.dict:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/d6c7737674b5336e2aea262275667719/align/NA12878-chr20/NA12878-chr20-coverage.callable-vrsubset.bed:/var/lib/cwl/stgb804fbf1-6c51-42fa-a2f2-e364dc1dd0fc/NA12878-chr20-coverage.callable-vrsubset.bed:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/11bce35340f7b5d1492f051cb82d9a75:/var/spool/cwl:rw \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/tmp/GY6wfA:/tmp:rw \ | |
| --workdir=/var/spool/cwl \ | |
| --read-only=true \ | |
| --user=1000 \ | |
| --rm \ | |
| --env=TMPDIR=/tmp \ | |
| --env=HOME=/var/spool/cwl \ | |
| --env=MPLCONFIGDIR=. \ | |
| quay.io/bcbio/bcbio-align \ | |
| bcbio_nextgen.py \ | |
| runfn \ | |
| combine_sample_regions \ | |
| cwl \ | |
| sentinel_runtime=cores,1,ram,3072 \ | |
| sentinel_parallel=multi-combined \ | |
| sentinel_outputs=config__algorithm__callable_regions,config__algorithm__non_callable_regions,config__algorithm__callable_count \ | |
| sentinel_inputs=regions__callable:var,regions__nblock:var,config__algorithm__nomap_split_size:var,config__algorithm__nomap_split_targets:var,reference__fasta__base:var,description:var | |
| [job combine_sample_regions] completed success | |
| [step combine_sample_regions] completed success | |
| [job batch_for_variantcall] Output of job will be cached in /home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/70e016609483ad6696d73b529f46b337 | |
| [job batch_for_variantcall] /home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/70e016609483ad6696d73b529f46b337$ docker \ | |
| run \ | |
| -i \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/collections/hg38/validation/giab-NA12878/truth_small_variants.vcf.gz.tbi:/var/lib/cwl/stg0d08e2d3-013a-4e6c-b5c0-d185a81caecf/truth_small_variants.vcf.gz.tbi:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/collections/hg38/coverage/problem_regions/repeats/LCR.bed.gz:/var/lib/cwl/stgf2d84db8-05f6-446e-9b58-2e3e61e39eb0/LCR.bed.gz:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/d6c7737674b5336e2aea262275667719/bedprep/NA12878-chr20-coverage.callable-vrsubset-callableblocks.bed:/var/lib/cwl/stg09d7cde2-7aae-4152-8cb3-ac64ed67c5f2/NA12878-chr20-coverage.callable-vrsubset-callableblocks.bed:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/collections/hg38/snpeff--GRCh38.86-wf.tar.gz:/var/lib/cwl/stg7febd3de-28ae-488c-be11-5f3cfc784f44/snpeff--GRCh38.86-wf.tar.gz:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/collections/hg38/validation/giab-NA12878/truth_regions.bed:/var/lib/cwl/stg8cdc2572-f649-484a-8e0d-603d5b867c68/truth_regions.bed:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/collections/hg38/coverage/problem_regions/repeats/LCR.bed.gz.tbi:/var/lib/cwl/stgf2d84db8-05f6-446e-9b58-2e3e61e39eb0/LCR.bed.gz.tbi:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/collections/hg38/seq/hg38.fa:/var/lib/cwl/stg2edfd8a1-225c-4cd8-b0ed-bca3768e5c1b/hg38.fa:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/11bce35340f7b5d1492f051cb82d9a75/regions/NA12878-chr20-analysis_blocks.bed:/var/lib/cwl/stg25bdb63e-e6ab-428f-87ef-17ad0a4d17d9/NA12878-chr20-analysis_blocks.bed:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/collections/hg38/validation/giab-NA12878/truth_small_variants.vcf.gz:/var/lib/cwl/stg0d08e2d3-013a-4e6c-b5c0-d185a81caecf/truth_small_variants.vcf.gz:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/collections/hg38/seq/hg38.fa.fai:/var/lib/cwl/stg2edfd8a1-225c-4cd8-b0ed-bca3768e5c1b/hg38.fa.fai:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/d3d1bf8df7088fcbd617ba0b72e96a52/align/NA12878-chr20/NA12878-chr20-sort.bam:/var/lib/cwl/stg31f07ec2-6ad3-432f-b283-b3d1e245a924/NA12878-chr20-sort.bam:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/collections/hg38/seq/hg38.dict:/var/lib/cwl/stg2edfd8a1-225c-4cd8-b0ed-bca3768e5c1b/hg38.dict:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/collections/hg38/variation/dbsnp-147.vcf.gz.tbi:/var/lib/cwl/stg606931de-52d1-4836-8f6b-a4941784187c/dbsnp-147.vcf.gz.tbi:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/d6c7737674b5336e2aea262275667719/align/NA12878-chr20/NA12878-chr20-sort-callable_sample.bed:/var/lib/cwl/stg27518a4f-d4b2-45f6-8057-7cf83eeae669/NA12878-chr20-sort-callable_sample.bed:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/d3d1bf8df7088fcbd617ba0b72e96a52/align/NA12878-chr20/NA12878-chr20-sort.bam.bai:/var/lib/cwl/stg31f07ec2-6ad3-432f-b283-b3d1e245a924/NA12878-chr20-sort.bam.bai:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/collections/hg38/variation/dbsnp-147.vcf.gz:/var/lib/cwl/stg606931de-52d1-4836-8f6b-a4941784187c/dbsnp-147.vcf.gz:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/collections/hg38/rtg--hg38.sdf-wf.tar.gz:/var/lib/cwl/stgbaaaaaf3-0767-498d-bd61-dd0b8b860045/rtg--hg38.sdf-wf.tar.gz:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/70e016609483ad6696d73b529f46b337:/var/spool/cwl:rw \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/tmp/Exu2mh:/tmp:rw \ | |
| --workdir=/var/spool/cwl \ | |
