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  • AsoBioInfo
    Member
    • Dec 2011
    • 37
    #1

    Cufflinks Error: "Segmentation Fault"

    Hello,

    I encountered an error while running Cufflinks,

    Processing bundle [ chr21:38067174-38362536 ] with 89 non-redundant alignments
    Warning: large bundle encountered...

    Processing bundle [ chr21:38408911-45747259 ] with 11249 non-redundant alignment s
    "Warning: nonsense gene merge, skipping

    Segmentation fault" and then it will terminate. I tried two times, it's the same.

    I have seen threads related to this error but unable to find a solution.

    The program will terminate. Maybe the alignment's number is big enough to handle. The problem is arising due to gtf file or .sam file? The error is related to memory (I think). If yes, how can I complete my command?

    Looking forward for your support!

    Thanks,
    Aso
    Tags: cufflinks, error, segmentation fault
  • bharati
    Member
    • Mar 2012
    • 38
    #2
    I got this error with cufflinks
    GffObj::getSpliced() error: improper genomic coordinate 19628622 on chrY for NR_028083

    Same error (with the same coordinates) was there for two different samples, is there any problem with gtf file which was parsed with cufflinks or something else?

    Please help me out I am stuck.

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