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  • seq_newbie
    Member
    • Jun 2011
    • 14

    #1

    cufflinks segmentation fault help please

    Hi,

    I get the output below when I run cufflinks using the command

    cufflinks -g /data/shared/genomes/Btau_4.0/Bos_taurus.Btau_4.0.62.gtf --frag-len-mean 201 --frag-len-std-dev 81 accepted_hits.bam

    I've tried -G and without any annotation file and I've also tried leaving it to use default frag-len-mean/std-dev values but it's the same each time and no output files are generated. Any help would be appreciated.

    Regards,

    K.

    here's the output

    cufflinks: /lib64/libz.so.1: no version information available (required by cufflinks)
    Warning: Could not connect to update server to verify current version. Please check at the Cufflinks website (http://cufflinks.cbcb.umd.edu).
    [17:24:11] Loading reference annotation.
    [17:24:14] Inspecting reads and determining fragment length distribution.
    > Processed 271810 loci. [*************************] 100%
    > Map Properties:
    > Total Map Mass: 12341530.00
    > Read Type: 36bp single-end
    > Fragment Length Distribution: Truncated Gaussian (user-specified)
    > Default Mean: 201
    > Default Std Dev: 81
    Segmentation fault
  • sunkorner
    Member
    • Jan 2011
    • 15

    #2
    This error could be due to insufficient memory

    Comment

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