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  • Tophat2 error ! Broken pipe!

    Hi all I am running tophat2 on my proton fastq data reads and have this error which I haven't faced before.
    Could you tell me what happened?!

    (Sorry for trouble every one , the problem has been sorted! because I didn't have enough space......)

    My command:
    tophat2 -o folder1 -p 12 --library-type fr-firststrand --keep-fasta-order --GTF genes.gtf Bowtie2Index sample1.fastq

    The error is:

    [2014-04-30 14:28:28] Beginning TopHat run (v2.0.10)
    -----------------------------------------------
    [2014-04-30 14:28:28] Checking for Bowtie
    Bowtie version: 2.1.0.0
    [2014-04-30 14:28:28] Checking for Samtools
    Samtools version: 0.1.19.0
    [2014-04-30 14:28:28] Checking for Bowtie index files (genome)..
    [2014-04-30 14:28:28] Checking for reference FASTA file
    [2014-04-30 14:28:28] Generating SAM header for ./Bos_taurus/Ensembl/Btau_4.0/Sequence/Bowtie2Index/genome
    [2014-04-30 14:28:30] Reading known junctions from GTF file
    [2014-04-30 14:28:33] Preparing reads
    left reads: min. length=16, max. length=320, 65134842 kept reads (3312 discarded)
    Warning: short reads (<20bp) will make TopHat quite slow and take large amount of memory because they are likely to be mapped in too many places
    [2014-04-30 14:43:49] Building transcriptome data files folder1/tmp/genes
    [2014-04-30 14:43:57] Building Bowtie index from genes.fa
    [2014-04-30 14:45:17] Mapping left_kept_reads to transcriptome genes with Bowtie2
    [2014-04-30 15:00:59] Resuming TopHat pipeline with unmapped reads
    [2014-04-30 15:00:59] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2
    Traceback (most recent call last):
    File "/software/bin/tophat", line 4084, in <module>
    sys.exit(main())
    File "/software/bin/tophat", line 4050, in main
    user_supplied_deletions)
    File "/software/bin/tophat", line 3541, in spliced_alignment
    segment_len)
    File "/software/bin/tophat", line 2977, in split_reads
    split_record(read_name, read_seq, read_quals, out_segfiles, offsets, params.read_params.color)
    File "/software/bin/tophat", line 2925, in split_record
    print >> f, "%s|%d:%d:%d" % (read_name,last_seq_offset,seg_num, len(offsets) - 1)
    IOError: [Errno 32] Broken pipe
    Last edited by super0925; 05-02-2014, 07:01 AM. Reason: sorry for trouble every one , it is sorted!!!

  • #2
    tophat is a Python script that calls a number of helper programs (Bowtie2 plus a number of TopHat-specific programs). The broken pipe implies a problem communicating with one of the sub-programs, most likely because it died unexpectedly.

    You might try looking in folder1/logs for a run.log file that will show all of the sub-commands that tophat runs. There should also be per-sub-command .log files as well that you could look through with the goal of figuring out (1) which command died and (2) whether it left a more specific error message anywhere.

    Comment


    • #3
      Just to add to par's response, if there isn't a per-command log, then just run the last command you find in the run log manually and you'll see the (typically vastly more informative) error message.

      Comment

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