Traceback (most recent call last):

 "/group/ngs/src/bcbio-nextgen/0.8.1a/rhel6-x64/anaconda/lib/python2.7/site-packages/bcbio/distributed/ipythontasks.py", line 38, in _setup_logging
yield config

 "/group/ngs/src/bcbio-nextgen/0.8.1a/rhel6-x64/anaconda/lib/python2.7/site-packages/bcbio/distributed/ipythontasks.py", line 79, in process_alignment
return ipython.zip_args(apply(sample.process_alignment, *args))

 "/group/ngs/src/bcbio-nextgen/0.8.1a/rhel6-x64/anaconda/lib/python2.7/site-packages/bcbio/pipeline/sample.py", line 114, in process_alignment
data)

 "/group/ngs/src/bcbio-nextgen/0.8.1a/rhel6-x64/anaconda/lib/python2.7/site-packages/bcbio/pipeline/cleanbam.py", line 30, in picard_prep
return _filter_bad_reads(rg_bam, ref_file, data)

 "/group/ngs/src/bcbio-nextgen/0.8.1a/rhel6-x64/anaconda/lib/python2.7/site-packages/bcbio/pipeline/cleanbam.py", line 51, in _filter_bad_reads
do.run(cmd, "Filter problem reads")

 "/group/ngs/src/bcbio-nextgen/0.8.1a/rhel6-x64/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 22, in run
_do_run(cmd, checks, log_stdout)

 "/group/ngs/src/bcbio-nextgen/0.8.1a/rhel6-x64/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 121, in _do_run
raise subprocess.CalledProcessError(exitcode, error_msg)CalledProcessError: Command '/group/ngs/src/bcbio-nextgen/0.8.1a/rhel6-x64/bin/gatk-framework -Xms2000m -Xmx5500m -XX:+UseSerialGC -Djava.io.tmpdir=/ngs/scratch/bcbiotmp/tmp5xA31j -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T PrintReads -R /ngs/reference_data/genomes/Hsapiens/hg19/seq/hg19.fa -I /gpfs/ngs/oncology/Analysis/external/EXT_018_SRP042620/variant/work/bamclean/SRR1313121/SRR1313121-reorder-fixrgs.bam --out /gpfs/ngs/oncology/Analysis/external/EXT_018_SRP042620/variant/work/bamclean/SRR1313121/tx/tmpS4dmrL/SRR1313121-reorder-fixrgs-gatkfilter.bam --filter_mismatching_base_and_quals --filter_bases_not_stored --filter_reads_with_N_cigar
Traceback (most recent call last):

 "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run
_do_run(cmd, checks, log_stdout)

 "/iron/bioinfo/share/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; /iron/bioinfo/share/bcbio/anaconda/bin/python /iron/bioinfo/share/bcbio/anaconda/bin/tophat --library-type=fr-unstranded --no-mixed --rg-id=Test1 --no-coverage-search --rg-library=illumina --rg-platform-unit=Test1 --rg-sample=Test1 --GTF=/iron/bioinfo/src/bcbio-nextgen/tests/data/genomes/mm9/rnaseq/ref-transcripts.gtf --output-dir=/iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/align/Test1/mm9/tx/tmpXoYYTr/Test1_tophat --no-convert-bam /iron/bioinfo/src/bcbio-nextgen/tests/data/genomes/mm9/bowtie2/mm9 /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/trimmed/Hsapiens_Mmusculus_1_Test1.trimmed.fq.gz