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  • cufflinks-0.9.1 Hangs

    Hi All,

    Using the new verison of TopHat, then the new version of Cufflinks here..

    The program stalls/hangs at 13% complete- multiple times now..

    The command:

    Code:
    /home/macmanes/cufflinks-0.9.1/cufflinks -N -r /media/hd_/tophat-1.1/social/tophat_out/tucomrna.fa --num-importance-samples 5000 --max-mle-iterations 20000 -p 15 /media/hd_/tophat-1.1/solitary/tophat_out/accepted_hits.bam
    Screen output:

    Code:
    [20:13:29] Inspecting reads and determining fragment length distribution.
    > Processing Locus 253055:2-223                [***                      ]  13%
    Any idea why it is hanging? Sat like this (13%) for 12 hours today..

  • #2
    Would you be willing to make this dataset available so I could try to find out what's happening?

    -Adam
    [email protected]

    Comment


    • #3
      Was there a solution to this?
      I ran cufflinks 0.9.3 yesterday and although it says 100%, cufflinks still seems to be running:
      Code:
      [16:08:03] Assembling transcripts and estimating abundances.
      > Processing Locus X:124110855-124110905     [*************************] 100%
      Thanks in advance for any suggestions.

      Comment


      • #4
        The SAM file is 21G

        Comment


        • #5
          @joro,

          Can you try running with verbose processing (-v) and post the last few lines before it hangs?

          Comment

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