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  • tophat error

    Hi,

    when i am executing tophat like this:
    ./tophat -r 430 /mnt/FILE/zv9genome/zvgenome ../ex1/t_1 ../ex1/t_2

    i got this exception:

    [Sat Feb 4 18:00:11 2012] Beginning TopHat run (v1.4.0)
    -----------------------------------------------
    [Sat Feb 4 18:00:11 2012] Preparing output location ./tophat_out/
    [Sat Feb 4 18:00:11 2012] Checking for Bowtie index files
    [Sat Feb 4 18:00:11 2012] Checking for reference FASTA file
    [Sat Feb 4 18:00:11 2012] Checking for Bowtie
    Bowtie version: 0.12.7.0
    [Sat Feb 4 18:00:11 2012] Checking for Samtools
    Samtools Version: 0.1.18
    [Sat Feb 4 18:00:11 2012] Generating SAM header for /mnt/FILE/zv9genome/zvgenome
    format: fastq
    quality scale: phred33 (default)
    [Sat Feb 4 18:00:24 2012] Preparing reads
    left reads: min. length=101, count=5992
    right reads: min. length=101, count=5967
    [Sat Feb 4 18:00:24 2012] Mapping left_kept_reads against zvgenome with Bowtie

    gzip: stdout: Broken pipe
    [Sat Feb 4 18:00:27 2012] Processing bowtie hits

    Warning: junction database is empty!
    [Sat Feb 4 18:02:17 2012] Processing bowtie hits
    [FAILED]
    Error executing: /mnt/FILE/tophat-1.4.0.Linux_x86_64/bam_merge ./tophat_out/tmp/left_kept_reads.candidates_and_unspl.bam ./tophat_out/tmp/left_kept_reads.candidates.bam ./tophat_out/tmp/left_kept_reads.unspl.bam

    is the error result of the gzip broken pipe or from the junction database is empty?
    Do anyone know what is the gzip exception?

    Best,
    Pap

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