Traceback (most recent call last):


 "/gpfs/software/bcbio/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 22, in run

_do_run(cmd, checks, log_stdout, env=env)


 "/gpfs/software/bcbio/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 102, in _do_run

raise subprocess.CalledProcessError(exitcode, error_msg)
CalledProcessError: Command 'set -o pipefail; export OMP_NUM_THREADS=1 && export LC_ALL=C && delly -t DEL -g /gpfs/software/bcbio/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /gpfs/software/cancer_pipeline_test/project/work/bcbiotx/tmpedzpc5/syn3-tumor-sort-syn3-svs-7-DEL.vcf -x /gpfs/software/cancer_pipeline_test/project/work/structural/syn3-tumor/delly/syn3-tumor-sort-syn3-svs-7-DEL-exclude-7-delly.bed /gpfs/software/cancer_pipeline_test/project/work/align/syn3-tumor/syn3-tumor-sort.bam /gpfs/software/cancer_pipeline_test/project/work/align/syn3-normal/syn3-normal-sort.bam

Traceback (most recent call last):


 "/path/to/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run

_do_run(cmd, checks, log_stdout)


 "/path/to/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run

raise subprocess.CalledProcessError(exitcode, error_msg)
CalledProcessError: Command 'set -o pipefail; /path/to/bcbio/anaconda/bin/freebayes -f /path/to/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --genotype-qualities --strict-vcf --ploidy 2 --targets /path/to/work/freebayes/9/13657-9_0_141213431-regions-nolcr.bed --min-repeat-entropy 1 --no-partial-observations --min-alternate-fraction 0.1 --pooled-discrete --pooled-continuous --report-genotype-likelihood-max --allele-balance-priors-off /path/to/work/bamprep/13657T/9/13657T-sort-9_0_141213431-prep.bam /path/to/work/bamprep/13657N/9/13657N-sort-9_0_141213431-prep.bam | bcftools filter -i 'ALT="<*>" || QUAL > 5' | /path/to/bcbio/anaconda/bin/py -x 'bcbio.variation.freebayes.call_somatic(x)' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDX]/, "N", $4) } {print}' | bcftools annotate -x FMT/DPR | bcftools view -a - | /path/to/bcbio/anaconda/bin/py -x 'bcbio.variation.freebayes.remove_missingalt(x)' | vcfallelicprimitives -t DECOMPOSED --keep-geno | vcffixup - | vcfstreamsort | vt normalize -n -r /path/to/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -q - | vcfuniqalleles | bgzip -c > /path/to/work/freebayes/9/tx/tmpn5ZPOD/13657-9_0_141213431.vcf.gz
