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  • Cufflinks 2.0.2 segmentation fault on long fragments

    I have a systematic segmentation fault problem with cufflinks (v.2.0.2), which is independent of the dataset analyzed and caused by the input parameters --frag-len-mean (m) and --frag-len-mean (s), arguably because I've got unusual fragment mean length and SD.
    (This is not like the other cufflinks segmentation fault reported, which is at a different step in the run).

    The process stops when estimating frag length distribution, right after the "Inspecting bundle ..." output:
    Code:
    cufflinks -q -u -p 1 -m 800 -s 200 -g $GTF -M $MASK -b $GENOME.fa data.bam
    [10:14:40] Loading reference annotation.
    [10:14:43] Loading reference annotation.
    [10:14:43] Inspecting reads and determining fragment length distribution.
    Processed 189391 loci.
    > Map Properties:
    >       Normalized Map Mass: 52735571.57
    >       Raw Map Mass: 52735571.57
    Segmentation fault
    I've tried requesting lots of memory, but it didn't make a difference, and I also get the same result using cufflinks' test_data.sam with the S.cerevisiae genome, suggesting that insufficient memory is not the issue.
    Using another GTF or changing cufflinks version (I've tried the last three) also didn't make a difference.

    Any of the following changes independently allowed cufflinks to run smoothly:
    • using -G instead of -g AND not providing a genome (-b)
    • removing the -m and -s parameters
    • reducing -m and -s to something more "normal", like 500 and 100 respectively.


    Any help would be greatly appreciated,
    Pierre-Luc

  • #2
    Did you solve the problem? I have the same error as you, but occurring in the next step of "Inspecting reads and determining fragment length distribution."

    I found another post (http://seqanswers.com/forums/showthread.php?t=27951) where Anelda suggested to have the genome.fa and GTF in same order of chromosome. I'll like to try it.

    Comment


    • #3
      No, I couldn't solve it other than by making the changes I mention in the post.
      In my case at least it was not a matter of sorting.

      Comment


      • #4
        Originally posted by plger View Post
        No, I couldn't solve it other than by making the changes I mention in the post.
        In my case at least it was not a matter of sorting.
        What do you mean specifically when you say 'sorting'?

        Comment

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