stderr.txt

/home/ubuntu/envs/env-ga4gh-dream/bin/cwltool 1.0.20170217172322
Resolved 'main-NA12878-platinum-chr20.cwl' to 'file:///home/ubuntu/ga4gh_dream_testing/bcbio/NA12878-platinum-chr20-workflow/main-NA12878-platinum-chr20.cwl'
[job alignment_to_rec] Output of job will be cached in /home/ubuntu/ga4gh_dream_testing/bcbio/NA12878-platinum-chr20-workflow/cache/68761c321fc424b99b4ba5719b935567
['docker', 'pull', 'quay.io/bcbio/bcbio-base']
Using default tag: latest
latest: Pulling from bcbio/bcbio-base
75c416ea735c: Pulling fs layer
c6ff40b6d658: Pulling fs layer
a7050fc1f338: Pulling fs layer
f0ffb5cf6ba9: Pulling fs layer
be232718519c: Pulling fs layer
2834eb77be41: Pulling fs layer
f0ffb5cf6ba9: Waiting
be232718519c: Waiting
2834eb77be41: Waiting
c6ff40b6d658: Verifying Checksum
c6ff40b6d658: Download complete
a7050fc1f338: Verifying Checksum
a7050fc1f338: Download complete
f0ffb5cf6ba9: Verifying Checksum
f0ffb5cf6ba9: Download complete
be232718519c: Verifying Checksum
be232718519c: Download complete
75c416ea735c: Verifying Checksum
75c416ea735c: Download complete
75c416ea735c: Pull complete
c6ff40b6d658: Pull complete
a7050fc1f338: Pull complete
f0ffb5cf6ba9: Pull complete
be232718519c: Pull complete
2834eb77be41: Download complete
2834eb77be41: Pull complete
Digest: sha256:c6a3a7a48fbc08805622b6a0fb9aae81b0b95408bc622b132dc75ea1bf200b23
Status: Downloaded newer image for quay.io/bcbio/bcbio-base:latest
[job alignment_to_rec] /home/ubuntu/ga4gh_dream_testing/bcbio/NA12878-platinum-chr20-workflow/cache/68761c321fc424b99b4ba5719b935567$ docker \
    run \
    -i \
    --volume=/home/ubuntu/ga4gh_dream_testing/bcbio/biodata/collections/hg38/seq/hg38.fa:/var/lib/cwl/stgec81339d-c6d1-4efe-bcf0-dad4d294ffae/hg38.fa:ro \
    --volume=/home/ubuntu/ga4gh_dream_testing/bcbio/biodata/giab/na12878/NA12878-platinum-chr20.bam:/var/lib/cwl/stge916b06b-8844-464f-80d3-9e8c5bf52744/NA12878-platinum-chr20.bam:ro \
    --volume=/home/ubuntu/ga4gh_dream_testing/bcbio/biodata/collections/hg38/seq/hg38.fa.fai:/var/lib/cwl/stgec81339d-c6d1-4efe-bcf0-dad4d294ffae/hg38.fa.fai:ro \
    --volume=/home/ubuntu/ga4gh_dream_testing/bcbio/biodata/giab/na12878/NA12878-platinum-chr20.bam.bai:/var/lib/cwl/stge916b06b-8844-464f-80d3-9e8c5bf52744/NA12878-platinum-chr20.bam.bai:ro \
    --volume=/home/ubuntu/ga4gh_dream_testing/bcbio/biodata/collections/hg38/seq/hg38.dict:/var/lib/cwl/stgec81339d-c6d1-4efe-bcf0-dad4d294ffae/hg38.dict:ro \
    --volume=/home/ubuntu/ga4gh_dream_testing/bcbio/biodata/collections/hg38/bwa-wf.tar.gz:/var/lib/cwl/stg2e153fa2-56e8-4cf6-9769-5ceacd2cd018/bwa-wf.tar.gz:ro \
    --volume=/home/ubuntu/ga4gh_dream_testing/bcbio/NA12878-platinum-chr20-workflow/cache/68761c321fc424b99b4ba5719b935567:/var/spool/cwl:rw \
    --volume=/home/ubuntu/ga4gh_dream_testing/bcbio/NA12878-platinum-chr20-workflow/tmp/eYDuwv:/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_dream_testing/bcbio/NA12878-platinum-chr20-workflow/cache/6f0a8446c18e5b61b8ae525dcf73fd9a
[job prep_samples_to_rec] /home/ubuntu/ga4gh_dream_testing/bcbio/NA12878-platinum-chr20-workflow/cache/6f0a8446c18e5b61b8ae525dcf73fd9a$ docker \
    run \
    -i \
    --volume=/home/ubuntu/ga4gh_dream_testing/bcbio/biodata/collections/hg38/seq/hg38.fa.fai:/var/lib/cwl/stg0674d683-eaf3-4ce1-b8f7-0e41ee565e4e/hg38.fa.fai:ro \
    --volume=/home/ubuntu/ga4gh_dream_testing/bcbio/biodata/collections/hg38/seq/hg38.dict:/var/lib/cwl/stg0674d683-eaf3-4ce1-b8f7-0e41ee565e4e/hg38.dict:ro \
