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tophat Error running running 'prep_reads'

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  • tophat Error running running 'prep_reads'

    Hi, Naive here, i'm getting an error from tophat with mac os x 10.6


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    tophat -o /tophatoutput/ --solexa1.3-quals /bowtie-0-1.12.7/indexes/mm9 a.fastq

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    [Wed Oct 12 13:31:31 2011] Beginning TopHat run (v1.3.2)
    -----------------------------------------------
    [Wed Oct 12 13:31:31 2011] Preparing output location /tophatoutput/
    [Wed Oct 12 13:31:31 2011] Checking for Bowtie index files
    [Wed Oct 12 13:31:31 2011] Checking for reference FASTA file
    Warning: Could not find FASTA file /bowtie-0-1.12.7/indexes/mm9.fa
    [Wed Oct 12 13:31:31 2011] Reconstituting reference FASTA file from Bowtie index
    Executing: /bowtie-0-1.12.7/indexes/mm9 > /tmp/mm9.fa
    [Wed Oct 12 13:34:42 2011] Checking for Bowtie
    Bowtie version: 0.12.7.0
    [Wed Oct 12 13:34:42 2011] Checking for Samtools
    Samtools Version: 0.1.18
    [Wed Oct 12 13:34:42 2011] Generating SAM header for /bowtie-0-1.12.7/indexes/mm9
    [Wed Oct 12 13:35:36 2011] Preparing reads
    format: fastq
    quality scale: phred64 (reads generated with GA pipeline version >= 1.3)
    [FAILED]
    Error running 'prep_reads'
    terminate called after throwing an instance of 'int'

    -------

    i have never seen such an error before, something wrong on command line?
    Last edited by victoryhe; 10-12-2011, 10:22 AM.

  • #2
    quality scale: phred64 (reads generated with GA pipeline version >= 1.3)
    FAILED

    Here lies the problem. Are you sure --solexa1.3-quals is right? Could you paste here a complete fastq read (header + read + quality)?

    Comment


    • #3
      thanks! without the solexa option, it works.

      Comment

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