Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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

                Latest Articles

                Collapse

                • seqadmin
                  Strategies for Sequencing Challenging Samples
                  by seqadmin


                  Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
                  03-22-2024, 06:39 AM
                • seqadmin
                  Techniques and Challenges in Conservation Genomics
                  by seqadmin



                  The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

                  Avian Conservation
                  Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
                  03-08-2024, 10:41 AM

                ad_right_rmr

                Collapse

                News

                Collapse

                Topics Statistics Last Post
                Started by seqadmin, 03-27-2024, 06:37 PM
                0 responses
                12 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 03-27-2024, 06:07 PM
                0 responses
                11 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 03-22-2024, 10:03 AM
                0 responses
                53 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 03-21-2024, 07:32 AM
                0 responses
                68 views
                0 likes
                Last Post seqadmin  
                Working...
                X