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  • ruggedtextile
    Member
    • Nov 2011
    • 18
    #1

    bcl2fastq 2.0 barcode mismatch option

    I'm trying to run bcl2fastq with the barcode-mismatch option set to 3. Unfortunately setting this option to anything other than the default seems to result in runaway memory usage (fills and eventually kills a 128GB machine). Is this a known bug? The version I am using is:

    BCL to FASTQ file converter
    bcl2fastq v02.14.01.07
    Copyright (c) 2007-2013 Illumina, Inc.
    Tags: None
  • IsmailM
    Junior Member
    • Apr 2013
    • 7
    #2
    BCL to FASTQ file converter
    bcl2fastq v02.14.01.07
    Copyright (c) 2007-2013 Illumina, Inc.

    This version has so many bugs in it. You should just upgrade to their new version 2.15. Also, which is kind of lame of illumina, but they will not support version 2.14.

    3 mismatches? That's a lot of mismatches in at most a 8 barcode sequence.

    Comment

    • ruggedtextile
      Member
      • Nov 2011
      • 18
      #3
      Yes, I upgraded. 2.14 was a car crash bug-wise.

      Re: 3 mismatches - yes the experiment was a bit of a car crash as well (over clustered), just trying to see what we can salvage.

      Comment

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