Test suite fails

Hi-
I've managed to install bcbio but am having some trouble with the test suite.  There seem to be issues with freebayes and perhaps also with gatk.  I just installed bcbio and then upgraded with bcbio_nextgen.py upgrade -u stable --tools --data.  I'd appreciate any help as I am very much looking forward to running the pipeline.
Thanks,
Daniel
ue Apr 21 14:31:49 tests > ./run_tests.sh
Check for the presence of runs in an Illumina SampleSheet. ... ok
Convert CSV Illumina SampleSheet to YAML. ... ok
Test variant calling with GATK pipeline. ... [2015-04-21T18:32Z] Resource requests: bwa, sambamba, samtools; memory: 2.00; cores: 16, 1, 16
[2015-04-21T18:32Z] Configuring 1 jobs to run, using 1 cores each with 2.00g of memory reserved for each job
[2015-04-21T18:32Z] Timing: organize samples
[2015-04-21T18:32Z] multiprocessing: organize_samples
[2015-04-21T18:32Z] Using input YAML configuration: /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/automated/run_info-variantcall.yaml
[2015-04-21T18:32Z] Checking sample YAML configuration: /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/automated/run_info-variantcall.yaml
[2015-04-21T18:32Z] Testing minimum versions of installed programs
[2015-04-21T18:32Z] Timing: alignment preparation
[2015-04-21T18:32Z] multiprocessing: prep_align_inputs
[2015-04-21T18:32Z] Resource requests: ; memory: 1.00; cores: 1
[2015-04-21T18:32Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-04-21T18:32Z] bgzip input file
[2015-04-21T18:32Z] bgzip input file
[2015-04-21T18:32Z] Resource requests: ; memory: 1.00; cores: 1
[2015-04-21T18:32Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-04-21T18:32Z] Index input with grabix: 7_100326_FC6107FAAXX_1_fastq.txt.gz
[2015-04-21T18:32Z] Index input with grabix: 7_100326_FC6107FAAXX_2_fastq.txt.gz
[2015-04-21T18:32Z] multiprocessing: disambiguate_split
[2015-04-21T18:32Z] Timing: alignment
[2015-04-21T18:32Z] multiprocessing: process_alignment
[2015-04-21T18:32Z] Aligning lane 7_100326_FC6107FAAXX with bwa aligner
[2015-04-21T18:32Z] bwa mem alignment from fastq: Test1
[2015-04-21T18:32Z] samblaster: Version 0.1.21
[2015-04-21T18:32Z] samblaster: Inputting from stdin
[2015-04-21T18:32Z] samblaster: Outputting to stdout
[2015-04-21T18:32Z] samblaster: Opening /dev/fd/62 for write.
[2015-04-21T18:32Z] samblaster: Opening /dev/fd/63 for write.
[2015-04-21T18:32Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2015-04-21T18:32Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-04-21T18:32Z] [M::mem_pestat] (25, 50, 75) percentile: (129, 150, 174)
[2015-04-21T18:32Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (39, 264)
[2015-04-21T18:32Z] [M::mem_pestat] mean and std.dev: (151.57, 30.80)
[2015-04-21T18:32Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 309)
[2015-04-21T18:32Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-04-21T18:32Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2015-04-21T18:32Z] samblaster: Loaded 2 header sequence entries.
[2015-04-21T18:32Z] [main] Version: 0.7.12-r1039
[2015-04-21T18:32Z] [main] CMD: /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/bwa mem -M -t 1 -R @RG\tID:7\tPL:illumina\tPU:7_100326_FC6107FAAXX\tSM:Test1 -v 1 /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/genomes/hg19/bwa/hg19.fa /dev/fd/63 /dev/fd/62
[2015-04-21T18:32Z] [main] Real time: 0.702 sec; CPU: 0.665 sec
[2015-04-21T18:32Z] samblaster: Output 0 discordant read pairs to /dev/fd/62
[2015-04-21T18:32Z] samblaster: Output 0 split reads to /dev/fd/63
[2015-04-21T18:32Z] samblaster: Marked 102 of 9000 (1.13%) read ids as duplicates using 1384k memory in 0.014S CPU seconds and 0S wall time.
[2015-04-21T18:32Z] Index BAM file: 7_100326_FC6107FAAXX-sort-1_36000-sr.bam
[2015-04-21T18:32Z] Index BAM file: 7_100326_FC6107FAAXX-sort-1_36000-disc.bam
[2015-04-21T18:32Z] Aligning lane 7_100326_FC6107FAAXX with bwa aligner
[2015-04-21T18:32Z] bwa mem alignment from fastq: Test1
[2015-04-21T18:32Z] samblaster: Version 0.1.21
[2015-04-21T18:32Z] samblaster: Inputting from stdin
[2015-04-21T18:32Z] samblaster: Outputting to stdout
[2015-04-21T18:32Z] samblaster: Opening /dev/fd/62 for write.
[2015-04-21T18:32Z] samblaster: Opening /dev/fd/63 for write.
[2015-04-21T18:32Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2015-04-21T18:32Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-04-21T18:32Z] [M::mem_pestat] (25, 50, 75) percentile: (129, 150, 175)
[2015-04-21T18:32Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (37, 267)
[2015-04-21T18:32Z] [M::mem_pestat] mean and std.dev: (151.74, 31.08)
[2015-04-21T18:32Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 313)
[2015-04-21T18:32Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-04-21T18:32Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2015-04-21T18:32Z] samblaster: Loaded 2 header sequence entries.
[2015-04-21T18:32Z] samblaster: Output 1 discordant read pairs to /dev/fd/62
[2015-04-21T18:32Z] samblaster: Output 2 split reads to /dev/fd/63
[2015-04-21T18:32Z] samblaster: Marked 108 of 9000 (1.20%) read ids as duplicates using 1388k memory in [main] Version: 0.7.12-r1039
[2015-04-21T18:32Z] 0.014S CPU seconds and [main] CMD:1S wall time.
[2015-04-21T18:32Z]  /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/bwa mem -M -t 1 -R @RG\tID:7\tPL:illumina\tPU:7_100326_FC6107FAAXX\tSM:Test1 -v 1 /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/genomes/hg19/bwa/hg19.fa /dev/fd/63 /dev/fd/62
[2015-04-21T18:32Z] [main] Real time: 0.711 sec; CPU: 0.669 sec
[2015-04-21T18:32Z] Index BAM file: 7_100326_FC6107FAAXX-sort-36001_72000-sr.bam
[2015-04-21T18:32Z] Index BAM file: 7_100326_FC6107FAAXX-sort-36001_72000-disc.bam
[2015-04-21T18:32Z] Aligning lane 7_100326_FC6107FAAXX with bwa aligner
[2015-04-21T18:32Z] bwa mem alignment from fastq: Test1
[2015-04-21T18:32Z] samblaster: Version 0.1.21
[2015-04-21T18:32Z] samblaster: Inputting from stdin
[2015-04-21T18:32Z] samblaster: Outputting to stdout
[2015-04-21T18:32Z] samblaster: Opening /dev/fd/62 for write.
[2015-04-21T18:32Z] samblaster: Opening /dev/fd/63 for write.
[2015-04-21T18:32Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2015-04-21T18:32Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-04-21T18:32Z] [M::mem_pestat] (25, 50, 75) percentile: (129, 149, 175)
[2015-04-21T18:32Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (37, 267)
[2015-04-21T18:32Z] [M::mem_pestat] mean and std.dev: (151.37, 30.95)
[2015-04-21T18:32Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 313)
[2015-04-21T18:32Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-04-21T18:32Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2015-04-21T18:32Z] samblaster: Loaded 2 header sequence entries.
[2015-04-21T18:32Z] samblaster: Output 1 discordant read pairs to /dev/fd/62
[2015-04-21T18:32Z] [main] Version: 0.7.12-r1039
[2015-04-21T18:32Z] [main] CMD:samblaster: Output 2 split reads to /dev/fd/63
[2015-04-21T18:32Z]  /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/bwa mem -M -t 1 -R @RG\tID:7\tPL:illumina\tPU:7_100326_FC6107FAAXX\tSM:Test1 -v 1 /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/genomes/hg19/bwa/hg19.fa /dev/fd/63 /dev/fd/62samblaster: Marked 108 of 9000 (1.20%) read ids as duplicates using 1384k memory in
[2015-04-21T18:32Z] [main] Real time: 0.723 sec; CPU: 0.685 sec
[2015-04-21T18:32Z] 0.014S CPU seconds and 1S wall time.
[2015-04-21T18:32Z] Index BAM file: 7_100326_FC6107FAAXX-sort-72001_108000-sr.bam
[2015-04-21T18:32Z] Index BAM file: 7_100326_FC6107FAAXX-sort-72001_108000-disc.bam
[2015-04-21T18:32Z] Aligning lane 7_100326_FC6107FAAXX with bwa aligner
[2015-04-21T18:32Z] bwa mem alignment from fastq: Test1
[2015-04-21T18:32Z] samblaster: Version 0.1.21
[2015-04-21T18:32Z] samblaster: Inputting from stdin
[2015-04-21T18:32Z] samblaster: Outputting to stdout
[2015-04-21T18:32Z] samblaster: Opening /dev/fd/62 for write.
[2015-04-21T18:32Z] samblaster: Opening /dev/fd/63 for write.
[2015-04-21T18:32Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2015-04-21T18:32Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-04-21T18:32Z] [M::mem_pestat] (25, 50, 75) percentile: (128, 150, 175)
[2015-04-21T18:32Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (34, 269)
[2015-04-21T18:32Z] [M::mem_pestat] mean and std.dev: (151.09, 31.43)
[2015-04-21T18:32Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 316)
[2015-04-21T18:32Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-04-21T18:32Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2015-04-21T18:32Z] samblaster: Loaded 2 header sequence entries.
[2015-04-21T18:32Z] [main] Version: 0.7.12-r1039
[2015-04-21T18:32Z] [main] CMD: /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/bwa mem -M -t 1 -R @RG\tID:7\tPL:illumina\tPU:7_100326_FC6107FAAXX\tSM:Test1 -v 1 /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/genomes/hg19/bwa/hg19.fa /dev/fd/63 /dev/fd/62
[2015-04-21T18:32Z] [main] Real time: 0.682 sec; CPU: 0.639 sec
[2015-04-21T18:32Z] samblaster: Output 0 discordant read pairs to /dev/fd/62
[2015-04-21T18:32Z] samblaster: Output 0 split reads to /dev/fd/63
[2015-04-21T18:32Z] samblaster: Marked 105 of 9000 (1.17%) read ids as duplicates using 1384k memory in 0.017S CPU seconds and 1S wall time.
[2015-04-21T18:32Z] Index BAM file: 7_100326_FC6107FAAXX-sort-108001_144000-sr.bam
[2015-04-21T18:32Z] Index BAM file: 7_100326_FC6107FAAXX-sort-108001_144000-disc.bam
[2015-04-21T18:32Z] Aligning lane 7_100326_FC6107FAAXX with bwa aligner
[2015-04-21T18:32Z] bwa mem alignment from fastq: Test1
[2015-04-21T18:32Z] samblaster: Version 0.1.21
[2015-04-21T18:32Z] samblaster: Inputting from stdin
[2015-04-21T18:32Z] samblaster: Outputting to stdout
[2015-04-21T18:32Z] samblaster: Opening /dev/fd/62 for write.
[2015-04-21T18:32Z] samblaster: Opening /dev/fd/63 for write.
[2015-04-21T18:32Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2015-04-21T18:32Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-04-21T18:32Z] [M::mem_pestat] (25, 50, 75) percentile: (129, 150, 175)
[2015-04-21T18:32Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (37, 267)
[2015-04-21T18:32Z] [M::mem_pestat] mean and std.dev: (151.76, 31.66)
[2015-04-21T18:32Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 313)
[2015-04-21T18:32Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-04-21T18:32Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2015-04-21T18:32Z] samblaster: Loaded 2 header sequence entries.
[2015-04-21T18:32Z] [main] Version: 0.7.12-r1039
[2015-04-21T18:32Z] [main] CMD: /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/bwa mem -M -t 1 -R @RG\tID:7\tPL:illumina\tPU:7_100326_FC6107FAAXX\tSM:Test1 -v 1 /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/genomes/hg19/bwa/hg19.fa /dev/fd/63 /dev/fd/62
[2015-04-21T18:32Z] [main] Real time: 0.357 sec; CPU: 0.342 sec
[2015-04-21T18:32Z] samblaster: Output 3 discordant read pairs to /dev/fd/62
[2015-04-21T18:32Z] samblaster: Output 0 split reads to /dev/fd/63
[2015-04-21T18:32Z] samblaster: Marked 31 of 4164 (0.74%) read ids as duplicates using 1340k memory in 0.005S CPU seconds and 0S wall time.
[2015-04-21T18:32Z] Index BAM file: 7_100326_FC6107FAAXX-sort-144001_160656-sr.bam
[2015-04-21T18:32Z] Index BAM file: 7_100326_FC6107FAAXX-sort-144001_160656-disc.bam
[2015-04-21T18:32Z] multiprocessing: delayed_bam_merge
[2015-04-21T18:32Z] Merge bam files to 7_100326_FC6107FAAXX-sort-sr.bam
[2015-04-21T18:32Z] Merge bam files to 7_100326_FC6107FAAXX-sort-disc.bam
[2015-04-21T18:32Z] Merge bam files to 7_100326_FC6107FAAXX-sort.bam
[2015-04-21T18:32Z] Timing: callable regions
[2015-04-21T18:32Z] multiprocessing: prep_samples
[2015-04-21T18:32Z] Prepare cleaned BED file : Test1
[2015-04-21T18:32Z] bgzip variant_regions-variantcall.bed
[2015-04-21T18:32Z] tabix index variant_regions-variantcall.bed.gz
[2015-04-21T18:32Z] Prepare merged BED file : Test1
[2015-04-21T18:32Z] bgzip variant_regions-variantcall-merged.bed
[2015-04-21T18:32Z] tabix index variant_regions-variantcall-merged.bed.gz
[2015-04-21T18:32Z] multiprocessing: postprocess_alignment
[2015-04-21T18:32Z] Resource requests: ; memory: 1.00; cores: 1
[2015-04-21T18:32Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-04-21T18:32Z] multiprocessing: calc_callable_loci
[2015-04-21T18:32Z] bedtools genomecov: chrM : 7_100326_FC6107FAAXX-sort.bam
[2015-04-21T18:32Z] bedtools genomecov: chr22 : 7_100326_FC6107FAAXX-sort.bam
[2015-04-21T18:32Z] multiprocessing: combine_bed
Processing reference #1 (chrM)
Processing reference #2 (chr22)
[2015-04-21T18:32Z] Identify high coverage regions
[2015-04-21T18:32Z] Processing reference #1 (chrM)
[2015-04-21T18:32Z] Processing reference #2 (chr22)
[2015-04-21T18:32Z] multiprocessing: combine_sample_regions
[2015-04-21T18:32Z] Identified 2 parallel analysis blocks
Block sizes:
  min: 5000
  5%: 5479.75
  25%: 7398.75
  median: 9797.5
  75%: 12196.25
  95%: 14115.25
  99%: 14499.05
  max: 14595
Between block sizes:
[]