    --volume=/home/ubuntu/ga4gh_dream_testing/bcbio/biodata/collections/hg38/seq/hg38.fa:/var/lib/cwl/stg0674d683-eaf3-4ce1-b8f7-0e41ee565e4e/hg38.fa:ro \
    --volume=/home/ubuntu/ga4gh_dream_testing/bcbio/NA12878-platinum-chr20-workflow/cache/6f0a8446c18e5b61b8ae525dcf73fd9a:/var/spool/cwl:rw \
    --volume=/home/ubuntu/ga4gh_dream_testing/bcbio/NA12878-platinum-chr20-workflow/tmp/_PqfEC:/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_samples] Output of job will be cached in /home/ubuntu/ga4gh_dream_testing/bcbio/NA12878-platinum-chr20-workflow/cache/3d481177f6ca7fdfade0bb77a1b80add
['docker', 'pull', 'quay.io/bcbio/bcbio-align']
Using default tag: latest
latest: Pulling from bcbio/bcbio-align
75c416ea735c: Already exists
c6ff40b6d658: Already exists
a7050fc1f338: Already exists
f0ffb5cf6ba9: Already exists
be232718519c: Already exists
2834eb77be41: Already exists
b8ab66395517: Pulling fs layer
74bad9141b53: Pulling fs layer
b8ab66395517: Verifying Checksum
b8ab66395517: Download complete
b8ab66395517: Pull complete
74bad9141b53: Download complete
74bad9141b53: Pull complete
Digest: sha256:a5820aed2a672840cf6f5064b08e2da16380b2e1b1611ff7fa2951a46cf7805b
Status: Downloaded newer image for quay.io/bcbio/bcbio-align:latest
[job prep_samples] /home/ubuntu/ga4gh_dream_testing/bcbio/NA12878-platinum-chr20-workflow/cache/3d481177f6ca7fdfade0bb77a1b80add$ docker \
    run \
    -i \
    --volume=/home/ubuntu/ga4gh_dream_testing/bcbio/biodata/collections/hg38/seq/hg38.fa:/var/lib/cwl/stgea975d72-d847-4a01-a865-90fa582d35fd/hg38.fa:ro \
    --volume=/home/ubuntu/ga4gh_dream_testing/bcbio/biodata/collections/hg38/seq/hg38.dict:/var/lib/cwl/stgea975d72-d847-4a01-a865-90fa582d35fd/hg38.dict:ro \
    --volume=/home/ubuntu/ga4gh_dream_testing/bcbio/biodata/collections/hg38/seq/hg38.fa.fai:/var/lib/cwl/stgea975d72-d847-4a01-a865-90fa582d35fd/hg38.fa.fai:ro \
    --volume=/home/ubuntu/ga4gh_dream_testing/bcbio/NA12878-platinum-chr20-workflow/cache/3d481177f6ca7fdfade0bb77a1b80add:/var/spool/cwl:rw \
    --volume=/home/ubuntu/ga4gh_dream_testing/bcbio/NA12878-platinum-chr20-workflow/tmp/_svp28:/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 prep_align_inputs] Output of job will be cached in /home/ubuntu/ga4gh_dream_testing/bcbio/NA12878-platinum-chr20-workflow/cache/b6bf2ae717a8a53502deba4b8127d679
[job prep_align_inputs] /home/ubuntu/ga4gh_dream_testing/bcbio/NA12878-platinum-chr20-workflow/cache/b6bf2ae717a8a53502deba4b8127d679$ docker \
    run \
    -i \
    --volume=/home/ubuntu/ga4gh_dream_testing/bcbio/biodata/collections/hg38/seq/hg38.fa:/var/lib/cwl/stg8d58e29e-9947-4954-8a57-e9b6bcf7b09e/hg38.fa:ro \
    --volume=/home/ubuntu/ga4gh_dream_testing/bcbio/biodata/collections/hg38/seq/hg38.dict:/var/lib/cwl/stg8d58e29e-9947-4954-8a57-e9b6bcf7b09e/hg38.dict:ro \
    --volume=/home/ubuntu/ga4gh_dream_testing/bcbio/biodata/collections/hg38/seq/hg38.fa.fai:/var/lib/cwl/stg8d58e29e-9947-4954-8a57-e9b6bcf7b09e/hg38.fa.fai:ro \
    --volume=/home/ubuntu/ga4gh_dream_testing/bcbio/biodata/giab/na12878/NA12878-platinum-chr20.bam:/var/lib/cwl/stg95a2edd0-faa0-4602-bd5e-0ecb01186681/NA12878-platinum-chr20.bam:ro \
    --volume=/home/ubuntu/ga4gh_dream_testing/bcbio/biodata/giab/na12878/NA12878-platinum-chr20.bam.bai:/var/lib/cwl/stg95a2edd0-faa0-4602-bd5e-0ecb01186681/NA12878-platinum-chr20.bam.bai:ro \
    --volume=/home/ubuntu/ga4gh_dream_testing/bcbio/biodata/collections/hg38/bwa-wf.tar.gz:/var/lib/cwl/stgd56a6a0e-ac3d-4976-a637-b3d6e8307004/bwa-wf.tar.gz:ro \
