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  • Cufflinks stuck at assembling transcript and initializong abundances step

    Dear authors of cufflinks,

    I have many samples that gives me headache. I have paired end RNAseq data that were generated by Illumina Hiseq 2000. I hard trim the reads at Q score of 30 (~75bp). Tophat runs fine and I get about ~15G bam file. When I feed this file to Cufflinks cufflinks gets stuck in the middle. When I examine the standard error output the message is as follows.

    [08:47:58] Assembling transcripts and initializing abundances for multi-read correction.
    > Processing Locus chr14:50319624-50319752 [***** ] 23%

    When I monitor the process it shows that cufflinks is running.
    I have multiple files like this that seem to be stuck at random chromosomal places
    Anyone had similar experiences? and any solutions?
    What would cause this problem?
    Any way to get around this problem?
    Thank you very much.
    Last edited by Him26; 10-05-2012, 03:12 PM.

  • #2
    I'm having the same problem now, did you ever find a solution?

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