[2015-04-21T18:32Z] Timing: coverage
[2015-04-21T18:32Z] Resource requests: freebayes, gatk, gatk-haplotype, picard, samtools; memory: 3.50, 3.50, 3.50, 2.00; cores: 1, 1, 1, 1, 16
[2015-04-21T18:32Z] Configuring 1 jobs to run, using 1 cores each with 3.50g of memory reserved for each job
[2015-04-21T18:32Z] Timing: alignment post-processing
[2015-04-21T18:32Z] multiprocessing: piped_bamprep
[2015-04-21T18:32Z] Timing: variant calling
[2015-04-21T18:32Z] multiprocessing: variantcall_sample
[2015-04-21T18:32Z] Genotyping with samtools: ('chrM', 0, 5000) 7_100326_FC6107FAAXX-sort.bam
[2015-04-21T18:32Z] Variant calling with samtools : Test1
[2015-04-21T18:32Z] [mpileup] 1 samples in 1 input files
[2015-04-21T18:32Z] <mpileup> Set max per-file depth to 8000
[2015-04-21T18:32Z] tabix index TestBatch1-chrM_0_5000-raw.vcf.gz
[2015-04-21T18:32Z] Genotyping with samtools: ('chr22', 0, 14595) 7_100326_FC6107FAAXX-sort.bam
[2015-04-21T18:32Z] Variant calling with samtools : Test1
[2015-04-21T18:32Z] [mpileup] 1 samples in 1 input files
[2015-04-21T18:32Z] <mpileup> Set max per-file depth to 8000
[2015-04-21T18:32Z] tabix index TestBatch1-chr22_0_14595-raw.vcf.gz
Traceback (most recent call last):
  File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/bcbio_nextgen.py", line 216, in <module>
    main(**kwargs)
  File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/bcbio_nextgen.py", line 42, in main
    run_main(**kwargs)
  File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 37, in run_main
    fc_dir, run_info_yaml)
  File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 81, in _run_toplevel
    for xs in pipeline.run(config, run_info_yaml, parallel, dirs, samples):
  File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 166, in run
    samples = genotype.parallel_variantcall_region(samples, run_parallel)
  File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/variation/genotype.py", line 165, in parallel_variantcall_region
    "vrn_file", ["region", "sam_ref", "config"]))
  File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/split.py", line 32, in grouped_parallel_split_combine
    final_output = parallel_fn(parallel_name, split_args)
  File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 28, in run_parallel
    return run_multicore(fn, items, config, parallel=parallel)
  File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 84, in run_multicore
    for data in joblib.Parallel(parallel["num_jobs"])(joblib.delayed(fn)(x) for x in items):
  File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 653, in __call__
    self.dispatch(function, args, kwargs)
  File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 400, in dispatch
    job = ImmediateApply(func, args, kwargs)
  File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 138, in __init__
    self.results = func(*args, **kwargs)
  File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/utils.py", line 149, in wrapper
    return apply(f, *args, **kwargs)
  File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multitasks.py", line 103, in variantcall_sample
    return genotype.variantcall_sample(*args)
  File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/variation/genotype.py", line 246, in variantcall_sample
    call_file = caller_fn(align_bams, items, sam_ref, assoc_files, region, call_file)
  File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/variation/gatk.py", line 87, in haplotype_caller
    region, out_file)
  File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/variation/gatk.py", line 35, in _shared_gatk_call_prep
    for a in annotation.get_gatk_annotations(config):
  File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/variation/annotation.py", line 25, in get_gatk_annotations
    if broad_runner.gatk_type() == "restricted":
  File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/broad/__init__.py", line 315, in gatk_type
    if LooseVersion(self.gatk_major_version()) > LooseVersion("2.3"):
  File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/broad/__init__.py", line 326, in gatk_major_version
    full_version = self.get_gatk_version()
  File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/broad/__init__.py", line 298, in get_gatk_version
    gatk_jar = self._get_jar("GenomeAnalysisTK", ["GenomeAnalysisTKLite"])
  File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/broad/__init__.py", line 377, in _get_jar
    raise ValueError("Could not find jar %s in %s:%s" % (command, self._picard_ref, self._gatk_dir))
ValueError: Could not find jar GenomeAnalysisTK in /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/share/java/picard:/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/share/java/gatk
ERROR
Allow BAM files as input to pipeline. ... [2015-04-21T18:32Z] Resource requests: bwa, sambamba, samtools; memory: 2.00; cores: 16, 1, 16
[2015-04-21T18:32Z] Configuring 1 jobs to run, using 1 cores each with 2.00g of memory reserved for each job
[2015-04-21T18:32Z] Timing: organize samples
[2015-04-21T18:32Z] multiprocessing: organize_samples
[2015-04-21T18:32Z] Using input YAML configuration: /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/automated/run_info-bam.yaml
[2015-04-21T18:32Z] Checking sample YAML configuration: /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/automated/run_info-bam.yaml
[2015-04-21T18:32Z] Testing minimum versions of installed programs
[2015-04-21T18:32Z] Timing: alignment preparation
[2015-04-21T18:32Z] multiprocessing: prep_align_inputs
[2015-04-21T18:32Z] BAM to bgzipped fastq
[2015-04-21T18:32Z] [V] 80349
[2015-04-21T18:32Z] [V] MemUsage(size=44.5039,rss=4.53125,peak=1169.03) wall clock time 64045700
[2015-04-21T18:32Z] Resource requests: ; memory: 1.00; cores: 1
[2015-04-21T18:32Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-04-21T18:32Z] Index input with grabix: 7_100326_FC6107FAAXX-1.fq.gz
[2015-04-21T18:32Z] Index input with grabix: 7_100326_FC6107FAAXX-2.fq.gz
[2015-04-21T18:32Z] multiprocessing: disambiguate_split
[2015-04-21T18:32Z] Timing: alignment
[2015-04-21T18:32Z] multiprocessing: process_alignment
[2015-04-21T18:32Z] Aligning lane Test1 with bwa aligner
[2015-04-21T18:32Z] bwa mem alignment from fastq: Test1
[2015-04-21T18:32Z] samblaster: Version 0.1.21
[2015-04-21T18:32Z] samblaster: Inputting from stdin
[2015-04-21T18:32Z] samblaster: Outputting to stdout
[2015-04-21T18:32Z] samblaster: Opening /dev/fd/62 for write.
[2015-04-21T18:32Z] samblaster: Opening /dev/fd/63 for write.
[2015-04-21T18:32Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2015-04-21T18:32Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-04-21T18:32Z] [M::mem_pestat] (25, 50, 75) percentile: (128, 148, 174)
[2015-04-21T18:32Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (36, 266)
[2015-04-21T18:32Z] [M::mem_pestat] mean and std.dev: (150.33, 30.95)
[2015-04-21T18:32Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 312)
[2015-04-21T18:32Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-04-21T18:32Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2015-04-21T18:32Z] samblaster: Loaded 2 header sequence entries.
[2015-04-21T18:32Z] [main] Version: 0.7.12-r1039
[2015-04-21T18:32Z] [main] CMD: /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/bwa mem -M -t 1 -R @RG\tID:7\tPL:illumina\tPU:Test1\tSM:Test1 -v 1 /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/genomes/hg19/bwa/hg19.fa /dev/fd/63 /dev/fd/62
[2015-04-21T18:32Z] [main] Real time: 1.083 sec; CPU: 1.016 sec
[2015-04-21T18:32Z] samblaster: Output 0 discordant read pairs to /dev/fd/62
[2015-04-21T18:32Z] samblaster: Output 2 split reads to /dev/fd/63
[2015-04-21T18:32Z] samblaster: Marked 803 of 15000 (5.35%) read ids as duplicates using 1492k memory in 0.023S CPU seconds and 1S wall time.
[2015-04-21T18:32Z] Index BAM file: Test1-sort-1_60000-sr.bam
[2015-04-21T18:32Z] Index BAM file: Test1-sort-1_60000-disc.bam
[2015-04-21T18:32Z] Aligning lane Test1 with bwa aligner
[2015-04-21T18:32Z] bwa mem alignment from fastq: Test1
[2015-04-21T18:32Z] samblaster: Version 0.1.21
[2015-04-21T18:32Z] samblaster: Inputting from stdin
[2015-04-21T18:32Z] samblaster: Outputting to stdout
[2015-04-21T18:32Z] samblaster: Opening /dev/fd/62 for write.
[2015-04-21T18:32Z] samblaster: Opening /dev/fd/63 for write.
[2015-04-21T18:32Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2015-04-21T18:32Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-04-21T18:32Z] [M::mem_pestat] (25, 50, 75) percentile: (129, 150, 175)
[2015-04-21T18:32Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (37, 267)
[2015-04-21T18:32Z] [M::mem_pestat] mean and std.dev: (151.92, 31.15)
[2015-04-21T18:32Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 313)
[2015-04-21T18:32Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-04-21T18:32Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2015-04-21T18:32Z] samblaster: Loaded 2 header sequence entries.
[2015-04-21T18:32Z] [main] Version: 0.7.12-r1039
[2015-04-21T18:32Z] [main] CMD: /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/bwa mem -M -t 1 -R @RG\tID:7\tPL:illumina\tPU:Test1\tSM:Test1 -vsamblaster: Output 2 discordant read pairs to /dev/fd/62
[2015-04-21T18:32Z]  1 /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/genomes/hg19/bwa/hg19.fasamblaster: Output 2 split reads to /dev/fd/63
[2015-04-21T18:32Z]  /dev/fd/63 /dev/fd/62
[2015-04-21T18:32Z] [main] Real time: 1.076 sec; CPU: 1.013 sec
[2015-04-21T18:32Z] samblaster: Marked 735 of 15000 (4.90%) read ids as duplicates using 1496k memory in 0.021S CPU seconds and 1S wall time.
[2015-04-21T18:32Z] Index BAM file: Test1-sort-60001_120000-sr.bam
[2015-04-21T18:32Z] Index BAM file: Test1-sort-60001_120000-disc.bam
[2015-04-21T18:32Z] Aligning lane Test1 with bwa aligner
[2015-04-21T18:32Z] bwa mem alignment from fastq: Test1
[2015-04-21T18:32Z] samblaster: Version 0.1.21
[2015-04-21T18:32Z] samblaster: Inputting from stdin
[2015-04-21T18:32Z] samblaster: Outputting to stdout
[2015-04-21T18:32Z] samblaster: Opening /dev/fd/62 for write.
[2015-04-21T18:32Z] samblaster: Opening /dev/fd/63 for write.
[2015-04-21T18:32Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2015-04-21T18:32Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-04-21T18:32Z] [M::mem_pestat] (25, 50, 75) percentile: (130, 151, 176)
[2015-04-21T18:32Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (38, 268)
[2015-04-21T18:32Z] [M::mem_pestat] mean and std.dev: (152.52, 31.30)
[2015-04-21T18:32Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 314)
[2015-04-21T18:32Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-04-21T18:32Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2015-04-21T18:32Z] samblaster: Loaded 2 header sequence entries.
[2015-04-21T18:32Z] [main] Version: 0.7.12-r1039
[2015-04-21T18:32Z] [main] CMD: /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/bwa mem -M -t 1 -Rsamblaster: Output 3 discordant read pairs to /dev/fd/62
[2015-04-21T18:32Z]  @RG\tID:7\tPL:illumina\tPU:Test1\tSM:Test1 -vsamblaster: Output 0 split reads to /dev/fd/63
[2015-04-21T18:32Z]  1 /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/genomes/hg19/bwa/hg19.fa /dev/fd/63 /dev/fd/62
[2015-04-21T18:32Z] [main] Real time: 0.743 sec; CPU: 0.701 sec
[2015-04-21T18:32Z] samblaster: Marked 517 of 10164 (5.09%) read ids as duplicates using 1376k memory in 0.013S CPU seconds and 1S wall time.
[2015-04-21T18:32Z] Index BAM file: Test1-sort-120001_160656-sr.bam
[2015-04-21T18:32Z] Index BAM file: Test1-sort-120001_160656-disc.bam
[2015-04-21T18:32Z] multiprocessing: delayed_bam_merge
[2015-04-21T18:32Z] Merge bam files to Test1-sort-sr.bam
[2015-04-21T18:32Z] Merge bam files to Test1-sort-disc.bam
[2015-04-21T18:32Z] Merge bam files to Test1-sort.bam
[2015-04-21T18:32Z] Timing: callable regions
[2015-04-21T18:32Z] multiprocessing: prep_samples
[2015-04-21T18:32Z] Prepare cleaned BED file : Test1
[2015-04-21T18:32Z] bgzip variant_regions-bam.bed
[2015-04-21T18:32Z] tabix index variant_regions-bam.bed.gz
[2015-04-21T18:32Z] Prepare merged BED file : Test1
[2015-04-21T18:32Z] bgzip variant_regions-bam-merged.bed
[2015-04-21T18:32Z] tabix index variant_regions-bam-merged.bed.gz
[2015-04-21T18:32Z] multiprocessing: postprocess_alignment
[2015-04-21T18:32Z] Resource requests: ; memory: 1.00; cores: 1
[2015-04-21T18:32Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-04-21T18:32Z] multiprocessing: calc_callable_loci
[2015-04-21T18:32Z] bedtools genomecov: chrM : Test1-sort.bam
[2015-04-21T18:32Z] bedtools genomecov: chr22 : Test1-sort.bam
[2015-04-21T18:32Z] multiprocessing: combine_bed
Processing reference #1 (chrM)
Processing reference #2 (chr22)
[2015-04-21T18:32Z] Identify high coverage regions
[2015-04-21T18:32Z] Processing reference #1 (chrM)
[2015-04-21T18:32Z] Processing reference #2 (chr22)
[2015-04-21T18:32Z] multiprocessing: combine_sample_regions
[2015-04-21T18:32Z] Identified 4 parallel analysis blocks
Block sizes:
  min: 372
  5%: 466.2
  25%: 843.0
  median: 2000.0
  75%: 5874.0
  95%: 12771.6
  99%: 14151.12
  max: 14496
Between block sizes:
  min: 632
  5%: 650.4
  25%: 724.0
  median: 816.0
  75%: 908.0
  95%: 981.6
  99%: 996.32
  max: 1000