    --volume=/home/ubuntu/ga4gh_dream_testing/bcbio/NA12878-platinum-chr20-workflow/cache/b6bf2ae717a8a53502deba4b8127d679:/var/spool/cwl:rw \
    --volume=/home/ubuntu/ga4gh_dream_testing/bcbio/NA12878-platinum-chr20-workflow/tmp/Z7KaZc:/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_dream_testing/bcbio/NA12878-platinum-chr20-workflow/cache/6475f4142293b0fdaa9e56a6e9525b6a
[job process_alignment] /home/ubuntu/ga4gh_dream_testing/bcbio/NA12878-platinum-chr20-workflow/cache/6475f4142293b0fdaa9e56a6e9525b6a$ docker \
    run \
    -i \
    --volume=/home/ubuntu/ga4gh_dream_testing/bcbio/biodata/collections/hg38/seq/hg38.fa:/var/lib/cwl/stgfa80d16b-5f40-4734-8c84-07bb36d7927c/hg38.fa:ro \
    --volume=/home/ubuntu/ga4gh_dream_testing/bcbio/biodata/collections/hg38/seq/hg38.dict:/var/lib/cwl/stgfa80d16b-5f40-4734-8c84-07bb36d7927c/hg38.dict:ro \
    --volume=/home/ubuntu/ga4gh_dream_testing/bcbio/biodata/collections/hg38/seq/hg38.fa.fai:/var/lib/cwl/stgfa80d16b-5f40-4734-8c84-07bb36d7927c/hg38.fa.fai:ro \
    --volume=/home/ubuntu/ga4gh_dream_testing/bcbio/NA12878-platinum-chr20-workflow/cache/b6bf2ae717a8a53502deba4b8127d679/align_prep/NA12878-platinum-chr20-1.fq.gz:/var/lib/cwl/stg59b2deb1-941c-40f8-8ec2-e1aff8d102b4/NA12878-platinum-chr20-1.fq.gz:ro \
    --volume=/home/ubuntu/ga4gh_dream_testing/bcbio/biodata/giab/na12878/NA12878-platinum-chr20.bam:/var/lib/cwl/stg7bd6256c-3777-45ca-be6a-f0ececa52262/NA12878-platinum-chr20.bam:ro \
    --volume=/home/ubuntu/ga4gh_dream_testing/bcbio/NA12878-platinum-chr20-workflow/cache/b6bf2ae717a8a53502deba4b8127d679/align_prep/NA12878-platinum-chr20-2.fq.gz.gbi:/var/lib/cwl/stg85085a93-7d9a-4b76-92e2-27d0cf8812ab/NA12878-platinum-chr20-2.fq.gz.gbi:ro \
    --volume=/home/ubuntu/ga4gh_dream_testing/bcbio/NA12878-platinum-chr20-workflow/cache/b6bf2ae717a8a53502deba4b8127d679/align_prep/NA12878-platinum-chr20-2.fq.gz:/var/lib/cwl/stg85085a93-7d9a-4b76-92e2-27d0cf8812ab/NA12878-platinum-chr20-2.fq.gz:ro \
    --volume=/home/ubuntu/ga4gh_dream_testing/bcbio/NA12878-platinum-chr20-workflow/cache/b6bf2ae717a8a53502deba4b8127d679/align_prep/NA12878-platinum-chr20-1.fq.gz.gbi:/var/lib/cwl/stg59b2deb1-941c-40f8-8ec2-e1aff8d102b4/NA12878-platinum-chr20-1.fq.gz.gbi:ro \
    --volume=/home/ubuntu/ga4gh_dream_testing/bcbio/biodata/giab/na12878/NA12878-platinum-chr20.bam.bai:/var/lib/cwl/stg7bd6256c-3777-45ca-be6a-f0ececa52262/NA12878-platinum-chr20.bam.bai:ro \
    --volume=/home/ubuntu/ga4gh_dream_testing/bcbio/biodata/collections/hg38/bwa-wf.tar.gz:/var/lib/cwl/stge264f8a4-32c8-4393-9a80-d417f5d30cf6/bwa-wf.tar.gz:ro \
    --volume=/home/ubuntu/ga4gh_dream_testing/bcbio/NA12878-platinum-chr20-workflow/cache/6475f4142293b0fdaa9e56a6e9525b6a:/var/spool/cwl:rw \
    --volume=/home/ubuntu/ga4gh_dream_testing/bcbio/NA12878-platinum-chr20-workflow/tmp/EsLlQt:/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
Traceback (most recent call last):
  File "/usr/local/bin/bcbio_nextgen.py", line 219, in <module>
    runfn.process(kwargs["args"])
  File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/distributed/runfn.py", line 56, in process
    out = fn(fnargs)
  File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/utils.py", line 50, in wrapper
    return apply(f, *args, **kwargs)
  File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/distributed/multitasks.py", line 93, in process_alignment
    return sample.process_alignment(*args)
