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  • TopHat Error: Splice sequence indexing failed with err =255

    I run tophat-2.0.5.Linux_x86_64 on real and test_ref data and get the same error:

    $ tophat -r 20 test_ref reads_1.fq reads_2.fq
    [2012-09-24 16:15:37] Beginning TopHat run (v2.0.5)
    -----------------------------------------------
    [2012-09-24 16:15:37] Checking for Bowtie
    Bowtie 2 not found, checking for older version..
    Bowtie version: 0.12.7.0
    [2012-09-24 16:15:37] Checking for Samtools
    Samtools version: 0.1.18.0
    [2012-09-24 16:15:37] Checking for Bowtie index files
    [2012-09-24 16:15:37] Checking for reference FASTA file
    [2012-09-24 16:15:37] Generating SAM header for test_ref
    format: fastq
    quality scale: phred33 (default)
    [2012-09-24 16:15:39] Preparing reads
    left reads: min. length=75, max. length=75, 100 kept reads (0 discarded)
    right reads: min. length=75, max. length=75, 100 kept reads (0 discarded)
    [2012-09-24 16:15:39] Mapping left_kept_reads to genome test_ref with Bowtie
    [2012-09-24 16:15:40] Mapping left_kept_reads_seg1 to genome test_ref with Bowtie (1/3)
    [2012-09-24 16:15:40] Mapping left_kept_reads_seg2 to genome test_ref with Bowtie (2/3)
    [2012-09-24 16:15:40] Mapping left_kept_reads_seg3 to genome test_ref with Bowtie (3/3)
    [2012-09-24 16:15:40] Mapping right_kept_reads to genome test_ref with Bowtie
    [2012-09-24 16:15:41] Mapping right_kept_reads_seg1 to genome test_ref with Bowtie (1/3)
    [2012-09-24 16:15:41] Mapping right_kept_reads_seg2 to genome test_ref with Bowtie (2/3)
    [2012-09-24 16:15:41] Mapping right_kept_reads_seg3 to genome test_ref with Bowtie (3/3)
    [2012-09-24 16:15:41] Searching for junctions via segment mapping
    [2012-09-24 16:15:42] Retrieving sequences for splices
    [2012-09-24 16:15:42] Indexing splices
    [FAILED]
    Error: Splice sequence indexing failed with err =255

    What do I miss?

  • #2
    OK. I found that the last version of Bowtie (0.12.8.0) does not show this error.
    So it looks like it's a bug in the old version of Bowtie (0.12.7.0).

    Comment

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