[2015-04-21T18:32Z] Timing: coverage
[2015-04-21T18:32Z] multiprocessing: coverage_summary
[2015-04-21T18:32Z] Prepare cleaned BED file : Test1
[2015-04-21T18:32Z] bgzip coverage_transcripts-bam.bed
[2015-04-21T18:32Z] tabix index coverage_transcripts-bam.bed.gz
[2015-04-21T18:32Z] Prep chanjo database
[2015-04-21T18:32Z] Chanjo coverage : Test1
[2015-04-21T18:32Z] Resource requests: freebayes, gatk, picard; memory: 3.50, 3.50; cores: 1, 1, 1
[2015-04-21T18:32Z] Configuring 1 jobs to run, using 1 cores each with 3.50g of memory reserved for each job
[2015-04-21T18:32Z] Timing: alignment post-processing
[2015-04-21T18:32Z] multiprocessing: piped_bamprep
[2015-04-21T18:32Z] Timing: variant calling
[2015-04-21T18:32Z] multiprocessing: variantcall_sample
[2015-04-21T18:32Z] Genotyping with FreeBayes
[2015-04-21T18:32Z] /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/freebayes: unrecognized option '--experimental-gls'
[2015-04-21T18:32Z] did you mean --use-best-n-alleles ?
[2015-04-21T18:32Z] terminate called after throwing an instance of 'std::out_of_range'
[2015-04-21T18:32Z]   what():  basic_string::substr
[2015-04-21T18:32Z] terminate called after throwing an instance of 'std::out_of_range'
[2015-04-21T18:32Z]   what():  basic_string::substr
[2015-04-21T18:32Z] terminate called after throwing an instance of 'std::out_of_range'
[2015-04-21T18:32Z]   what():  basic_string::substr
[2015-04-21T18:32Z] terminate called after throwing an instance of 'std::out_of_range'
[2015-04-21T18:32Z]   what():  basic_string::substr
[2015-04-21T18:32Z] terminate called after throwing an instance of 'std::out_of_range'
[2015-04-21T18:32Z]   what():  basic_string::substr
[2015-04-21T18:32Z] /bin/bash: line 1: 28283 Exit 1                  /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/freebayes -f /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -b /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort.bam --ploidy 1 --targets /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/test_automated_output/freebayes/chrM/TestBatch1-chrM_0_1000-raw-regions.bed --min-repeat-entropy 1 --experimental-gls
[2015-04-21T18:32Z] Uncaught exception occurred
Traceback (most recent call last):
  File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run
    _do_run(cmd, checks, log_stdout)
  File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/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; /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/freebayes -f /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -b /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort.bam --ploidy 1 --targets /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/test_automated_output/freebayes/chrM/TestBatch1-chrM_0_1000-raw-regions.bed --min-repeat-entropy 1 --experimental-gls | /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/vcffilter -f 'QUAL > 5' -s | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDX]/, "N", $4) } {print}' | vcfallelicprimitives --keep-geno | vcffixup - | vcfstreamsort | vt normalize -r /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -q - 2> /dev/null | vcfuniqalleles | bgzip -c > /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/test_automated_output/tmptest/bcbiotx/49b5f73b-8550-435c-ba57-9119af47268b/tmp70DH2m/TestBatch1-chrM_0_1000-raw.vcf.gz
/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/freebayes: unrecognized option '--experimental-gls'
did you mean --use-best-n-alleles ?
terminate called after throwing an instance of 'std::out_of_range'
  what():  basic_string::substr
terminate called after throwing an instance of 'std::out_of_range'
  what():  basic_string::substr
terminate called after throwing an instance of 'std::out_of_range'
  what():  basic_string::substr
terminate called after throwing an instance of 'std::out_of_range'
  what():  basic_string::substr
terminate called after throwing an instance of 'std::out_of_range'
  what():  basic_string::substr
/bin/bash: line 1: 28283 Exit 1                  /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/freebayes -f /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -b /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort.bam --ploidy 1 --targets /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/test_automated_output/freebayes/chrM/TestBatch1-chrM_0_1000-raw-regions.bed --min-repeat-entropy 1 --experimental-gls
     28284 Aborted                 (core dumped) | /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/vcffilter -f 'QUAL > 5' -s
     28285 Done                    | awk -F'	' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDX]/, "N", $4) } {print}'
     28286 Aborted                 (core dumped) | vcfallelicprimitives --keep-geno
     28287 Aborted                 (core dumped) | vcffixup -
     28288 Aborted                 (core dumped) | vcfstreamsort
     28289                       | vt normalize -r /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -q - 2> /dev/null
     28290 Aborted                 (core dumped) | vcfuniqalleles
     28291 Done                    | bgzip -c > /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/test_automated_output/tmptest/bcbiotx/49b5f73b-8550-435c-ba57-9119af47268b/tmp70DH2m/TestBatch1-chrM_0_1000-raw.vcf.gz
' returned non-zero exit status 134
Traceback (most recent call last):
  File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/bcbio_nextgen.py", line 216, in <module>
    main(**kwargs)
  File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/bcbio_nextgen.py", line 42, in main
    run_main(**kwargs)
  File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 37, in run_main
    fc_dir, run_info_yaml)
  File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 81, in _run_toplevel
    for xs in pipeline.run(config, run_info_yaml, parallel, dirs, samples):
  File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 166, in run
    samples = genotype.parallel_variantcall_region(samples, run_parallel)
  File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/variation/genotype.py", line 165, in parallel_variantcall_region
    "vrn_file", ["region", "sam_ref", "config"]))
  File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/split.py", line 32, in grouped_parallel_split_combine
    final_output = parallel_fn(parallel_name, split_args)
  File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 28, in run_parallel
    return run_multicore(fn, items, config, parallel=parallel)
  File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 84, in run_multicore
    for data in joblib.Parallel(parallel["num_jobs"])(joblib.delayed(fn)(x) for x in items):
  File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 653, in __call__
    self.dispatch(function, args, kwargs)
  File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 400, in dispatch
    job = ImmediateApply(func, args, kwargs)
  File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 138, in __init__
    self.results = func(*args, **kwargs)
  File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/utils.py", line 149, in wrapper
    return apply(f, *args, **kwargs)
  File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multitasks.py", line 103, in variantcall_sample
    return genotype.variantcall_sample(*args)
  File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/variation/genotype.py", line 246, in variantcall_sample
    call_file = caller_fn(align_bams, items, sam_ref, assoc_files, region, call_file)
  File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/variation/freebayes.py", line 77, in run_freebayes
    assoc_files, region, out_file)
  File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/variation/freebayes.py", line 112, in _run_freebayes_caller
    do.run(cmd.format(**locals()), "Genotyping with FreeBayes", {})
  File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run
    _do_run(cmd, checks, log_stdout)
  File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run
    raise subprocess.CalledProcessError(exitcode, error_msg)
subprocess.CalledProcessError: Command 'set -o pipefail; /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/freebayes -f /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -b /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort.bam --ploidy 1 --targets /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/test_automated_output/freebayes/chrM/TestBatch1-chrM_0_1000-raw-regions.bed --min-repeat-entropy 1 --experimental-gls | /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/vcffilter -f 'QUAL > 5' -s | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDX]/, "N", $4) } {print}' | vcfallelicprimitives --keep-geno | vcffixup - | vcfstreamsort | vt normalize -r /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -q - 2> /dev/null | vcfuniqalleles | bgzip -c > /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/test_automated_output/tmptest/bcbiotx/49b5f73b-8550-435c-ba57-9119af47268b/tmp70DH2m/TestBatch1-chrM_0_1000-raw.vcf.gz
/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/freebayes: unrecognized option '--experimental-gls'
did you mean --use-best-n-alleles ?
terminate called after throwing an instance of 'std::out_of_range'
  what():  basic_string::substr
terminate called after throwing an instance of 'std::out_of_range'
  what():  basic_string::substr
terminate called after throwing an instance of 'std::out_of_range'
  what():  basic_string::substr
terminate called after throwing an instance of 'std::out_of_range'
  what():  basic_string::substr
terminate called after throwing an instance of 'std::out_of_range'
  what():  basic_string::substr
/bin/bash: line 1: 28283 Exit 1                  /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/freebayes -f /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -b /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort.bam --ploidy 1 --targets /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/test_automated_output/freebayes/chrM/TestBatch1-chrM_0_1000-raw-regions.bed --min-repeat-entropy 1 --experimental-gls
     28284 Aborted                 (core dumped) | /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/vcffilter -f 'QUAL > 5' -s
     28285 Done                    | awk -F'	' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDX]/, "N", $4) } {print}'
     28286 Aborted                 (core dumped) | vcfallelicprimitives --keep-geno
     28287 Aborted                 (core dumped) | vcffixup -
     28288 Aborted                 (core dumped) | vcfstreamsort
     28289                       | vt normalize -r /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -q - 2> /dev/null
     28290 Aborted                 (core dumped) | vcfuniqalleles
     28291 Done                    | bgzip -c > /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/test_automated_output/tmptest/bcbiotx/49b5f73b-8550-435c-ba57-9119af47268b/tmp70DH2m/TestBatch1-chrM_0_1000-raw.vcf.gz
' returned non-zero exit status 134
ERROR
Create a project template from input files and metadata configuration. ... variant_regions ../data/100326_FC6107FAAXX/test.bed
sex female
description 7_1
batch 1a
variant_regions ../data/100326_FC6107FAAXX/test.bed
sex
description 8_1
batch 1a
Configuration file created at: /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/test_automated_output/100326/config/100326.yaml
Edit to finalize and run with:
  cd /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/test_automated_output/100326/work
  bcbio_nextgen.py ../config/100326.yaml
ok
Identify programs and versions used in analysis. ... [{'program': 'bcbio-nextgen', 'version': '0.8.7'}, {'program': 'alientrimmer', 'version': '0.3.2'}, {'program': 'bamtools', 'version': '2.3.0'}, {'program': 'bcbio_variation', 'version': '0.2.4'}, {'program': 'bcftools', 'version': '1.2'}, {'program': 'bedtools', 'version': '2.23.0'}, {'program': 'biobambam', 'version': '0.0.182'}, {'program': 'bowtie2', 'version': '2.2.5'}, {'program': 'bwa', 'version': '0.7.12'}, {'program': 'chanjo', 'version': '2.3.2'}, {'program': 'cutadapt', 'version': '1.4.2'}, {'program': 'fastqc', 'version': '0.11.3'}, {'program': 'featurecounts', 'version': '1.4.4'}, {'program': 'freebayes', 'version': '0.9.21-7'}, {'program': 'gatk-framework', 'version': '3.2-4'}, {'program': 'gemini', 'version': '0.7.0'}, {'program': 'htseq', 'version': '0.6.1'}, {'program': 'mutect', 'version': '1.1.5'}, {'program': 'novoalign', 'version': '3.02.10'}, {'program': 'novosort', 'version': 'V3.00.02'}, {'program': 'oncofuse', 'version': '1.0.9'}, {'program': 'picard', 'version': '1.96'}, {'program': 'platypus-variant', 'version': '<IP_ADDRESS>'}, {'program': 'qualimap', 'version': '30-03-15'}, {'program': 'rnaseqc', 'version': '1.1.7'}, {'program': 'samtools', 'version': '1.2'}, {'program': 'snpeff', 'version': '4.1c'}, {'program': 'tophat', 'version': '2.0.9'}, {'program': 'varscan', 'version': '2.3.7'}, {'program': 'vcflib', 'version': '2015-03-13'}, {'program': 'vt', 'version': '2015-03-26'}, {'program': 'cn.mops', 'version': ''}, {'program': 'cufflinks', 'version': ''}, {'program': 'sambamba', 'version': ''}, {'program': 'gatk', 'version': ''}]