  File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/pipeline/sample.py", line 117, in process_alignment
    data = align_to_sort_bam(fastq1, fastq2, aligner, data)
  File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.py", line 65, in align_to_sort_bam
    names, align_dir, data)
  File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.py", line 119, in _align_from_fastq
    out = align_fn(fastq1, fastq2, align_ref, names, align_dir, data)
  File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.py", line 163, in align_pipe
    names, rg_info, data)
  File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.py", line 174, in _align_mem
    [do.file_nonempty(tx_out_file), do.file_reasonable_size(tx_out_file, fastq_file)])
  File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 22, in run
    _do_run(cmd, checks, log_stdout, env=env)
  File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 102, in _do_run
    raise subprocess.CalledProcessError(exitcode, error_msg)
subprocess.CalledProcessError: Command 'set -o pipefail; unset JAVA_HOME && /usr/local/share/bcbio-nextgen/anaconda/bin/bwa mem   -c 250 -M -t 8  -R '@RG\tID:NA12878-chr20\tPL:illumina\tPU:1_2017-07-13_NA12878-platinum-chr20\tSM:NA12878-chr20' -v 1 /var/spool/cwl/wf-inputs/bwa/hg38.fa /var/lib/cwl/stg59b2deb1-941c-40f8-8ec2-e1aff8d102b4/NA12878-platinum-chr20-1.fq.gz /var/lib/cwl/stg85085a93-7d9a-4b76-92e2-27d0cf8812ab/NA12878-platinum-chr20-2.fq.gz  | /usr/local/share/bcbio-nextgen/anaconda/share/bwakit-0.7.12-0/k8 /usr/local/share/bcbio-nextgen/anaconda/share/bwakit-0.7.12-0/bwa-postalt.js -p /var/spool/cwl/align/NA12878-chr20/hla/NA12878-chr20-sort.bam.hla /var/spool/cwl/wf-inputs/bwa/hg38.fa.alt | bamsormadup inputformat=sam threads=8 tmpfile=/var/spool/cwl/bcbiotx/tmpQKCMCM/NA12878-chr20-sort-sorttmp-markdup SO=coordinate indexfilename=/var/spool/cwl/bcbiotx/tmpQKCMCM/NA12878-chr20-sort.bam.bai > /var/spool/cwl/bcbiotx/tmpQKCMCM/NA12878-chr20-sort.bam
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 541)
[M::mem_pestat] mean and std.dev: (224.88, 93.94)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 659)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RR
[V] 9644354	14:09:57773099	MemUsage(size=3682.29,rss=1895.35,peak=3899.95)	AutoArrayMemUsage(memusage=3102.5,peakmemusage=3257.96,maxmem=1.75922e+13)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (96, 194, 270)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 618)
[M::mem_pestat] mean and std.dev: (181.73, 97.57)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 792)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (274, 318, 362)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (98, 538)
[M::mem_pestat] mean and std.dev: (317.56, 69.96)
[M::mem_pestat] low and high boundaries for proper pairs: (10, 626)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (25, 33, 154)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 412)
[M::mem_pestat] mean and std.dev: (52.17, 53.46)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 541)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (168, 239, 307)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 585)
[M::mem_pestat] mean and std.dev: (227.48, 101.78)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 724)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[V] 10618618	15:10:22459400	MemUsage(size=3682.29,rss=1895.35,peak=3899.95)	AutoArrayMemUsage(memusage=3102.64,peakmemusage=3257.96,maxmem=1.75922e+13)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (96, 200, 260)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 588)
