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  • Error when running TopHat

    this is the first time I run Tophat, and I cannot get it to work.
    I have two test fastq files, each one containing 10 reads. They align well to hg19 with bowtie:
    bowtie --phred64-quals indexes/h_sapiens_37_asm -1 test_1.fastq -2 test_2.fastq

    # reads processed: 10
    # reads with at least one reported alignment: 5 (50.00%)
    # reads that failed to align: 5 (50.00%)
    Reported 5 paired-end alignments to 1 output stream(s)

    However, tophat complains:

    tophat --keep-tmp -r 15 -o test --phred64-quals indexes/h_sapiens_37_asm test_1.fastq test_2.fastq
    I get the following output, again and again with different settings:
    [Tue Jul 12 15:06:45 2011] Beginning TopHat run (v1.3.0)
    [Tue Jul 12 15:06:45 2011] Preparing output location test/
    [Tue Jul 12 15:06:45 2011] Checking for Bowtie index files
    [Tue Jul 12 15:06:45 2011] Checking for reference FASTA file
    [Tue Jul 12 15:06:45 2011] Checking for Bowtie
    Bowtie version:
    [Tue Jul 12 15:06:45 2011] Checking for Samtools
    Samtools Version: 0.1.15
    [Tue Jul 12 15:06:45 2011] Generating SAM header for indexes/h_sapiens_37_asm
    [Tue Jul 12 15:06:48 2011] Preparing reads
    format: fastq
    quality scale: phred64 (reads generated with GA pipeline version >= 1.3)
    Left reads: min. length=53, count=10
    Right reads: min. length=53, count=10
    [Tue Jul 12 15:06:48 2011] Mapping left_kept_reads against h_sapiens_37_asm with Bowtie
    Error at mkfifo(test/tmp/31660.bwt_unmapped.z.fifo). [Errno 5] Input/output error
    If anyone knows what is going on, I would be so thankful...

  • #2
    mkfifo errors in TopHat v1.3.1

    I am also unable to get the mkfifo portions of the code that were introduced in Tophat v1.3.0 and v1.3.1 to work on my system. I thought I had circumvented this problem by using the --no-unmapped-fifo option, but then it failed much later in the merge_sort.fifo portion of the code.

    As a temporary solution, I have continued to use v1.2.0, though I would like to try out the new features in 1.3.1, so it would be great to understand what may be causing these errors.

    I am certainly not an expert in the nuances of Linux, so I am not sure what the problem is. I don't have root permissions where bowtie is installed on my system - would that make a difference?

    I look forward to a resolution to this problem.



    • #3
      well, I finally got the answer to my problem. I'll paste it here, since it may be useful for others...
      Here is what the developers of Tophat told me by email:

      This seems to be an error related to the underlying file system -- some file systems do not support the mkfifo() call that Tophat currently uses. For example, if the underlying partition/volume that is hosting the tophat output directory is a Windows (NTFS) volume, mkfifo() will fail. We will address this problem in the next release (removing the mkfifo() call), but until then the only solution to this is to redirect's tophat output (using -o/--output-dir) to (or run tophat in) a directory which resides on a different volume/partition which uses a file system that supports mkfifo(). Using a local directory with a native file system usually works for this. Of course you must also make sure that you have enough space on this output volume, as the output and temporary files are quite large (about twice the size of the original data).
      That was indeed my case (NTFS volume). I changed to another volume, and it worked.
      Hope that helps!


      • #4
        This problem seems to have been resolved in the latest version of TopHat (according to release notes) 1.3.2 beta.


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