ok
Parallel combination of VCF files, split by chromosome. ... [2015-04-21 18:32:56.193702] DEBUG: bcbio-nextgen: Resource requests: ; memory: 1.00; cores: 1
[2015-04-21 18:32:56.193936] DEBUG: bcbio-nextgen: Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-04-21 18:32:56.195213] DEBUG: bcbio-nextgen: Resource requests: ; memory: 1.00; cores: 1
[2015-04-21 18:32:56.195378] DEBUG: bcbio-nextgen: Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-04-21 18:32:56.203212] DEBUG: bcbio-nextgen: bgzip S1-variants.vcf
[2015-04-21 18:32:56.203423] DEBUG: bcbio-nextgen-commands: /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/bgzip -c /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/S1-variants.vcf > /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/tx/tmp3y5lRr/S1-variants.vcf.gz
[2015-04-21 18:32:56.262698] DEBUG: bcbio-nextgen: tabix index S1-variants.vcf.gz
[2015-04-21 18:32:56.263109] DEBUG: bcbio-nextgen-commands: /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/tabix -f -p vcf /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/tx/tmpkPEylO/S1-variants.vcf.gz
[2015-04-21 18:32:56.306572] DEBUG: bcbio-nextgen: bgzip S2-variants.vcf
[2015-04-21 18:32:56.306956] DEBUG: bcbio-nextgen-commands: /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/bgzip -c /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/S2-variants.vcf > /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/tx/tmpRHr718/S2-variants.vcf.gz
[2015-04-21 18:32:56.379842] DEBUG: bcbio-nextgen: tabix index S2-variants.vcf.gz
[2015-04-21 18:32:56.380255] DEBUG: bcbio-nextgen-commands: /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/tabix -f -p vcf /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/tx/tmpYi2uWL/S2-variants.vcf.gz
[2015-04-21 18:32:56.419102] INFO: bcbio-nextgen: multiprocessing: merge_variant_files
[2015-04-21 18:32:59.469904] DEBUG: bcbio-nextgen: Resource requests: ; memory: 1.00; cores: 1
[2015-04-21 18:32:59.470254] DEBUG: bcbio-nextgen: Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-04-21 18:32:59.477983] DEBUG: bcbio-nextgen: Merge variants
[2015-04-21 18:32:59.478220] DEBUG: bcbio-nextgen-commands: /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/bcftools merge -O z -r chrM `cat /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/S1_S2-combined-regions/S1_S2-combined-chrM-files.txt` > /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/S1_S2-combined-regions/tx/tmp9HUWQr/S1_S2-combined-chrM.vcf.gz
[2015-04-21 18:32:59.550320] DEBUG: bcbio-nextgen: tabix index S1_S2-combined-chrM.vcf.gz
[2015-04-21 18:32:59.550760] DEBUG: bcbio-nextgen-commands: /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/tabix -f -p vcf /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/S1_S2-combined-regions/tx/tmpz55Tlk/S1_S2-combined-chrM.vcf.gz
[2015-04-21 18:32:59.591847] DEBUG: bcbio-nextgen: Resource requests: ; memory: 1.00; cores: 1
[2015-04-21 18:32:59.592227] DEBUG: bcbio-nextgen: Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-04-21 18:32:59.600571] DEBUG: bcbio-nextgen: Merge variants
[2015-04-21 18:32:59.600825] DEBUG: bcbio-nextgen-commands: /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/bcftools merge -O z -r chr22 `cat /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/S1_S2-combined-regions/S1_S2-combined-chr22-files.txt` > /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/S1_S2-combined-regions/tx/tmp4IVTnm/S1_S2-combined-chr22.vcf.gz
[2015-04-21 18:32:59.666032] DEBUG: bcbio-nextgen: tabix index S1_S2-combined-chr22.vcf.gz
[2015-04-21 18:32:59.666444] DEBUG: bcbio-nextgen-commands: /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/tabix -f -p vcf /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/S1_S2-combined-regions/tx/tmppAHUGK/S1_S2-combined-chr22.vcf.gz
[2015-04-21 18:32:59.705793] INFO: bcbio-nextgen: multiprocessing: concat_variant_files
[2015-04-21 18:32:59.710353] DEBUG: bcbio-nextgen: Resource requests: ; memory: 1.00; cores: 1
[2015-04-21 18:32:59.710655] DEBUG: bcbio-nextgen: Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-04-21 18:32:59.721204] DEBUG: bcbio-nextgen: Concat variant files
[2015-04-21 18:32:59.721464] DEBUG: bcbio-nextgen-commands: /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/gatk-framework org.broadinstitute.gatk.tools.CatVariants -R /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -V /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/S1_S2-combined-files.list -out /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/tx/tmpmKs_VR/S1_S2-combined.vcf.gz -assumeSorted -Xms500m -Xmx3500m -XX:+UseSerialGC
[2015-04-21 18:33:01.238067] DEBUG: bcbio-nextgen: INFO  14:33:01,235 HelpFormatter - -------------------------------------------------------
[2015-04-21 18:33:01.238365] DEBUG: bcbio-nextgen: INFO  14:33:01,237 HelpFormatter - Program Name: org.broadinstitute.gatk.tools.CatVariants
[2015-04-21 18:33:01.242439] DEBUG: bcbio-nextgen: INFO  14:33:01,241 HelpFormatter - Program Args: -R /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -V /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/S1_S2-combined-files.list -out /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/tx/tmpmKs_VR/S1_S2-combined.vcf.gz -assumeSorted
[2015-04-21 18:33:01.248780] DEBUG: bcbio-nextgen: INFO  14:33:01,247 HelpFormatter - Executing as<EMAIL_ADDRESS>on Linux 2.6.32-431.17.1.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_25-b15.
[2015-04-21 18:33:01.249255] DEBUG: bcbio-nextgen: INFO  14:33:01,248 HelpFormatter - Date/Time: 2015/04/21 14:33:01
[2015-04-21 18:33:01.249853] DEBUG: bcbio-nextgen: INFO  14:33:01,249 HelpFormatter - -------------------------------------------------------
[2015-04-21 18:33:01.250287] DEBUG: bcbio-nextgen: INFO  14:33:01,249 HelpFormatter - -------------------------------------------------------
[2015-04-21 18:33:01.374665] DEBUG: bcbio-nextgen: ..
ok
Exclude samples from VCF files. ... [2015-04-21 18:33:01.571781] DEBUG: bcbio-nextgen: Exclude samples: ['S1']
[2015-04-21 18:33:01.571932] DEBUG: bcbio-nextgen-commands: /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/bcftools view -O z -s S2  /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/S1_S2-combined.vcf.gz > /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/tx/tmpHZezPx/S1_S2-combined-exclude.vcf.gz
ok
Split a VCF file into SNPs and indels, then combine back together. ... [2015-04-21 18:33:01.734482] DEBUG: bcbio-nextgen: Subset to SNPs and indels
[2015-04-21 18:33:01.734639] DEBUG: bcbio-nextgen-commands: /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/bcftools view -O v /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/S1-variants.vcf --types snps > /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/tx/tmpKL8NuT/S1-variants-snp.vcf
[2015-04-21 18:33:01.779786] DEBUG: bcbio-nextgen: Subset to SNPs and indels
[2015-04-21 18:33:01.780166] DEBUG: bcbio-nextgen-commands: /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/bcftools view -O v /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/S1-variants.vcf --exclude-types snps > /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/tx/tmpQvfuhy/S1-variants-indel.vcf
[2015-04-21 18:33:01.820177] DEBUG: bcbio-nextgen: Resource requests: ; memory: 1.00; cores: 1
[2015-04-21 18:33:01.820576] DEBUG: bcbio-nextgen: Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-04-21 18:33:01.826282] DEBUG: bcbio-nextgen: bgzip S1-variants-snp.vcf
[2015-04-21 18:33:01.826525] DEBUG: bcbio-nextgen-commands: /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/bgzip -c /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/S1-variants-snp.vcf > /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/tx/tmpo7ZdLe/S1-variants-snp.vcf.gz
[2015-04-21 18:33:01.882115] DEBUG: bcbio-nextgen: tabix index S1-variants-snp.vcf.gz
[2015-04-21 18:33:01.882536] DEBUG: bcbio-nextgen-commands: /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/tabix -f -p vcf /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/tx/tmpl6LQD2/S1-variants-snp.vcf.gz
[2015-04-21 18:33:01.921801] DEBUG: bcbio-nextgen: bgzip S1-variants-indel.vcf
[2015-04-21 18:33:01.922174] DEBUG: bcbio-nextgen-commands: /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/bgzip -c /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/S1-variants-indel.vcf > /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/tx/tmpB1oyij/S1-variants-indel.vcf.gz
[2015-04-21 18:33:01.983260] DEBUG: bcbio-nextgen: tabix index S1-variants-indel.vcf.gz
[2015-04-21 18:33:01.983702] DEBUG: bcbio-nextgen-commands: /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/tabix -f -p vcf /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/tx/tmpdFiUo6/S1-variants-indel.vcf.gz
[2015-04-21 18:33:02.019826] DEBUG: bcbio-nextgen: Combine variant files
[2015-04-21 18:33:02.020242] DEBUG: bcbio-nextgen-commands: /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/gatk-framework -Xms500m -Xmx3500m -XX:+UseSerialGC -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --out /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/tx/tmpvxzezw/S1-variants-merge.vcf.gz --variant:v0 /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/S1-variants-snp.vcf.gz --variant:v1 /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/S1-variants-indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null
[2015-04-21 18:33:03.742108] DEBUG: bcbio-nextgen: INFO  14:33:03,739 HelpFormatter - ---------------------------------------------------------------------------------
[2015-04-21 18:33:03.742417] DEBUG: bcbio-nextgen: INFO  14:33:03,741 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-04-21 18:33:03.742523] DEBUG: bcbio-nextgen: INFO  14:33:03,742 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-04-21 18:33:03.742675] DEBUG: bcbio-nextgen: INFO  14:33:03,742 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-04-21 18:33:03.746487] DEBUG: bcbio-nextgen: INFO  14:33:03,746 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --out /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/tx/tmpvxzezw/S1-variants-merge.vcf.gz --variant:v0 /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/S1-variants-snp.vcf.gz --variant:v1 /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/S1-variants-indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null
[2015-04-21 18:33:03.752190] DEBUG: bcbio-nextgen: INFO  14:33:03,751 HelpFormatter - Executing as<EMAIL_ADDRESS>on Linux 2.6.32-431.17.1.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_25-b15.
[2015-04-21 18:33:03.752387] DEBUG: bcbio-nextgen: INFO  14:33:03,752 HelpFormatter - Date/Time: 2015/04/21 14:33:03
[2015-04-21 18:33:03.752705] DEBUG: bcbio-nextgen: INFO  14:33:03,752 HelpFormatter - ---------------------------------------------------------------------------------
[2015-04-21 18:33:03.752902] DEBUG: bcbio-nextgen: INFO  14:33:03,752 HelpFormatter - ---------------------------------------------------------------------------------
[2015-04-21 18:33:04.238007] DEBUG: bcbio-nextgen: INFO  14:33:04,237 GenomeAnalysisEngine - Strictness is SILENT
[2015-04-21 18:33:04.291948] DEBUG: bcbio-nextgen: INFO  14:33:04,291 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-04-21 18:33:04.333379] DEBUG: bcbio-nextgen: WARN  14:33:04,333 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-04-21 18:33:04.333569] DEBUG: bcbio-nextgen: WARN  14:33:04,333 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-04-21 18:33:04.396877] DEBUG: bcbio-nextgen: INFO  14:33:04,396 GenomeAnalysisEngine - Preparing for traversal
[2015-04-21 18:33:04.398497] DEBUG: bcbio-nextgen: INFO  14:33:04,397 GenomeAnalysisEngine - Done preparing for traversal
[2015-04-21 18:33:04.399304] DEBUG: bcbio-nextgen: INFO  14:33:04,398 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-04-21 18:33:04.400016] DEBUG: bcbio-nextgen: INFO  14:33:04,399 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-04-21 18:33:04.400516] DEBUG: bcbio-nextgen: INFO  14:33:04,400 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-04-21 18:33:04.509009] DEBUG: bcbio-nextgen: INFO  14:33:04,508 ProgressMeter -            done        12.0     0.0 s       2.5 h       45.7%     0.0 s       0.0 s
[2015-04-21 18:33:04.509667] DEBUG: bcbio-nextgen: INFO  14:33:04,509 ProgressMeter - Total runtime 0.11 secs, 0.00 min, 0.00 hours
ok
Select a sample from a VCF file. ... [2015-04-21 18:33:04.621034] DEBUG: bcbio-nextgen: Select sample: S2
[2015-04-21 18:33:04.621266] DEBUG: bcbio-nextgen-commands: /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/bcftools view -O z  /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/S1_S2-combined.vcf.gz -s S2 > /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/tx/tmp8iNTPN/S1_S2-combined-sampleselect.vcf.gz
[2015-04-21 18:33:04.686302] DEBUG: bcbio-nextgen: tabix index S1_S2-combined-sampleselect.vcf.gz
[2015-04-21 18:33:04.686757] DEBUG: bcbio-nextgen-commands: /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/tabix -f -p vcf /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/tx/tmpKedODQ/S1_S2-combined-sampleselect.vcf.gz
ok
Ensure we can correctly find paired fastq files. ... ok

