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  • Bowtie2 - segmentation fault due to --sam-RG

    Hi,
    Just tried to move my stuff to a new machine with Ubuntu 11.10 (not sure if that is the problem here) with no donut. I cannot add any --sam-RG since it causes "seg fault". Anyone had similar problem ?

    issue #2, tried to run it without any RG header and got this:

    Only read 402653184 bytes (out of 715335926) from reference index file hg19.4.bt2
    Error: Encountered internal Bowtie 2 exception (#1)


    truncated index ?

    Its being run on i7 machine with 6gb (4+2). Bowtie1 works just fine.

    I hope that someone can help....
    Last edited by memento; 02-02-2012, 05:34 AM.

  • #2
    See this:
    http://sourceforge.net/projects/bowt.../topic/4882702

    Comment


    • #3
      Thanks a lot! So basically, bowtie2 is not usable if one wants to use it with picard/GATK down the line....

      Comment


      • #4
        So basically, bowtie2 is not usable if one wants to use it with picard/GATK down the line....
        If you don't want to wait for the next beta, you can always download the trunk / development version, or modify the SAM headers using a few different tools (presumably including Picard), or use a script and/or text editor to edit the SAM headers in a more direct fashion.

        Yay for FOSS and plain-text file formats.

        Comment

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