20180202_errorlog

20180202_errorlog

[2018-02-02T09:01Z] System YAML configuration: /mnt/nfsfile/NAS6/zhenghank/bin/bcbio/galaxy/bcbio_system.yaml
[2018-02-02T09:01Z] Resource requests: bwa, sambamba, samtools; memory: 3.00, 3.00, 3.00; cores: 16, 16, 16
[2018-02-02T09:01Z] Configuring 1 jobs to run, using 10 cores each with 30.1g of memory reserved for each job
[2018-02-02T09:01Z] Timing: organize samples
[2018-02-02T09:01Z] multiprocessing: organize_samples
[2018-02-02T09:01Z] Using input YAML configuration: /mnt/nfsfile/yourgene-academic-workspace-pool2/zhenghank/All_projects/OD20171203-CLA252/bcbio_test/OD20171203-merged/config/OD20171203-merged.yaml
[2018-02-02T09:01Z] Checking sample YAML configuration: /mnt/nfsfile/yourgene-academic-workspace-pool2/zhenghank/All_projects/OD20171203-CLA252/bcbio_test/OD20171203-merged/config/OD20171203-merged.yaml
[2018-02-02T09:01Z] Testing minimum versions of installed programs
[2018-02-02T09:01Z] Timing: alignment preparation
[2018-02-02T09:01Z] multiprocessing: prep_align_inputs
[2018-02-02T09:01Z] Skipping trimming of T-LA-F03_S17_PE_cutadapt_QC.
[2018-02-02T09:01Z] Resource requests: ; memory: 1.00; cores: 1
[2018-02-02T09:01Z] Configuring 2 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2018-02-02T09:01Z] multiprocessing: disambiguate_split
[2018-02-02T09:01Z] Timing: alignment
[2018-02-02T09:01Z] multiprocessing: process_alignment
[2018-02-02T09:01Z] Aligning lane T-LA-F03_S17_PE_cutadapt_QC with bwa aligner
[2018-02-02T09:01Z] Timing: callable regions
[2018-02-02T09:01Z] multiprocessing: prep_samples
[2018-02-02T09:01Z] multiprocessing: postprocess_alignment
[2018-02-02T09:01Z] T-LA-F03_S17_PE_cutadapt_QC: Assigned coverage as 'genome' with 91.8% genome coverage and 0.0% offtarget coverage
[2018-02-02T09:01Z] multiprocessing: combine_sample_regions
[2018-02-02T09:01Z] Identified 64 parallel analysis blocks
Block sizes:
  min: 17683
  5%: 17990.95
  25%: 29205.25
  median: 40849.5
  75%: 58494.75
  95%: 145777.9
  99%: 170117.39
  max: 176321
Between block sizes:
  min: 271
  5%: 276.7
  25%: 387.5
  median: 1131.0
  75%: 2508.5
  95%: 6215.0
  99%: 9608.08
  max: 13555

[2018-02-02T09:01Z] multiprocessing: calculate_sv_bins
[2018-02-02T09:01Z] CNVkit target
[2018-02-02T09:01Z] Traceback (most recent call last):
[2018-02-02T09:01Z]   File "/mnt/nfsfile/NAS6/zhenghank/bin/bcbio/anaconda/bin/cnvkit.py", line 13, in <module>
[2018-02-02T09:01Z]     args.func(args)
[2018-02-02T09:01Z]   File "/home/zhenghank/zhenghank/bin/bcbio/anaconda/lib/python2.7/site-packages/cnvlib/commands.py", line 229, in _cmd_target
[2018-02-02T09:01Z]     regions = tabio.read_auto(args.interval)
[2018-02-02T09:01Z]   File "/home/zhenghank/zhenghank/bin/bcbio/anaconda/lib/python2.7/site-packages/skgenome/tabio/__init__.py", line 108, in read_auto
[2018-02-02T09:01Z]     fmt = sniff_region_format(infile)
[2018-02-02T09:01Z]   File "/home/zhenghank/zhenghank/bin/bcbio/anaconda/lib/python2.7/site-packages/skgenome/tabio/__init__.py", line 253, in sniff_region_format
[2018-02-02T09:01Z]     % (fname, ', '.join(format_patterns.keys()), line))
[2018-02-02T09:01Z] ValueError: File '/mnt/nfsfile/yourgene-academic-workspace-pool2/zhenghank/All_projects/OD20171203-CLA252/bcbio_test/OD20171203-merged/work/bedprep/T-LA-F03_S17_PE_cutadapt_QC-variant_regions.quantized-vrsubset-callableblocks.bed' does not appear to be a recognized format! (Any of: text, tab, interval, refflat, gff, bed)