======================================================================
ERROR: Test variant calling with GATK pipeline.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/test_automated_analysis.py", line 263, in test_1_variantcall
    subprocess.check_call(cl)
  File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/subprocess.py", line 540, in check_call
    raise CalledProcessError(retcode, cmd)
CalledProcessError: Command '['bcbio_nextgen.py', '/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/test_automated_output/bcbio_system.yaml', '/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/automated/../100326_FC6107FAAXX', '/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/automated/run_info-variantcall.yaml']' returned non-zero exit status 1

======================================================================
ERROR: Allow BAM files as input to pipeline.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/test_automated_analysis.py", line 275, in test_5_bam
    subprocess.check_call(cl)
  File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/subprocess.py", line 540, in check_call
    raise CalledProcessError(retcode, cmd)
CalledProcessError: Command '['bcbio_nextgen.py', '/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/test_automated_output/bcbio_system.yaml', '/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/automated/run_info-bam.yaml']' returned non-zero exit status 1

----------------------------------------------------------------------
Ran 11 tests in 70.706s

FAILED (errors=2)

Hi @dfcrmuser,
Sorry for the trouble. There are some programs we aren't allowed to distribute, and the GATK toolkit is one of them. You have to download it and install it manually. Here is a description about how to do that:
http://bcbio-nextgen.readthedocs.org/en/latest/contents/installation.html#extra-software-and-data
Hopefully that will get you up and going. Let us know if that fixes the issue.

Sorry about the problems. In addition to Rory's suggestion, you should also update to the latest development version:
bcbio_nextgen.py upgrade -u development

Apologies, some of the options for freebayes changed since the last release. We plan to have a new release this week which will resolve this. Hope this gets you running cleanly.

