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  • tophat segment-search failed with err=-11 segmentation fault

    Hello all.

    I am using tophat 2.0.6 to map pair end reads of 60 bp length. The command is:

    tophat -p 8 -r 240 -G ~/index/hg19.knownGene.gtf --transcriptome-index=~/index/hg19.knownGene -o tophat_out ~/ucsc/hg19 hm_1.fastq hm_2.fastq

    However, the job failed and printed the following error:


    segment_juncs v2.0.6 (3670M)
    ---------------------------
    [samopen] SAM header is present: 84 sequences.
    Loading reference sequences...
    Loading chr1...done
    Loading chr2...done
    Loading chr3...done
    Loading chr4...done
    Loading chr5...done
    Loading chr6...done
    Loading chr7...done
    Loading chr8...done
    Loading chr9...done
    Loading chr10...done
    Loading chr11...done
    Loading chr12...done
    Loading chr13...done
    Loading chr14...done
    Loading chr15...done
    Loading chr16...done
    Loading chr17...done
    Loading chr18...done
    Loading chr19...done
    Loading chr20...done
    Loading chr21...done
    Loading chr22...done
    Loading chrX...done
    Loading chrY...done
    Loading chrM...done
    Loading ...done
    >> Performing segment-search:
    Loading left segment hits...
    Segmentation fault (core dumped)

    I googled but could not find any help.


    Any ideas on how to solve this?

    Thanks,

    Alex
    Last edited by webappl; 12-13-2012, 06:03 AM.

  • #2
    I found out that the problem was caused by using a wrong reference genome sequence file.

    Comment

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