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  • yet another "Error: segment-based junction search failed with err = -9"

    I have run into the same problem that are few people have encountered before when I am using TopHat to align 7 lanes of Illumina data to hg19. Since I am relatively new to tophat, can somebody give me a hint? Thanks!

    here are the screen output and segment_juncs.log:

    Code:
    [Fri Aug 20 14:58:12 2010] Beginning TopHat run (v1.0.13)
    -----------------------------------------------
    [Fri Aug 20 14:58:12 2010] Preparing output location /home/haiti/tmpdata/all_brn/tophat/
    [Fri Aug 20 14:58:12 2010] Checking for Bowtie index files
    [Fri Aug 20 14:58:12 2010] Checking for reference FASTA file
    [Fri Aug 20 14:58:12 2010] Checking for Bowtie
            Bowtie version:          0.12.5.0
    [Fri Aug 20 14:58:12 2010] Checking reads
            seed length:     35bp
            format:          fastq
            quality scale:   phred33 (default)
    [Fri Aug 20 15:31:58 2010] Reading known junctions from GFF file
            Warning: TopHat did not find any junctions in GFF file
    [Fri Aug 20 15:53:49 2010] Mapping reads against hg19 with Bowtie
    [Sat Aug 21 00:52:55 2010] Joining segment hits
    [Sat Aug 21 01:22:40 2010] Searching for junctions via segment mapping
            [FAILED]
    Error: segment-based junction search failed with err = -9
    segment_juncs.log
    Code:
    segment_juncs v1.0.13
    ---------------------------
    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
    Found 0 potential split-segment junctions
    Indexing extensions in /home/haiti/tmpdata/all_brn/tophat/tmp//left_kept_reads_missing.fq
    Total extensions: 637479408
    Looking for junctions by island end pairings
    Adding hits from segment file 0 to coverage map
    Map covers 325972654 bases
    Map covers 320327918 bases in sufficiently long segments
    Map contains 5580241 good islands
    276495363 are left looking bases
    276492492 are right looking bases
    Collecting potential splice sites in islands
    Last edited by liux; 08-24-2010, 09:51 AM. Reason: clarify

  • #2
    However, when I run lanes individually, no problems were reported at all.

    Anyone know the cause of the error?

    right now, I am align lanes individually, and plan to merge, sort and index them once all alignments are done. does this route have any potential problem?

    Thanks!

    Comment

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