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  • usha
    Junior Member
    • Sep 2013
    • 1
    #1

    Error in htseq-count. Large gaps in CIGAR string

    Hi,

    I am getting this error when I run htseq-count (version 0.5.4p3)

    Error occured in line 6684695 of file OUT.gsnap.combined.Control_72_Rep3_R1.fastq.uniq.
    Error: value too large to convert to int
    [Exception type: OverflowError, raised in _HTSeq.pyx:1120]

    The corresponding line in the input file is

    HISEQ:488:C3W46ACXX:4:2111:4082:52860 83 Chr08 6311469 40 28S2M4294966387N45M25S = 63083
    37 -3002 GAAAATTGAGGATGACTTAGAGGTCTCAAGATCGGCAATGCATCTGGAAAGAAGTGGATATCAATGACTAATGAGGAGAAGGTTAAATACTAT
    GATATAG DDDC@CCA>3FFFFFFFHFHEHHEEEEHF;;--0/9AEJIIIIH@GDJHHGJJIIHGHCJHGIIIHFEHHHEHEHIHGIIHEIIJIHDHFFHFFFFF@@@MD:Z:4T42 NH:i:1 HI:i:1 NM:i:1 SM:i:40 XQ:i:40 X2:i:0 XO:Z:CU XS:A:+

    I noticed that there is a very large gap in the CIGAR string. I used GSNAP to generate the alignments.

    Has anyone encountered this before?

    Thanks for your help
    Tags: count, gsnap output, htseq
  • Brian Bushnell
    Super Moderator
    • Jan 2014
    • 2709
    #2
    Looks like a bug in gsnap; you should report it. Then remove that read.

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