Thank you both for your prompt response.
I ran both the commands you described above and then retried the test suite.  I'm running this on an sge cluster.  I tried running it with 4 cores, each with 6 G of memory.  I ran it and was getting an error that the Java heap for GATK wasn't big enough, so I increased the size of the heap in the config/bcbio_system.yaml file.
Now I'm getting a seg fault in sambamba and some other errors (including heap errors).
Here's the output from the test suite:
Wed Apr 22 09:49:51 tests > ./run_tests.sh
Check for the presence of runs in an Illumina SampleSheet. ... ok
Convert CSV Illumina SampleSheet to YAML. ... ok
Test variant calling with GATK pipeline. ... [2015-04-22T13:50Z] Resource requests: bwa, sambamba, samtools; memory: 2.00, 2.00; cores: 16, 16, 16
[2015-04-22T13:50Z] Configuring 1 jobs to run, using 1 cores each with 2.00g of memory reserved for each job
[2015-04-22T13:50Z] Timing: organize samples
[2015-04-22T13:50Z] multiprocessing: organize_samples
[2015-04-22T13:50Z] Using input YAML configuration: /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/automated/run_info-variantcall.yaml
[2015-04-22T13:50Z] Checking sample YAML configuration: /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/automated/run_info-variantcall.yaml
[2015-04-22T13:50Z] Testing minimum versions of installed programs
[2015-04-22T13:50Z] Timing: alignment preparation
[2015-04-22T13:50Z] multiprocessing: prep_align_inputs
[2015-04-22T13:50Z] Resource requests: ; memory: 1.00; cores: 1
[2015-04-22T13:50Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-04-22T13:50Z] bgzip input file
[2015-04-22T13:50Z] bgzip input file
[2015-04-22T13:50Z] Resource requests: ; memory: 1.00; cores: 1
[2015-04-22T13:50Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-04-22T13:50Z] Index input with grabix: 7_100326_FC6107FAAXX_1_fastq.txt.gz
[2015-04-22T13:50Z] Index input with grabix: 7_100326_FC6107FAAXX_2_fastq.txt.gz
[2015-04-22T13:50Z] multiprocessing: disambiguate_split
[2015-04-22T13:50Z] Timing: alignment
[2015-04-22T13:50Z] multiprocessing: process_alignment
[2015-04-22T13:50Z] Aligning lane 7_100326_FC6107FAAXX with bwa aligner
[2015-04-22T13:50Z] bwa mem alignment from fastq: Test1
[2015-04-22T13:50Z] samblaster: Version 0.1.21
[2015-04-22T13:50Z] samblaster: Inputting from stdin
[2015-04-22T13:50Z] samblaster: Outputting to stdout
[2015-04-22T13:50Z] samblaster: Opening /dev/fd/62 for write.
[2015-04-22T13:50Z] samblaster: Opening /dev/fd/63 for write.
[2015-04-22T13:50Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2015-04-22T13:50Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-04-22T13:50Z] [M::mem_pestat] (25, 50, 75) percentile: (129, 150, 174)
[2015-04-22T13:50Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (39, 264)
[2015-04-22T13:50Z] [M::mem_pestat] mean and std.dev: (151.57, 30.80)
[2015-04-22T13:50Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 309)
[2015-04-22T13:50Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-04-22T13:50Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2015-04-22T13:50Z] samblaster: Loaded 2 header sequence entries.
[2015-04-22T13:50Z] [main] Version: 0.7.12-r1039
[2015-04-22T13:50Z] [main] CMD: /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/bwa mem -M -t 1 -R @RG\tID:7\tPL:illumina\tPU:7_100326_FC6107FAAXX\tSM:Test1 -v 1 /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/genomes/hg19/bwa/hg19.fa /dev/fd/63 /dev/fd/62
[2015-04-22T13:50Z] [main] Real time: 0.723 sec; CPU: 0.676 sec
[2015-04-22T13:50Z] samblaster: Output 0 discordant read pairs to /dev/fd/62
[2015-04-22T13:50Z] samblaster: Output 0 split reads to /dev/fd/63
[2015-04-22T13:50Z] samblaster: Marked 102 of 9000 (1.13%) read ids as duplicates using 1384k memory in 0.020S CPU seconds and 1S wall time.
[2015-04-22T13:50Z] Index BAM file: 7_100326_FC6107FAAXX-sort-1_36000-sr.bam
[2015-04-22T13:50Z] Index BAM file: 7_100326_FC6107FAAXX-sort-1_36000-disc.bam
[2015-04-22T13:50Z] Aligning lane 7_100326_FC6107FAAXX with bwa aligner
[2015-04-22T13:50Z] bwa mem alignment from fastq: Test1
[2015-04-22T13:50Z] samblaster: Version 0.1.21
[2015-04-22T13:50Z] samblaster: Inputting from stdin
[2015-04-22T13:50Z] samblaster: Outputting to stdout
[2015-04-22T13:50Z] samblaster: Opening /dev/fd/62 for write.
[2015-04-22T13:50Z] samblaster: Opening /dev/fd/63 for write.
[2015-04-22T13:50Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2015-04-22T13:50Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-04-22T13:50Z] [M::mem_pestat] (25, 50, 75) percentile: (129, 150, 175)
[2015-04-22T13:50Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (37, 267)
[2015-04-22T13:50Z] [M::mem_pestat] mean and std.dev: (151.74, 31.08)
[2015-04-22T13:50Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 313)
[2015-04-22T13:50Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-04-22T13:50Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2015-04-22T13:50Z] samblaster: Loaded 2 header sequence entries.
[2015-04-22T13:50Z] [main] Version: 0.7.12-r1039
[2015-04-22T13:50Z] [main] CMD: /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/bwa mem -M -t 1 -R @RG\tID:7\tPL:illumina\tPU:7_100326_FC6107FAAXX\tSM:Test1 -v 1 /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/genomes/hg19/bwa/hg19.fa /dev/fd/63 /dev/fd/62
[2015-04-22T13:50Z] [main] Real time: 0.716 sec; CPU: 0.673 sec
[2015-04-22T13:50Z] samblaster: Output 1 discordant read pairs to /dev/fd/62
[2015-04-22T13:50Z] samblaster: Output 2 split reads to /dev/fd/63
[2015-04-22T13:50Z] samblaster: Marked 108 of 9000 (1.20%) read ids as duplicates using 1384k memory in 0.016S CPU seconds and 1S wall time.
[2015-04-22T13:50Z] Index BAM file: 7_100326_FC6107FAAXX-sort-36001_72000-sr.bam
[2015-04-22T13:50Z] Index BAM file: 7_100326_FC6107FAAXX-sort-36001_72000-disc.bam
[2015-04-22T13:50Z] Aligning lane 7_100326_FC6107FAAXX with bwa aligner
[2015-04-22T13:50Z] bwa mem alignment from fastq: Test1
[2015-04-22T13:50Z] samblaster: Version 0.1.21
[2015-04-22T13:50Z] samblaster: Inputting from stdin
[2015-04-22T13:50Z] samblaster: Outputting to stdout
[2015-04-22T13:50Z] samblaster: Opening /dev/fd/62 for write.
[2015-04-22T13:50Z] samblaster: Opening /dev/fd/63 for write.
[2015-04-22T13:50Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2015-04-22T13:50Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-04-22T13:50Z] [M::mem_pestat] (25, 50, 75) percentile: (129, 149, 175)
[2015-04-22T13:50Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (37, 267)
[2015-04-22T13:50Z] [M::mem_pestat] mean and std.dev: (151.37, 30.95)
[2015-04-22T13:50Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 313)
[2015-04-22T13:50Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-04-22T13:50Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2015-04-22T13:50Z] samblaster: Loaded 2 header sequence entries.
[2015-04-22T13:50Z] [main] Version: 0.7.12-r1039
[2015-04-22T13:50Z] [main] CMD: /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/bwa mem -M -t 1 -R @RG\tID:7\tPL:illumina\tPU:7_100326_FC6107FAAXX\tSM:Test1 -v 1 /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/genomes/hg19/bwa/hg19.fa /dev/fd/63 /dev/fd/62
[2015-04-22T13:50Z] [main] Real time: 0.725 sec; CPU: 0.686 sec
[2015-04-22T13:50Z] samblaster: Output 1 discordant read pairs to /dev/fd/62
[2015-04-22T13:50Z] samblaster: Output 2 split reads to /dev/fd/63
[2015-04-22T13:50Z] samblaster: Marked 108 of 9000 (1.20%) read ids as duplicates using 1380k memory in 0.016S CPU seconds and 1S wall time.
[2015-04-22T13:50Z] Index BAM file: 7_100326_FC6107FAAXX-sort-72001_108000-sr.bam
[2015-04-22T13:50Z] Index BAM file: 7_100326_FC6107FAAXX-sort-72001_108000-disc.bam
[2015-04-22T13:50Z] Aligning lane 7_100326_FC6107FAAXX with bwa aligner
[2015-04-22T13:50Z] bwa mem alignment from fastq: Test1
[2015-04-22T13:50Z] samblaster: Version 0.1.21
[2015-04-22T13:50Z] samblaster: Inputting from stdin
[2015-04-22T13:50Z] samblaster: Outputting to stdout
[2015-04-22T13:50Z] samblaster: Opening /dev/fd/62 for write.
[2015-04-22T13:50Z] samblaster: Opening /dev/fd/63 for write.
[2015-04-22T13:50Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2015-04-22T13:50Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-04-22T13:50Z] [M::mem_pestat] (25, 50, 75) percentile: (128, 150, 175)
[2015-04-22T13:50Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (34, 269)
[2015-04-22T13:50Z] [M::mem_pestat] mean and std.dev: (151.09, 31.43)
[2015-04-22T13:50Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 316)
[2015-04-22T13:50Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-04-22T13:50Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2015-04-22T13:50Z] samblaster: Loaded 2 header sequence entries.
[2015-04-22T13:50Z] [main] Version: 0.7.12-r1039
[2015-04-22T13:50Z] [main] CMD: /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/bwa mem -M -t 1 -R @RG\tID:7\tPL:illumina\tPU:7_100326_FC6107FAAXX\tSM:Test1 -v 1 /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/genomes/hg19/bwa/hg19.fa /dev/fd/63 /dev/fd/62
[2015-04-22T13:50Z] [main] Real time: 0.724 sec; CPU: 0.677 sec
[2015-04-22T13:50Z] samblaster: Output 0 discordant read pairs to /dev/fd/62
[2015-04-22T13:50Z] samblaster: Output 0 split reads to /dev/fd/63
[2015-04-22T13:50Z] samblaster: Marked 105 of 9000 (1.17%) read ids as duplicates using 1380k memory in 0.018S CPU seconds and 0S wall time.
[2015-04-22T13:50Z] Index BAM file: 7_100326_FC6107FAAXX-sort-108001_144000-sr.bam
[2015-04-22T13:50Z] Index BAM file: 7_100326_FC6107FAAXX-sort-108001_144000-disc.bam
[2015-04-22T13:50Z] Aligning lane 7_100326_FC6107FAAXX with bwa aligner
[2015-04-22T13:50Z] bwa mem alignment from fastq: Test1
[2015-04-22T13:50Z] samblaster: Version 0.1.21
[2015-04-22T13:50Z] samblaster: Inputting from stdin
[2015-04-22T13:50Z] samblaster: Outputting to stdout
[2015-04-22T13:50Z] samblaster: Opening /dev/fd/62 for write.
[2015-04-22T13:50Z] samblaster: Opening /dev/fd/63 for write.
[2015-04-22T13:50Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2015-04-22T13:50Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-04-22T13:50Z] [M::mem_pestat] (25, 50, 75) percentile: (129, 150, 175)
[2015-04-22T13:50Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (37, 267)
[2015-04-22T13:50Z] [M::mem_pestat] mean and std.dev: (151.76, 31.66)
[2015-04-22T13:50Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 313)
[2015-04-22T13:50Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-04-22T13:50Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2015-04-22T13:50Z] samblaster: Loaded 2 header sequence entries.
[2015-04-22T13:50Z] [main] Version: 0.7.12-r1039
[2015-04-22T13:50Z] [main] CMD: /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/bwa mem -M -t 1 -R @RG\tID:7\tPL:illumina\tPU:7_100326_FC6107FAAXX\tSM:Test1 -v 1 /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/genomes/hg19/bwa/hg19.fa /dev/fd/63 /dev/fd/62
[2015-04-22T13:50Z] [main] Real time: 0.374 sec; CPU: 0.350 sec
[2015-04-22T13:50Z] samblaster: Output 3 discordant read pairs to /dev/fd/62
[2015-04-22T13:50Z] samblaster: Output 0 split reads to /dev/fd/63
[2015-04-22T13:50Z] samblaster: Marked 31 of 4164 (0.74%) read ids as duplicates using 1340k memory in 0.006S CPU seconds and 0S wall time.
[2015-04-22T13:50Z] Index BAM file: 7_100326_FC6107FAAXX-sort-144001_160656-sr.bam
[2015-04-22T13:50Z] Index BAM file: 7_100326_FC6107FAAXX-sort-144001_160656-disc.bam
[2015-04-22T13:50Z] multiprocessing: delayed_bam_merge
[2015-04-22T13:50Z] Merge bam files to 7_100326_FC6107FAAXX-sort-sr.bam
[2015-04-22T13:50Z] Merge bam files to 7_100326_FC6107FAAXX-sort-disc.bam
[2015-04-22T13:50Z] Merge bam files to 7_100326_FC6107FAAXX-sort.bam
[2015-04-22T13:50Z] Timing: callable regions
[2015-04-22T13:50Z] multiprocessing: prep_samples
[2015-04-22T13:50Z] Prepare cleaned BED file : Test1
[2015-04-22T13:50Z] bgzip variant_regions-variantcall.bed
[2015-04-22T13:50Z] tabix index variant_regions-variantcall.bed.gz
[2015-04-22T13:50Z] Prepare merged BED file : Test1
[2015-04-22T13:50Z] bgzip variant_regions-variantcall-merged.bed
[2015-04-22T13:50Z] tabix index variant_regions-variantcall-merged.bed.gz
[2015-04-22T13:50Z] multiprocessing: postprocess_alignment
[2015-04-22T13:50Z] Resource requests: ; memory: 1.00; cores: 1
[2015-04-22T13:50Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-04-22T13:50Z] multiprocessing: calc_callable_loci
[2015-04-22T13:50Z] bedtools genomecov: chrM : 7_100326_FC6107FAAXX-sort.bam
[2015-04-22T13:50Z] /bin/bash: line 1: 18310 Segmentation fault      (core dumped) /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/sambamba view -F 'mapping_quality > 0' -L /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable-split/tx/tmpF65QQl/7_100326_FC6107FAAXX-sort-chrM-callable-regions.bed -f bam -l 1 /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort.bam
[2015-04-22T13:50Z] Uncaught exception occurred
Traceback (most recent call last):
File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run
_do_run(cmd, checks, log_stdout)

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/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; /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/sambamba view -F 'mapping_quality > 0' -L /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable-split/tx/tmpF65QQl/7_100326_FC6107FAAXX-sort-chrM-callable-regions.bed -f bam -l 1 /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort.bam | /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/bedtools genomecov -split -ibam stdin -bga -g /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa.fai -max 70001 > /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable-split/tx/tmpF65QQl/tx/tmpCrajOz/7_100326_FC6107FAAXX-sort-chrM-callable-genomecov.bed
/bin/bash: line 1: 18310 Segmentation fault      (core dumped) /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/sambamba view -F 'mapping_quality > 0' -L /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable-split/tx/tmpF65QQl/7_100326_FC6107FAAXX-sort-chrM-callable-regions.bed -f bam -l 1 /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort.bam
 18311 Done                    | /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/bedtools genomecov -split -ibam stdin -bga -g /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa.fai -max 70001 > /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable-split/tx/tmpF65QQl/tx/tmpCrajOz/7_100326_FC6107FAAXX-sort-chrM-callable-genomecov.bed

' returned non-zero exit status 139
Traceback (most recent call last):
File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/bcbio_nextgen.py", line 216, in
main(**kwargs)

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/bcbio_nextgen.py", line 42, in main
run_main(**kwargs)

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 36, in run_main
fc_dir, run_info_yaml)

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 79, in _run_toplevel
for xs in pipeline.run(config, run_info_yaml, parallel, dirs, samples):

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 148, in run
samples = run_parallel("postprocess_alignment", samples)