[M::mem_pestat] mean and std.dev: (178.67, 101.46)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 752)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (274, 318, 363)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (96, 541)
[M::mem_pestat] mean and std.dev: (317.63, 70.29)
[M::mem_pestat] low and high boundaries for proper pairs: (7, 630)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (169, 243, 293)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 541)
[M::mem_pestat] mean and std.dev: (227.52, 92.80)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 665)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RR
[V] 11577779	16:16:72896700	MemUsage(size=3682.29,rss=1895.61,peak=3899.95)	AutoArrayMemUsage(memusage=3102.8,peakmemusage=3257.96,maxmem=1.75922e+13)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (103, 183, 255)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 559)
[M::mem_pestat] mean and std.dev: (180.14, 99.06)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 711)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (275, 319, 364)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (97, 542)
[M::mem_pestat] mean and std.dev: (318.32, 70.83)
[M::mem_pestat] low and high boundaries for proper pairs: (8, 631)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (182, 265, 604)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1448)
[M::mem_pestat] mean and std.dev: (328.83, 232.35)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1870)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (153, 207, 258)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 468)
[M::mem_pestat] mean and std.dev: (207.53, 85.90)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 573)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (112, 193, 282)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 622)
[M::mem_pestat] mean and std.dev: (184.79, 102.93)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 792)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (276, 319, 364)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (100, 540)
[M::mem_pestat] mean and std.dev: (319.13, 70.48)
[M::mem_pestat] low and high boundaries for proper pairs: (12, 628)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (173, 221, 286)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 512)
[M::mem_pestat] mean and std.dev: (221.30, 85.71)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 625)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RR
[V] 13461264	31:36:53056900	MemUsage(size=3682.29,rss=1890.26,peak=3899.95)	AutoArrayMemUsage(memusage=3103.1,peakmemusage=3257.96,maxmem=1.75922e+13)
libmaus2::bambam::SamInfo::parseSamLine: defect SAM line (less than 11 columns): ERR194147.687693754	163		NaN	NaN
/usr/local/share/bcbio-nextgen/anaconda/share/biobambam-2.0.72-0/bin/../lib/libmaus2.so.2(libmaus2::util::StackTrace::StackTrace()+0x55)[0x7f87723ae155]
bamsormadup(libmaus2::exception::LibMausException::LibMausException()+0x20)[0x41f740]
bamsormadup()[0x45ccab]
bamsormadup()[0x45d044]
bamsormadup()[0x47a37e]
bamsormadup(libmaus2::parallel::PosixThread::dispatch(void*)+0x14)[0x41cdb4]
/lib/x86_64-linux-gnu/libpthread.so.0(+0x76ba)[0x7f87710b06ba]
/lib/x86_64-linux-gnu/libc.so.6(clone+0x6d)[0x7f876f5f33dd]
' returned non-zero exit status 1