| --read-only=true \ | |
| --user=1000 \ | |
| --rm \ | |
| --env=TMPDIR=/tmp \ | |
| --env=HOME=/var/spool/cwl \ | |
| --env=MPLCONFIGDIR=. \ | |
| quay.io/bcbio/bcbio-base \ | |
| bcbio_nextgen.py \ | |
| runfn \ | |
| batch_for_variantcall \ | |
| cwl \ | |
| sentinel_runtime=cores,1,ram,3072 \ | |
| sentinel_parallel=multi-batch \ | |
| 'sentinel_outputs=batch_rec:description;config__algorithm__validate;reference__fasta__base;reference__snpeff;config__algorithm__variantcaller;config__algorithm__coverage_interval;metadata__batch;config__algorithm__validate_regions;genome_build;metadata__phenotype;genome_resources__aliases__human;config__algorithm__tools_off;genome_resources__variation__dbsnp;genome_resources__variation__cosmic;reference__genome_context;analysis;config__algorithm__tools_on;config__algorithm__variant_regions;genome_resources__aliases__ensembl;reference__rtg;genome_resources__aliases__snpeff;align_bam;regions__sample_callable;config__algorithm__callable_regions' \ | |
| sentinel_inputs=analysis:var,genome_build:var,align_bam:var,config__algorithm__callable_regions:var,metadata__batch:var,metadata__phenotype:var,regions__sample_callable:var,config__algorithm__variantcaller:var,config__algorithm__coverage_interval:var,config__algorithm__variant_regions:var,config__algorithm__validate:var,config__algorithm__validate_regions:var,config__algorithm__tools_on:var,config__algorithm__tools_off:var,reference__fasta__base:var,reference__rtg:var,reference__genome_context:var,genome_resources__variation__cosmic:var,genome_resources__variation__dbsnp:var,genome_resources__aliases__ensembl:var,genome_resources__aliases__human:var,genome_resources__aliases__snpeff:var,reference__snpeff:var,description:var | |
| [job batch_for_variantcall] completed success | |
| [step batch_for_variantcall] completed success | |
| [job pipeline_summary] Output of job will be cached in /home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/a59f44ab1bd9ce0da9d54eff78c5684b | |
| [job pipeline_summary] /home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/a59f44ab1bd9ce0da9d54eff78c5684b$ docker \ | |
| run \ | |
| -i \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/d3d1bf8df7088fcbd617ba0b72e96a52/align/NA12878-chr20/NA12878-chr20-sort.bam.bai:/var/lib/cwl/stg7b3ef782-83cf-49a8-9ed2-28fe754e804b/NA12878-chr20-sort.bam.bai:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/d3d1bf8df7088fcbd617ba0b72e96a52/align/NA12878-chr20/NA12878-chr20-sort.bam:/var/lib/cwl/stg7b3ef782-83cf-49a8-9ed2-28fe754e804b/NA12878-chr20-sort.bam:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/collections/hg38/seq/hg38.fa:/var/lib/cwl/stg2067de01-f0d1-4e0f-8468-6d59b145bfbc/hg38.fa:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/collections/hg38/seq/hg38.dict:/var/lib/cwl/stg2067de01-f0d1-4e0f-8468-6d59b145bfbc/hg38.dict:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/collections/hg38/seq/hg38.fa.fai:/var/lib/cwl/stg2067de01-f0d1-4e0f-8468-6d59b145bfbc/hg38.fa.fai:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/d6c7737674b5336e2aea262275667719/bedprep/NA12878-chr20-coverage.callable-vrsubset-callableblocks-merged.bed:/var/lib/cwl/stg10557f41-cc41-45e5-831f-71dfe47ab843/NA12878-chr20-coverage.callable-vrsubset-callableblocks-merged.bed:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/d6c7737674b5336e2aea262275667719/bedprep/NA12878-chr20-coverage.callable-vrsubset-callableblocks.bed:/var/lib/cwl/stg74ca6b9c-d162-43ca-8777-2331114dc162/NA12878-chr20-coverage.callable-vrsubset-callableblocks.bed:ro \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/a59f44ab1bd9ce0da9d54eff78c5684b:/var/spool/cwl:rw \ | |
| --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/tmp/eHAe3K:/tmp:rw \ | |
| --workdir=/var/spool/cwl \ | |
| --read-only=true \ | |
| --user=1000 \ | |
| --rm \ | |
| --env=TMPDIR=/tmp \ | |
| --env=HOME=/var/spool/cwl \ | |
| --env=MPLCONFIGDIR=. \ | |
| quay.io/bcbio/bcbio-qc \ | |
| bcbio_nextgen.py \ | |
| runfn \ | |
| pipeline_summary \ | |
| cwl \ | |
| sentinel_runtime=cores,8,ram,24576 \ | |
| sentinel_parallel=multi-parallel \ | |
| 'sentinel_outputs=qcout_rec:summary__qc;summary__metrics;description;reference__fasta__base;config__algorithm__coverage_interval;genome_build;config__algorithm__tools_off;config__algorithm__qc;analysis;config__algorithm__tools_on;config__algorithm__variant_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__coverage;config__algorithm__coverage_merged' \ | |
| sentinel_inputs=qc_rec:record | |
| [job pipeline_summary] completed success | |
| [job pipeline_summary_2] Using cached output in /home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/a59f44ab1bd9ce0da9d54eff78c5684b | |
| Workflow error, try again with --debug for more information: | |
| Output file path /var/lib/cwl/stg2067de01-f0d1-4e0f-8468-6d59b145bfbc/hg38.fa must be within designated output directory (/var/spool/cwl) or an input file pass through. |
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