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tophat error: Report generation failed with err = -11

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  • tophat error: Report generation failed with err = -11

    I hope someone can advise or assist me with a tophat error. terminal output is below. error is:

    Report generation failed with err = -11

    I'm just starting to work with tophat. Ran it once on a single set of paired-end seqs and it finished OK. But then I got greedy and gave it 28 different sets of reads. Note that because of multiplexing samples this was not totally insane (I think) -- only 2 x 5.7e7 reads.

    My current analysis goal is to use these data to generate a Cufflinks annotation for a novel butterfly genome. samples are from different individuals and tissues.

    working on a linux cluster with 3TB diskspace and should have plenty of RAM/processors.

    Current plan is to rerun with more modest allowance of datasets to see what happens, and/or on offending dataset (if I can fish out that detail from logs -- suggestions on that front welcome as well...)

    Many Thanks, Jamie



    _______________________________________

    nice tophat -r 0 -i 20 -I 30000 -p 6 -g 20 --closure-search --min-closure-exon 20 --min-closure-intron 20 --min-coverage-intron 20 --min-segment-intron 20 --max-segment-intron 30000 indexes/melpomene



    [Wed Feb 9 16:58:56 2011] Beginning TopHat run (v1.2.0)
    -----------------------------------------------
    [Wed Feb 9 16:58:56 2011] Preparing output location edinburg_tophat_out/
    [Wed Feb 9 16:58:56 2011] Checking for Bowtie index files
    [Wed Feb 9 16:58:56 2011] Checking for reference FASTA file
    [Wed Feb 9 16:58:56 2011] Checking for Bowtie
    Bowtie version: 0.12.7.0
    [Wed Feb 9 16:58:56 2011] Checking for Samtools
    Samtools Version: 0.1.8
    [Wed Feb 9 16:58:57 2011] Checking reads
    min read length: 50bp, max read length: 54bp
    format: fastq
    quality scale: phred33 (default)
    [Wed Feb 9 17:54:48 2011] Mapping reads against melpomene with Bowtie
    [Wed Feb 9 18:16:40 2011] Joining segment hits
    [Wed Feb 9 18:33:04 2011] Mapping reads against melpomene with Bowtie(1/2)
    [Wed Feb 9 18:46:50 2011] Mapping reads against melpomene with Bowtie(2/2)
    [Wed Feb 9 18:59:05 2011] Mapping reads against melpomene with Bowtie
    [Wed Feb 9 19:25:20 2011] Joining segment hits
    [Wed Feb 9 19:42:15 2011] Mapping reads against melpomene with Bowtie(1/2)
    [Wed Feb 9 19:57:47 2011] Mapping reads against melpomene with Bowtie(2/2)
    [Wed Feb 9 20:11:15 2011] Searching for junctions via segment mapping
    [Wed Feb 9 23:00:46 2011] Searching for junctions via mate-pair closures
    [Wed Feb 9 23:14:54 2011] Retrieving sequences for splices
    [Wed Feb 9 23:17:05 2011] Indexing splices
    [Wed Feb 9 23:49:09 2011] Mapping reads against segment_juncs with Bowtie
    [Thu Feb 10 00:14:05 2011] Mapping reads against segment_juncs with Bowtie
    [Thu Feb 10 00:36:28 2011] Joining segment hits
    [Thu Feb 10 00:56:25 2011] Mapping reads against segment_juncs with Bowtie
    [Thu Feb 10 01:23:12 2011] Mapping reads against segment_juncs with Bowtie
    [Thu Feb 10 01:47:10 2011] Joining segment hits
    [Thu Feb 10 02:06:56 2011] Reporting output tracks
    [FAILED]
    Error: Report generation failed with err = -11

  • #2
    Okay, found at least one problem I was having. My data are in Illumina1.3 quality scores, which I failed to specify. Should have used '--solexa1.3-quals'. Hope this is the reason for the fail. Seems likely...

    If at first you don't succeed...

    Comment


    • #3
      ... you keep on failing until you figure out the problem. Which I have not. I reran with correct quality scoring specified and suffered the same fate. tophat err = -11 ? Anyone?

      jamie

      Comment


      • #4
        Splitting the dataset into 5 subsets and running each of those separately did not cause the same error. All 5 runs finished up just fine. So there is clearly something problematic about combining either that volume of data or that many different files... Don't know which.

        Comment


        • #5
          Hi Jamie,

          I have obtained the same error message with human paired-end data (~140 million of paired-end reads). It seems to come from the high number of reads, as it has worked previously with <100 million of paired-end reads. I have splitted the dataset to see if it works.
          How many reads do you have ?

          Emilie

          Comment


          • #6
            It works when I split my dataset in 3 chunks (~50 million of paired-end reads per chunk). It seems most probably that there is an issue with the size of the dataset.

            Comment


            • #7
              I agree... seems the most logical explanation for the run fail... but I'm a biologist and new to this, so hard to say for sure...

              Good luck,

              jamie

              Comment


              • #8
                Tmp directory too big

                I am getting this error too. I believe (atleast in my case) that it is due to disk getting full with the tmp directory. Just before giving this error, tophat says:

                Code:
                sort: close failed: -: No space left on device
                Errors are:
                Code:
                Report generation failed with err = -11
                or
                Code:
                Error: Report generation failed with err = 1

                Comment

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