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  • tophat error = -9?

    I ran tophat on some data yesterday, and got the following (error at bottom):


    matt@matt-desktop:~/Desktop/data/bowtie_trim_final$ tophat -o bowtiecap01 -r 100 --solexa1.3-quals -p4 mm9 s_5_1_sequence.txt s_5_2_sequence.txt

    [Fri Jun 25 09:14:19 2010] Beginning TopHat run (v1.0.11)
    -----------------------------------------------
    [Fri Jun 25 09:14:19 2010] Preparing output location bowtiecap01/
    [Fri Jun 25 09:14:19 2010] Checking for Bowtie index files
    [Fri Jun 25 09:14:19 2010] Checking for reference FASTA file
    Warning: Could not find FASTA file mm9.fa
    [Fri Jun 25 09:14:19 2010] Reconstituting reference FASTA file from Bowtie index
    [Fri Jun 25 09:30:53 2010] Checking for Bowtie
    Bowtie version: 0.12.5.0
    [Fri Jun 25 09:30:53 2010] Checking reads
    seed length: 27bp
    format: fastq
    quality scale: --solexa1.3-quals
    [Fri Jun 25 09:39:59 2010] Mapping reads against mm9 with Bowtie
    [Fri Jun 25 11:01:37 2010] Joining segment hits
    [Fri Jun 25 11:09:04 2010] Mapping reads against mm9 with Bowtie
    [Fri Jun 25 12:31:23 2010] Joining segment hits
    [Fri Jun 25 12:38:49 2010] Searching for junctions via segment mapping
    [Fri Jun 25 13:02:31 2010] Retrieving sequences for splices
    [Fri Jun 25 13:04:11 2010] Indexing splices
    [Fri Jun 25 13:06:23 2010] Mapping reads against segment_juncs with Bowtie
    [Fri Jun 25 13:23:43 2010] Joining segment hits
    [Fri Jun 25 13:31:33 2010] Mapping reads against segment_juncs with Bowtie
    [Fri Jun 25 13:50:14 2010] Joining segment hits
    [Fri Jun 25 13:58:13 2010] Reporting output tracks
    [FAILED]
    Error: Report generation failed with err = -9

    matt@matt-desktop:~/Desktop/data/bowtie_trim_final$

    I saw another thread about this error, with the suggestion that the fasta file was bad, but this file is being reconstituted during the analysis. Is this actually a problem? or is there something else wrong here?

    Thanks for any help,

    Matt

  • #2
    Too many reads

    Hi,

    I had the same problem. I have splitted my reads and then it worked !
    I first had more than 400 millions 50 bp reads, It worked with 1/5. I didn't try other split size.

    Martin

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