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 28, in run_parallel
return run_multicore(fn, items, config, parallel=parallel)

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 84, in run_multicore
for data in joblib.Parallel(parallel["num_jobs"])(joblib.delayed(fn)(x) for x in items):

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 653, in call
self.dispatch(function, args, kwargs)

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 400, in dispatch
job = ImmediateApply(func, args, kwargs)

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 138, in init
self.results = func(*args, **kwargs)

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/utils.py", line 49, in wrapper
return apply(f, *args, **kwargs)

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multitasks.py", line 35, in postprocess_alignment
return sample.postprocess_alignment(*args)

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/sample.py", line 156, in postprocess_alignment
callable.block_regions(data["work_bam"], ref_file, data["config"])

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/bam/callable.py", line 321, in block_regions
callable_bed = parallel_callable_loci(in_bam, ref_file, config)

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/bam/callable.py", line 48, in parallel_callable_loci
"callable_bed", ["config"])[0]

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/split.py", line 59, in parallel_split_combine
split_output = parallel_fn(parallel_name, split_args)

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 28, in run_parallel
return run_multicore(fn, items, config, parallel=parallel)

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 84, in run_multicore
for data in joblib.Parallel(parallel["num_jobs"])(joblib.delayed(fn)(x) for x in items):

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 653, in call
self.dispatch(function, args, kwargs)

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 400, in dispatch
job = ImmediateApply(func, args, kwargs)

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 138, in init
self.results = func(*args, **kwargs)

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/utils.py", line 49, in wrapper
return apply(f, *args, **kwargs)

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multitasks.py", line 143, in calc_callable_loci
return callable.calc_callable_loci(*args)

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 63, in wrapper
out = f(*args, **kwargs)

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/bam/callable.py", line 66, in calc_callable_loci
tx_out_file, data),

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/bam/callable.py", line 111, in _get_coverage_file
do.run(cmd.format(**locals()), "bedtools genomecov: %s" % (str(region)), data)

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run
_do_run(cmd, checks, log_stdout)

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run
raise subprocess.CalledProcessError(exitcode, error_msg)

subprocess.CalledProcessError: Command 'set -o pipefail; /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/sambamba view -F 'mapping_quality > 0' -L /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable-split/tx/tmpF65QQl/7_100326_FC6107FAAXX-sort-chrM-callable-regions.bed -f bam -l 1 /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort.bam | /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/bedtools genomecov -split -ibam stdin -bga -g /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa.fai -max 70001 > /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable-split/tx/tmpF65QQl/tx/tmpCrajOz/7_100326_FC6107FAAXX-sort-chrM-callable-genomecov.bed
/bin/bash: line 1: 18310 Segmentation fault      (core dumped) /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/sambamba view -F 'mapping_quality > 0' -L /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable-split/tx/tmpF65QQl/7_100326_FC6107FAAXX-sort-chrM-callable-regions.bed -f bam -l 1 /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort.bam
 18311 Done                    | /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/bedtools genomecov -split -ibam stdin -bga -g /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa.fai -max 70001 > /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable-split/tx/tmpF65QQl/tx/tmpCrajOz/7_100326_FC6107FAAXX-sort-chrM-callable-genomecov.bed

' returned non-zero exit status 139
ERROR
Allow BAM files as input to pipeline. ... [2015-04-22T13:50Z] Resource requests: bwa, sambamba, samtools; memory: 2.00, 2.00; cores: 16, 16, 16
[2015-04-22T13:50Z] Configuring 1 jobs to run, using 1 cores each with 2.00g of memory reserved for each job
[2015-04-22T13:50Z] Timing: organize samples
[2015-04-22T13:50Z] multiprocessing: organize_samples
[2015-04-22T13:50Z] Using input YAML configuration: /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/automated/run_info-bam.yaml
[2015-04-22T13:50Z] Checking sample YAML configuration: /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/automated/run_info-bam.yaml
[2015-04-22T13:50Z] Testing minimum versions of installed programs
[2015-04-22T13:50Z] Timing: alignment preparation
[2015-04-22T13:50Z] multiprocessing: prep_align_inputs
Traceback (most recent call last):
File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/bcbio_nextgen.py", line 216, in
main(**kwargs)

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/bcbio_nextgen.py", line 42, in main
run_main(**kwargs)

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 36, in run_main
fc_dir, run_info_yaml)

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 79, in _run_toplevel
for xs in pipeline.run(config, run_info_yaml, parallel, dirs, samples):

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 140, in run
samples = run_parallel("prep_align_inputs", samples)

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 28, in run_parallel
return run_multicore(fn, items, config, parallel=parallel)

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 84, in run_multicore
for data in joblib.Parallel(parallel["num_jobs"])(joblib.delayed(fn)(x) for x in items):

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 653, in call
self.dispatch(function, args, kwargs)

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 400, in dispatch
job = ImmediateApply(func, args, kwargs)

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 138, in init
self.results = func(*args, **kwargs)

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/utils.py", line 49, in wrapper
return apply(f, *args, **kwargs)

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multitasks.py", line 43, in prep_align_inputs
return alignprep.create_inputs(*args)

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/alignprep.py", line 37, in create_inputs
ready_files = _prep_grabix_indexes(data["files"], data["dirs"], data)

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/alignprep.py", line 156, in _prep_grabix_indexes
out = _bgzip_from_bam(in_files[0], dirs, data["config"])

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/alignprep.py", line 304, in _bgzip_from_bam
max_mem = int(resources.get("memory", "1073741824")) * cores  # 1Gb/core default

ValueError: invalid literal for int() with base 10: '2G'
ERROR
Create a project template from input files and metadata configuration. ... variant_regions ../data/100326_FC6107FAAXX/test.bed
sex female
description 7_1
batch 1a
variant_regions ../data/100326_FC6107FAAXX/test.bed
sex
description 8_1
batch 1a
Configuration file created at: /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/test_automated_output/100326/config/100326.yaml
Edit to finalize and run with:
cd /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/test_automated_output/100326/work
bcbio_nextgen.py ../config/100326.yaml
ok
Identify programs and versions used in analysis. ... [{'program': 'bcbio-nextgen', 'version': '0.8.8a0-5c3e6a5'}, {'program': 'alientrimmer', 'version': '0.3.2'}, {'program': 'bamtools', 'version': '2.3.0'}, {'program': 'bcbio_variation', 'version': '0.2.4'}, {'program': 'bcftools', 'version': '1.2'}, {'program': 'bedtools', 'version': '2.23.0'}, {'program': 'biobambam', 'version': '0.0.182'}, {'program': 'bowtie2', 'version': '2.2.5'}, {'program': 'bwa', 'version': '0.7.12'}, {'program': 'chanjo', 'version': '2.3.2'}, {'program': 'cutadapt', 'version': '1.4.2'}, {'program': 'fastqc', 'version': '0.11.3'}, {'program': 'featurecounts', 'version': '1.4.4'}, {'program': 'freebayes', 'version': '0.9.21-7'}, {'program': 'gatk', 'version': '3.3-0-g37228af'}, {'program': 'gatk-framework', 'version': '3.2-4'}, {'program': 'gemini', 'version': '0.7.0'}, {'program': 'htseq', 'version': '0.6.1'}, {'program': 'mutect', 'version': '1.1.5'}, {'program': 'novoalign', 'version': '3.02.10'}, {'program': 'novosort', 'version': 'V3.00.02'}, {'program': 'oncofuse', 'version': '1.0.9'}, {'program': 'picard', 'version': '1.96'}, {'program': 'platypus-variant', 'version': '<IP_ADDRESS>'}, {'program': 'qualimap', 'version': '30-03-15'}, {'program': 'rnaseqc', 'version': '1.1.7'}, {'program': 'samtools', 'version': '1.2'}, {'program': 'snpeff', 'version': '4.1c'}, {'program': 'tophat', 'version': '2.0.9'}, {'program': 'varscan', 'version': '2.3.7'}, {'program': 'vcflib', 'version': '2015-03-13'}, {'program': 'vt', 'version': '2015-03-26'}, {'program': 'cn.mops', 'version': ''}, {'program': 'cufflinks', 'version': ''}, {'program': 'sambamba', 'version': ''}]
ok
Parallel combination of VCF files, split by chromosome. ... [2015-04-22 13:50:40.412770] DEBUG: bcbio-nextgen: Resource requests: ; memory: 1.00; cores: 1
[2015-04-22 13:50:40.412948] DEBUG: bcbio-nextgen: Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-04-22 13:50:40.413716] DEBUG: bcbio-nextgen: Resource requests: ; memory: 1.00; cores: 1
[2015-04-22 13:50:40.413841] DEBUG: bcbio-nextgen: Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-04-22 13:50:40.425051] INFO: bcbio-nextgen: multiprocessing: merge_variant_files
[2015-04-22 13:50:43.540659] DEBUG: bcbio-nextgen: Resource requests: ; memory: 1.00; cores: 1
[2015-04-22 13:50:43.540848] DEBUG: bcbio-nextgen: Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-04-22 13:50:43.546526] DEBUG: bcbio-nextgen: Merge variants
[2015-04-22 13:50:43.546700] DEBUG: bcbio-nextgen-commands: /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/bcftools merge -O z -r chrM cat /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/S1_S2-combined-regions/S1_S2-combined-chrM-files.txt > /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/S1_S2-combined-regions/tx/tmp32g5kP/S1_S2-combined-chrM.vcf.gz
[2015-04-22 13:50:43.644841] DEBUG: bcbio-nextgen: tabix index S1_S2-combined-chrM.vcf.gz
[2015-04-22 13:50:43.645296] DEBUG: bcbio-nextgen-commands: /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/tabix -f -p vcf /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/S1_S2-combined-regions/tx/tmpLOe2eA/S1_S2-combined-chrM.vcf.gz
[2015-04-22 13:50:43.685156] DEBUG: bcbio-nextgen: Resource requests: ; memory: 1.00; cores: 1
[2015-04-22 13:50:43.685549] DEBUG: bcbio-nextgen: Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-04-22 13:50:43.692797] DEBUG: bcbio-nextgen: Merge variants
[2015-04-22 13:50:43.693066] DEBUG: bcbio-nextgen-commands: /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/bcftools merge -O z -r chr22 cat /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/S1_S2-combined-regions/S1_S2-combined-chr22-files.txt > /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/S1_S2-combined-regions/tx/tmpJWwzrR/S1_S2-combined-chr22.vcf.gz
[2015-04-22 13:50:43.765082] DEBUG: bcbio-nextgen: tabix index S1_S2-combined-chr22.vcf.gz
[2015-04-22 13:50:43.765504] DEBUG: bcbio-nextgen-commands: /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/tabix -f -p vcf /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/S1_S2-combined-regions/tx/tmpFolivc/S1_S2-combined-chr22.vcf.gz
[2015-04-22 13:50:43.801682] INFO: bcbio-nextgen: multiprocessing: concat_variant_files
[2015-04-22 13:50:43.807454] DEBUG: bcbio-nextgen: Resource requests: ; memory: 1.00; cores: 1
[2015-04-22 13:50:43.807747] DEBUG: bcbio-nextgen: Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-04-22 13:50:43.828898] DEBUG: bcbio-nextgen: Concat variant files
[2015-04-22 13:50:43.829205] DEBUG: bcbio-nextgen-commands: /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/gatk-framework org.broadinstitute.gatk.tools.CatVariants -R /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -V /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/S1_S2-combined-files.list -out /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/tx/tmp7QbDcz/S1_S2-combined.vcf.gz -assumeSorted -Xms750 -Xmx2000m -XX:+UseSerialGC
[2015-04-22 13:50:43.867681] DEBUG: bcbio-nextgen: Error occurred during initialization of VM
[2015-04-22 13:50:43.868221] DEBUG: bcbio-nextgen: Too small initial heap
ERROR
Exclude samples from VCF files. ... ERROR
Split a VCF file into SNPs and indels, then combine back together. ... [2015-04-22 13:50:44.113497] DEBUG: bcbio-nextgen: Subset to SNPs and indels
[2015-04-22 13:50:44.113621] DEBUG: bcbio-nextgen-commands: /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/bcftools view -O v /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/S1-variants.vcf --types snps > /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/tx/tmpOGYNPm/S1-variants-snp.vcf
[2015-04-22 13:50:44.154102] DEBUG: bcbio-nextgen: [E::hts_open] fail to open file '/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/S1-variants.vcf'
[2015-04-22 13:50:44.154766] ERROR: bcbio-nextgen: Uncaught exception occurred
Traceback (most recent call last):
File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run
_do_run(cmd, checks, log_stdout)

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/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; /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/bcftools view -O v /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/S1-variants.vcf --types snps > /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/tx/tmpOGYNPm/S1-variants-snp.vcf
[E::hts_open] fail to open file '/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/S1-variants.vcf'
Failed to open /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/S1-variants.vcf: No such file or directory
' returned non-zero exit status 255
ERROR
Select a sample from a VCF file. ... FAIL
Ensure we can correctly find paired fastq files. ... ok
======================================================================
ERROR: Test variant calling with GATK pipeline.