[2018-02-02T09:01Z] First non-blank line:
[2018-02-02T09:01Z] NZ_CP022130.1	0	62322
[2018-02-02T09:01Z] Uncaught exception occurred
Traceback (most recent call last):
  File "/home/zhenghank/zhenghank/bin/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 23, in run
    _do_run(cmd, checks, log_stdout, env=env)
  File "/home/zhenghank/zhenghank/bin/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 103, in _do_run
    raise subprocess.CalledProcessError(exitcode, error_msg)
CalledProcessError: Command 'set -o pipefail; export TMPDIR=/mnt/nfsfile/yourgene-academic-workspace-pool2/zhenghank/All_projects/OD20171203-CLA252/bcbio_test/OD20171203-merged/work/bcbiotx/tmpO5V7Zb && /mnt/nfsfile/NAS6/zhenghank/bin/bcbio/anaconda/bin/cnvkit.py target /mnt/nfsfile/yourgene-academic-workspace-pool2/zhenghank/All_projects/OD20171203-CLA252/bcbio_test/OD20171203-merged/work/bedprep/T-LA-F03_S17_PE_cutadapt_QC-variant_regions.quantized-vrsubset-callableblocks.bed --split -o /mnt/nfsfile/yourgene-academic-workspace-pool2/zhenghank/All_projects/OD20171203-CLA252/bcbio_test/OD20171203-merged/work/bcbiotx/tmpO5V7Zb/T-LA-F03_S17_PE_cutadapt_QC-target.bed --avg-size 250
Traceback (most recent call last):
  File "/mnt/nfsfile/NAS6/zhenghank/bin/bcbio/anaconda/bin/cnvkit.py", line 13, in <module>
    args.func(args)
  File "/home/zhenghank/zhenghank/bin/bcbio/anaconda/lib/python2.7/site-packages/cnvlib/commands.py", line 229, in _cmd_target
    regions = tabio.read_auto(args.interval)
  File "/home/zhenghank/zhenghank/bin/bcbio/anaconda/lib/python2.7/site-packages/skgenome/tabio/__init__.py", line 108, in read_auto
    fmt = sniff_region_format(infile)
  File "/home/zhenghank/zhenghank/bin/bcbio/anaconda/lib/python2.7/site-packages/skgenome/tabio/__init__.py", line 253, in sniff_region_format
    % (fname, ', '.join(format_patterns.keys()), line))
ValueError: File '/mnt/nfsfile/yourgene-academic-workspace-pool2/zhenghank/All_projects/OD20171203-CLA252/bcbio_test/OD20171203-merged/work/bedprep/T-LA-F03_S17_PE_cutadapt_QC-variant_regions.quantized-vrsubset-callableblocks.bed' does not appear to be a recognized format! (Any of: text, tab, interval, refflat, gff, bed)
First non-blank line:
NZ_CP022130.1	0	62322
' returned non-zero exit status 1
Traceback (most recent call last):
  File "/home/zhenghank/zhenghank/bin/bcbio/tools/bin/bcbio_nextgen.py", line 241, in <module>
    main(**kwargs)
  File "/home/zhenghank/zhenghank/bin/bcbio/tools/bin/bcbio_nextgen.py", line 46, in main
    run_main(**kwargs)
  File "/home/zhenghank/zhenghank/bin/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 43, in run_main
    fc_dir, run_info_yaml)
  File "/home/zhenghank/zhenghank/bin/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 87, in _run_toplevel
    for xs in pipeline(config, run_info_yaml, parallel, dirs, samples):
  File "/home/zhenghank/zhenghank/bin/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 132, in variant2pipeline
    samples = run_parallel("calculate_sv_bins", [samples])
  File "/home/zhenghank/zhenghank/bin/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 "/home/zhenghank/zhenghank/bin/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 86, in run_multicore
    for data in joblib.Parallel(parallel["num_jobs"], batch_size=1)(joblib.delayed(fn)(x) for x in items):
  File "/home/zhenghank/zhenghank/bin/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 804, in __call__
