Sudden crash during runtime

[GoogleCodeExporter]

What steps will reproduce the problem?
1. Run analysis using version "0.5.0" from the SVN repo; pysam version "0.7.5"
2. Use default settings and "-p 4" on a 16 core machine

What is the expected output? What do you see instead?
Expected: results, instead: an error message in realigned_reads.log:

Traceback (most recent call last):
  File "/usr/local/lib/python2.7/dist-packages/chimerascan/pipeline/sam_to_bam_pesr.py", line 68, in <module>
    sys.exit(main())
  File "/usr/local/lib/python2.7/dist-packages/chimerascan/pipeline/sam_to_bam_pesr.py", line 65, in main
    return sam_to_bam_pesr(args.input_sam_file, args.input_fastq_file, args.output_bam_file)
  File "/usr/local/lib/python2.7/dist-packages/chimerascan/pipeline/sam_to_bam_pesr.py", line 34, in sam_to_bam_pesr
    assert r.qname == fqrec.qname
AssertionError
Error while flushing and closing output
terminate called after throwing an instance of 'int'


What version of the product are you using? On what operating system?
* chimerascan "0.5.0" (from SVN repo)
* pysam "0.7.5" (from tar.gz source)
* Debian, saucy

Please provide any additional information below.
The tool was running for quite some time:

Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
2013-11-04 15:53:41,981 - root - DEBUG - Reading transcript features
2013-11-04 15:53:42,861 - root - DEBUG - Creating genome SAM header
2013-11-04 15:53:45,063 - root - DEBUG - Creating transcript to genome map
2013-11-04 15:53:45,363 - root - DEBUG - Converting transcriptome to genome BAM
61460496 reads; of these:
  61460496 (100.00%) were paired; of these:
    21692002 (35.29%) aligned concordantly 0 times
    20838036 (33.90%) aligned concordantly exactly 1 time
    18930458 (30.80%) aligned concordantly >1 times
64.71% overall alignment rate
2013-11-04 22:07:04,670 - root - DEBUG - Paired fragments: 39768494
2013-11-04 22:07:04,748 - root - DEBUG - Unpaired fragments: 21692002
2013-11-04 22:07:04,758 - root - DEBUG - Found 122920992 fragments



I hope you can fix this issue; it occurs in all my samples.

Best regards,

Youri

Original issue reported on code.google.com by y.hoogst...@gmail.com on 5 Nov 2013 at 8:47