Traceback (most recent call last):
File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/test_automated_analysis.py", line 263, in test_1_variantcall
subprocess.check_call(cl)

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/subprocess.py", line 540, in check_call
raise CalledProcessError(retcode, cmd)

CalledProcessError: Command '['bcbio_nextgen.py', '/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/test_automated_output/bcbio_system.yaml', '/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/automated/../100326_FC6107FAAXX', '/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/automated/run_info-variantcall.yaml']' returned non-zero exit status 1
======================================================================
ERROR: Allow BAM files as input to pipeline.

Traceback (most recent call last):
File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/test_automated_analysis.py", line 275, in test_5_bam
subprocess.check_call(cl)

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/subprocess.py", line 540, in check_call
raise CalledProcessError(retcode, cmd)

CalledProcessError: Command '['bcbio_nextgen.py', '/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/test_automated_output/bcbio_system.yaml', '/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/automated/run_info-bam.yaml']' returned non-zero exit status 1
======================================================================
ERROR: Parallel combination of VCF files, split by chromosome.

Traceback (most recent call last):
File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/test_pipeline.py", line 60, in test_1_parallel_vcf_combine
vcfutils.parallel_combine_variants(files, self.combo_file, ref_file, config, run_parallel)

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/variation/vcfutils.py", line 422, in parallel_combine_variants
file_key, ["region", "sam_ref", "config"], split_outfile_i=0)

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/split.py", line 63, in parallel_split_combine
parallel_fn(combiner, combine_args)

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 28, in run_parallel
return run_multicore(fn, items, config, parallel=parallel)

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 84, in run_multicore
for data in joblib.Parallel(parallel["num_jobs"])(joblib.delayed(fn)(x) for x in items):

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 653, in call
self.dispatch(function, args, kwargs)

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 400, in dispatch
job = ImmediateApply(func, args, kwargs)

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 138, in init
self.results = func(*args, **kwargs)

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/utils.py", line 49, in wrapper
return apply(f, *args, **kwargs)

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multitasks.py", line 115, in concat_variant_files
return vcfutils.concat_variant_files(*args)

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/variation/vcfutils.py", line 286, in concat_variant_files
do.run(cmd, "Concat variant files", log_error=False)

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run
_do_run(cmd, checks, log_stdout)

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run
raise subprocess.CalledProcessError(exitcode, error_msg)

CalledProcessError: Command '/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/gatk-framework org.broadinstitute.gatk.tools.CatVariants -R /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -V /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/S1_S2-combined-files.list -out /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/tx/tmp7QbDcz/S1_S2-combined.vcf.gz -assumeSorted -Xms750 -Xmx2000m -XX:+UseSerialGC
Error occurred during initialization of VM
Too small initial heap
' returned non-zero exit status 1
======================================================================
ERROR: Exclude samples from VCF files.

Traceback (most recent call last):
File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/test_pipeline.py", line 80, in test_2_vcf_exclusion
vcfutils.exclude_samples(self.combo_file, out_file, to_exclude, ref_file, config)

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/variation/vcfutils.py", line 152, in exclude_samples
include, exclude = _get_exclude_samples(in_file, to_exclude)

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/variation/vcfutils.py", line 142, in _get_exclude_samples
for s in get_samples(in_file):

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/variation/vcfutils.py", line 130, in get_samples
with (gzip.open(in_file) if in_file.endswith(".gz") else open(in_file)) as in_handle:

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/gzip.py", line 34, in open
return GzipFile(filename, mode, compresslevel)

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/gzip.py", line 94, in init
fileobj = self.myfileobj = __builtin__.open(filename, mode or 'rb')

IOError: [Errno 2] No such file or directory: '/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/S1_S2-combined.vcf.gz'
======================================================================
ERROR: Split a VCF file into SNPs and indels, then combine back together.

Traceback (most recent call last):
File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/test_pipeline.py", line 92, in test_3_vcf_split_combine
snp_file, indel_file = vcfutils.split_snps_indels(fname, ref_file, config)

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/variation/vcfutils.py", line 122, in split_snps_indels
do.run(cmd.format(**locals()), "Subset to SNPs and indels")

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run
_do_run(cmd, checks, log_stdout)

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/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; /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/bcftools view -O v /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/S1-variants.vcf --types snps > /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/tx/tmpOGYNPm/S1-variants-snp.vcf
[E::hts_open] fail to open file '/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/S1-variants.vcf'
Failed to open /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/S1-variants.vcf: No such file or directory
' returned non-zero exit status 255
======================================================================
FAIL: Select a sample from a VCF file.

Traceback (most recent call last):
File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/test_pipeline.py", line 111, in test_4_vcf_sample_select
out_file = vcfutils.select_sample(fname, "S2", out_file, {})

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/variation/vcfutils.py", line 172, in select_sample
bgzip_and_index(in_file, config)

File "/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/anaconda/lib/python2.7/site-packages/bcbio/variation/vcfutils.py", line 441, in bgzip_and_index
assert not in_file == out_file, "Input file is bgzipped but not found: %s" % in_file

AssertionError: Input file is bgzipped but not found: /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/variants/S1_S2-combined.vcf.gz

Ran 11 tests in 48.868s
FAILED (errors=5, failures=1)
Here's the revised bcbio_system.yaml file:

Configuration file specifying system details for running an analysis pipeline
These pipeline apply generally across multiple projects. Adjust them in sample
specific configuration files when needed.
-- Base setup
Define resources to be used for individual programs on multicore machines.
These can be defined specifically for memory and processor availability.
- memory: Specify usage for memory intensive programs
- cores: Define cores that can be used for multicore programs.
- jvm_opts: specify details
- cmd: Command to launch the program, if not located on PATH.
- dir: Directory containing program associated data. Especially useful for
java jars
resources:
default options, used if other items below are not present
avoids needing to configure/adjust for every program
default:
memory: 4G

cores: 4

jvm_opts: ["-Xms750", "-Xmx3000m"]

log:
dir: log

tmp:
dir: null

ucsc_bigwig:
memory: 36g

bwa:
cmd: bwa

cores: 4

samtools:
memory: 3G

cores: 4

star:
memory: 4g

cores: 4

snap:
cores: 4

memory: 4G

kraken:
cores: 4

memory: 4g

qsignature:
cores: 1

memory: 2g

qsnp:
jvm_opts: ["-Xms750m", "-Xmx6g"]

gatk:
jvm_opts: ["-Xms500m", "-Xmx5000m"]

dir: /usr/local/share/java/gatk

gatk-haplotype:
jvm_opts: ["-Xms500m", "-Xmx5000m"]

gatk-vqsr:
jvm_opts: ["-Xms500m", "-Xmx5000m"]

picard:
jvm_opts: ["-Xms750m", "-Xmx5000m"]

dir: /usr/local/share/java/picard

snpeff:
jvm_opts: ["-Xms750m", "-Xmx6g"]

bcbio_variation:
jvm_opts: ["-Xms750m", "-Xmx5000m"]

dir: /usr/local/share/java/bcbio_variation

rnaseqc:
dir: /usr/local/share/java/RNA-SeQC

jvm_opts: ["-Xms750m", "-Xmx20g"]

mutect:
jvm_opts: ["-Xms750m", "-Xmx5000m"]

dir: /usr/local/share/java/mutect

varscan:
jvm_opts: ["-Xms750m", "-Xmx5000m"]

dir: /usr/local/share/java/varscan

vardict:
jvm_opts: ["-Xms750m", "-Xmx5000m"]

oncofuse:
jvm_opts: ["-Xms750m", "-Xmx5000m"]

dir: /usr/local/share/java/oncofuse

express:
memory: 8g

Location of galaxy configuration file, which has pointers to reference data
https://bcbio-nextgen.readthedocs.org/en/latest/contents/configuration.html#reference-genome-files
galaxy_config: universe_wsgi.ini
-- Additional options for specific integration, not required for standalone usage.
Galaxy integration. Required for retrieving information from Galaxy LIMS.
#galaxy_url: http://your/galaxy/url
#galaxy_api_key: your_galaxy_api_key
Details for hooking automated processing to a sequencer machine.
Not required if running standalone pipelines.
analysis:
# Can specify a different remote host to initiate
# the copy from. This is useful for NFS shared filesystems
# where you want to manage the copy from the base machine.
copy_user:
copy_host:
store_dir: /store4/solexadata
base_dir: /array0/projects/Sequencing
worker_program: nextgen_analysis_server.py

Daniel;
Sorry about the continued issues with installation. I dug through and identified two underlying problems (as an aide, it would be helpful if you could post error logs as a gist (https://gist.github.com/) and link to them from here -- it can be quite hard to work through some of the copy/paste):

There was a bug with the new default memory settings. I pushed a fix for this so if you update with bcbio_nextgen.py upgrade -u development it should fix that.

There is some kind of coredump going on with your sambamba and bedtools. This is the command line that is failing, although it's hard to debug separately because things are happening in a temporary directory:

/ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/sambamba view -F 'mapping_quality > 0' -L /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable-split/tx/tmpF65QQl/7_100326_FC6107FAAXX-sort-chrM-callable-regions.bed -f bam -l 1 /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort.bam | /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio/bin/bedtools genomecov -split -ibam stdin -bga -g /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa.fai -max 70001 > /ifs/scratch/c2b2/ngs_lab/db2175/Projects/PersonalizedCancer/FullPipeline/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable-split/tx/tmpF65QQl/tx/tmpCrajOz/7_100326_FC6107FAAXX-sort-chrM-callable-genomecov.bed

What type of system are you running this on? I can try to see if we can reproduce to figure out what is happening.
Hope this helps some and gets us moving a little forward.

Thanks for your continued interest in helping me get this set up.
Here's a gist with info about what system I'm on.
https://gist.github.com/dfcrmuser/54b350d6978bdf9d8033
I ran the command you suggested (it did not overwrite the bcbio_system.yaml file that I edited).  Here's the error message--looks pretty similar as the last time.
https://gist.github.com/dfcrmuser/585a0709746215f3412b

Daniel;
Thanks much for the additional details. The gist helps a lot to dig into it. The issues with all the failing final tests are all due to the GATK Java issue (https://gist.github.com/dfcrmuser/585a0709746215f3412b#file-testsuiteerrormessage-L524). These tests build off each other so the first failure triggers the rest.
The problem there is a typo in your specification of the GATK memory parameters -Xms750 -Xmx2000m -XX:+UseSerialGC. Your stack size specification (-Xms) has no units so I guess is 750 bytes which java complains about. If you edit this to Xms750m it should now work. You might have to re-pull the test files (S1-variants.vcf and S2-variants.vcf) if this failure resulted in deleting those, but otherwise you should hopefully be good to go.
The other 2 failing tests are due to the segfault in either sambamba or bedtools. I'm not sure what to suggest right now with that other than testing these tools to see if they work outside of bcbio. I'll try to spin up a Centos 6.5 machine and see if I can replicate/debug from my side as well.
Hope this helps.

Hi Daniel, it looks like this got partly resolved in #840. Closing it out for now since there hasn't been any action in a while, and the tools are a couple of versions ahead now which might have fixed the problem. Feel free to reopen if things aren't actually functioning.  Thanks!