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  • Tophat 2.0.0 is stuck

    Hello, I have a tophat process that seems stuck:

    Code:
    [2012-10-03 14:47:19] Beginning TopHat run (v2.0.0)
    -----------------------------------------------
    [2012-10-03 14:47:19] Checking for Bowtie
                      Bowtie version:        2.0.0.6
    [2012-10-03 14:47:19] Checking for Samtools
                    Samtools version:        0.1.18.0
    [2012-10-03 14:47:19] Checking for Bowtie index files
    [2012-10-03 14:47:19] Checking for Bowtie index files
    [2012-10-03 14:47:19] Checking for reference FASTA file
    [2012-10-03 14:47:19] Generating SAM header for ../alignment/expanded_genome2
            format:          fastq
            quality scale:   phred33 (default)
    [2012-10-03 14:47:56] Reading known junctions from GTF file
    [2012-10-03 14:48:01] Preparing reads
             left reads: min. length=50, count=29715271
            right reads: min. length=50, count=29535618
    [2012-10-03 15:02:14] Using pre-built transcriptome index..
    [2012-10-03 15:02:18] Mapping left_kept_reads against transcriptome genes with Bowtie2
    [2012-10-03 15:18:27] Mapping right_kept_reads against transcriptome genes with Bowtie2
    [2012-10-03 15:34:00] Converting left_kept_reads.m2g to genomic coordinates (map2gtf)
    [2012-10-03 15:40:53] Converting right_kept_reads.m2g to genomic coordinates (map2gtf)
    [2012-10-03 15:47:50] Resuming TopHat pipeline with unmapped reads
    [2012-10-03 15:48:14] Mapping left_kept_reads.m2g_um against expanded_genome2 with Bowtie2
    [2012-10-03 15:57:12] Mapping left_kept_reads.m2g_um_seg1 against expanded_genome2 with Bowtie2 (1/2)
    [2012-10-03 16:00:07] Mapping left_kept_reads.m2g_um_seg2 against expanded_genome2 with Bowtie2 (2/2)
    [2012-10-03 16:03:12] Mapping right_kept_reads.m2g_um against expanded_genome2 with Bowtie2
    [2012-10-03 16:12:05] Mapping right_kept_reads.m2g_um_seg1 against expanded_genome2 with Bowtie2 (1/2)
    [2012-10-03 16:15:47] Mapping right_kept_reads.m2g_um_seg2 against expanded_genome2 with Bowtie2 (2/2)
    [2012-10-03 16:19:25] Searching for junctions via segment mapping
    [2012-10-03 21:18:12] Retrieving sequences for splices
    [2012-10-03 21:20:47] Indexing splices
    [2012-10-03 21:33:14] Mapping left_kept_reads.m2g_um_seg1 against segment_juncs with Bowtie2 (1/2)
    ...since this step never took so long I'm beginning to wonder if maybe it is really stuck there...maybe there is a problem in the multicore approach. I see the process listed as running and using CPU but strace does not report any syscall and the virtual memory used is fixed...I am checking /proc/PID data but I am not sure which is the correct file to
    understand this kind of problems (maybe stack?).
    Anyone experienced this kind of problems? I don't see it listed as a solved issue in successive version so I am not sure if it's time-wise to stop it and try with a newer version.

    Thank you very much,
    E.G.

  • #2
    +1 to this. I had similar issues (perhaps the same one) with the tophat 2.0.4 and multicore. I now (painfully) only use single core and it works fine, albeit very slowly.

    Vincent

    Comment


    • #3
      Ouch, sad. Thanks, I will try to launch it in sigle core mode and see if it works (assuming that it will end before my contract does that ).

      Comment


      • #4
        Do you need to upgrade to Tophat 2? I got good alignment with Tophat 1.4 and Bowtie 1, and I'm wondering if I should upgrade. If it can only do one core at a time, I definitely won't.

        Comment


        • #5
          ...no luck. Even the single core process got stuck at that point...I'm working on a public dataset (GSE27003). I've added the --no-novel-juncs option and it has finished. I really do not understand what's the problem.

          Comment


          • #6
            I've had the same issues and my solution was to "upgrade" to Tophat 1.4.1.

            Comment


            • #7
              We've also had problems running Tophat 2 on multiple cores, usually it would fail at the point where multiple BAM files are merged into 1.
              However we found that running on 4 cores worked so have switched to that for now...

              Comment


              • #8
                Tophat 2 on a different dataset worked for me with different number of cores, ranging from 2 to 6. I'm wondering what could be the problem, even if in this peculiar case the problem is still there with a single core.

                Comment


                • #9
                  We're using TopHat2 on Ubuntu 12.0.4. Parts of the process take up the max number of threads (16 threads: -p 16). https://insilicodb.org

                  Comment

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