ioerrors galore

bcbio.log

"""
Traceback (most recent call last):
  File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 22, in run
    _do_run(cmd, checks)
  File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 113, in _do_run
    raise subprocess.CalledProcessError(exitcode, error_msg)
CalledProcessError: Command '/usr/local/share/bcbio-nextgen/anaconda/bin/cutadapt --times=2 --quality-base=33 --quality-cutoff=20 --format=fastq --minimum-length=0 --output=/glusterfs/netapp/infvol/PORT
ERJAMESJ/brca/work/trim/tx/tmpCEp9YB/111101_UNC13-SN749_0133_BC04U8ABXX.5_2_trimmed.fastq /glusterfs/netapp/infvol/PORTERJAMESJ/brcafqs/111101_UNC13-SN749_0133_BC04U8ABXX.5_2.fastq
Traceback (most recent call last):
  File "/usr/local/share/bcbio-nextgen/anaconda/bin/cutadapt", line 10, in <module>
    cutadapt.main()
  File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/cutadapt/scripts/cutadapt.py", line 793, in main
    reader = read_sequences(input_filename, quality_filename, colorspace=options.colorspace, fileformat=options.format)
  File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/cutadapt/scripts/cutadapt.py", line 236, in read_sequences
    return seqio.SequenceReader(seqfilename, colorspace, fileformat)
  File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/cutadapt/seqio.py", line 162, in SequenceReader
    return fastq_reader(file)
  File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/cutadapt/seqio.py", line 298, in __init__
    file = xopen(file, "r")
  File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/cutadapt/xopen.py", line 63, in xopen
    return open(filename, mode)
' returned non-zero exit status 1
"""

or

"""
[2014-03-03 11:56] torque-node172-16-1-196: Unexpected error
Traceback (most recent call last):
  File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/distributed/ipythontasks.py", line 34, in _setup_logging
    yield None
  File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/distributed/ipythontasks.py", line 51, in trim_lane
    return apply(lane.trim_lane, *args)
  File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/pipeline/lane.py", line 75, in trim_lane
    out_files = trim_read_through(to_trim, dirs, config)
  File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/bam/trim.py", line 71, in trim_read_through
    fixed_files = remove_short_reads(out_files, dirs, lane_config)
  File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/bam/trim.py", line 89, in remove_short_reads
    out_files = fastq.filter_reads_by_length(fastq1, fastq2, quality_format, min_length)
  File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/bam/fastq.py", line 78, in filter_reads_by_length
    for fq1_record, fq2_record in izip(fq1_in, fq2_in):
  File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/Bio/SeqIO/__init__.py", line 582, in parse
    for r in i:
  File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/Bio/SeqIO/QualityIO.py", line 1033, in FastqPhredIterator
    for title_line, seq_string, quality_string in FastqGeneralIterator(handle):
  File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/Bio/SeqIO/QualityIO.py", line 953, in FastqGeneralIterator
    % (title_line, seq_len, len(quality_string)))
ValueError: Lengths of sequence and quality values differs  for UNC13-SN749:179:C0V5LACXX:1:1203:2885:192813 2:N:0:GGCTAC (48 and 16518).
"""

or

"""
[2014-03-04 06:02] torque-node172-16-1-86: Unexpected error
Traceback (most recent call last):
  File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/distributed/ipythontasks.py", line 34, in _setup_logging
    yield None
  File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/distributed/ipythontasks.py", line 51, in trim_lane
    return apply(lane.trim_lane, *args)
  File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/pipeline/lane.py", line 75, in trim_lane
    out_files = trim_read_through(to_trim, dirs, config)
  File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/bam/trim.py", line 71, in trim_read_through
    fixed_files = remove_short_reads(out_files, dirs, lane_config)
  File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/bam/trim.py", line 89, in remove_short_reads
    out_files = fastq.filter_reads_by_length(fastq1, fastq2, quality_format, min_length)
  File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/bam/fastq.py", line 78, in filter_reads_by_length
    for fq1_record, fq2_record in izip(fq1_in, fq2_in):
  File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/Bio/SeqIO/__init__.py", line 582, in parse
    for r in i:
  File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/Bio/SeqIO/QualityIO.py", line 1033, in FastqPhredIterator
    for title_line, seq_string, quality_string in FastqGeneralIterator(handle):
  File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/Bio/SeqIO/QualityIO.py", line 922, in FastqGeneralIterator
    raise ValueError("Sequence and quality captions differ.")
ValueError: Sequence and quality captions differ.
"""