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  • tophat 1.3.0(Beta) closure search failed

    I tried to run tophat 1.3.0(Beta) with 90*2 illumina RNA-seq

    tophat -o tophat-output -F 0.1 -p 6 -r 10 --mate-std-dev 45 --solexa1.3-quals --library-type fr-firststrand -i 30 --min-closure-intron 30

    --min-coverage-intron 30 --closure-search --coverage-search --segment-length 30 ref polyA.1.fq polyA.2.fq


    The same data and parameters worked well with tophat 1.2.0


    [Tue Jun 7 01:43:17 2011] Beginning TopHat run (v1.3.0)
    -----------------------------------------------
    [Tue Jun 7 01:43:17 2011] Preparing output location tophat-output/
    [Tue Jun 7 01:43:17 2011] Checking for Bowtie index files
    [Tue Jun 7 01:43:17 2011] Checking for reference FASTA file
    [Tue Jun 7 01:43:17 2011] Checking for Bowtie
    Bowtie version: 0.12.7.0
    [Tue Jun 7 01:43:17 2011] Checking for Samtools
    Samtools Version: 0.1.12
    [Tue Jun 7 01:43:17 2011] Generating SAM header for ref
    [Tue Jun 7 01:43:17 2011] Preparing reads
    format: fastq
    quality scale: phred64 (reads generated with GA pipeline version >= 1.3)
    Left reads: min. length=90, count=11331560
    Right reads: min. length=90, count=11332998
    [Tue Jun 7 01:59:21 2011] Mapping left_kept_reads against ref with Bowtie
    [Tue Jun 7 02:08:18 2011] Processing bowtie hits
    [Tue Jun 7 02:19:24 2011] Mapping left_kept_reads_seg1 against ref with Bowtie (1/3)
    [Tue Jun 7 02:21:27 2011] Mapping left_kept_reads_seg2 against ref with Bowtie (2/3)
    [Tue Jun 7 02:23:34 2011] Mapping left_kept_reads_seg3 against ref with Bowtie (3/3)
    [Tue Jun 7 02:25:36 2011] Mapping right_kept_reads against ref with Bowtie
    [Tue Jun 7 02:34:46 2011] Processing bowtie hits
    [Tue Jun 7 02:45:21 2011] Mapping right_kept_reads_seg1 against ref with Bowtie (1/3)
    [Tue Jun 7 02:47:13 2011] Mapping right_kept_reads_seg2 against ref with Bowtie (2/3)
    [Tue Jun 7 02:49:07 2011] Mapping right_kept_reads_seg3 against ref with Bowtie (3/3)
    [Tue Jun 7 02:51:00 2011] Searching for junctions via segment mapping
    [Tue Jun 7 03:02:19 2011] Searching for junctions via mate-pair closures
    [FAILED]
    Error: closure-based junction search failed with err =-11

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