    while self.dispatch_one_batch(iterator):
  File "/home/zhenghank/zhenghank/bin/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 662, in dispatch_one_batch
    self._dispatch(tasks)
  File "/home/zhenghank/zhenghank/bin/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 570, in _dispatch
    job = ImmediateComputeBatch(batch)
  File "/home/zhenghank/zhenghank/bin/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 183, in __init__
    self.results = batch()
  File "/home/zhenghank/zhenghank/bin/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 72, in __call__
    return [func(*args, **kwargs) for func, args, kwargs in self.items]
  File "/home/zhenghank/zhenghank/bin/bcbio/anaconda/lib/python2.7/site-packages/bcbio/utils.py", line 52, in wrapper
    return apply(f, *args, **kwargs)
  File "/home/zhenghank/zhenghank/bin/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multitasks.py", line 291, in calculate_sv_bins
    return svregions.calculate_sv_bins(*args)
  File "/home/zhenghank/zhenghank/bin/bcbio/anaconda/lib/python2.7/site-packages/bcbio/structural/regions.py", line 45, in calculate_sv_bins
    cnv_group.work_dir, data)
  File "/home/zhenghank/zhenghank/bin/bcbio/anaconda/lib/python2.7/site-packages/bcbio/structural/cnvkit.py", line 427, in targets_w_bins
    do.run(_prep_cmd(cmd, tx_out_file), "CNVkit target")
  File "/home/zhenghank/zhenghank/bin/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 23, in run
    _do_run(cmd, checks, log_stdout, env=env)
  File "/home/zhenghank/zhenghank/bin/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 103, in _do_run
    raise subprocess.CalledProcessError(exitcode, error_msg)
subprocess.CalledProcessError: Command 'set -o pipefail; export TMPDIR=/mnt/nfsfile/yourgene-academic-workspace-pool2/zhenghank/All_projects/OD20171203-CLA252/bcbio_test/OD20171203-merged/work/bcbiotx/tmpO5V7Zb && /mnt/nfsfile/NAS6/zhenghank/bin/bcbio/anaconda/bin/cnvkit.py target /mnt/nfsfile/yourgene-academic-workspace-pool2/zhenghank/All_projects/OD20171203-CLA252/bcbio_test/OD20171203-merged/work/bedprep/T-LA-F03_S17_PE_cutadapt_QC-variant_regions.quantized-vrsubset-callableblocks.bed --split -o /mnt/nfsfile/yourgene-academic-workspace-pool2/zhenghank/All_projects/OD20171203-CLA252/bcbio_test/OD20171203-merged/work/bcbiotx/tmpO5V7Zb/T-LA-F03_S17_PE_cutadapt_QC-target.bed --avg-size 250
Traceback (most recent call last):
  File "/mnt/nfsfile/NAS6/zhenghank/bin/bcbio/anaconda/bin/cnvkit.py", line 13, in <module>
    args.func(args)
  File "/home/zhenghank/zhenghank/bin/bcbio/anaconda/lib/python2.7/site-packages/cnvlib/commands.py", line 229, in _cmd_target
    regions = tabio.read_auto(args.interval)
  File "/home/zhenghank/zhenghank/bin/bcbio/anaconda/lib/python2.7/site-packages/skgenome/tabio/__init__.py", line 108, in read_auto
    fmt = sniff_region_format(infile)
  File "/home/zhenghank/zhenghank/bin/bcbio/anaconda/lib/python2.7/site-packages/skgenome/tabio/__init__.py", line 253, in sniff_region_format
    % (fname, ', '.join(format_patterns.keys()), line))
ValueError: File '/mnt/nfsfile/yourgene-academic-workspace-pool2/zhenghank/All_projects/OD20171203-CLA252/bcbio_test/OD20171203-merged/work/bedprep/T-LA-F03_S17_PE_cutadapt_QC-variant_regions.quantized-vrsubset-callableblocks.bed' does not appear to be a recognized format! (Any of: text, tab, interval, refflat, gff, bed)
First non-blank line:
NZ_CP022130.1	0	62322
' returned non-zero exit status 1