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  • Is bowtie2 really this unstable?

    I am having the devil's own time running bowtie2 on a relatively modest set (at most 17 Mill reads) of RNA-seq data.

    I run it with the "-a" flag (report all alignments) or a "-k 2" (report 2) or the default to just report one alignment.

    I have paired-end reads. I have run them as paired end or as unpaired reads.

    I have run them against transcriptome or genome.

    Only a couple of times have I seen it actually run to completion. When it fails, it does not even give me a segmentation fault. Just keeps spinning for days on end with no output (to stdout or stderror). I am trying to build a pipeline by looking at hits to both genome and transcriptome but have never had it complete the runs against both. (It has only completed the mapping against the transcriptome on a couple of occasions).

    Is bowtie2 (supposedly still beta) really this unstable? Do others have experience with it running flawlessly?
    Kamalakar Gulukota,
    Director,
    Center for Bioinformatics and Computational Biology
    NorthShore University Health System, [email protected]

  • #2
    Which version are you running?

    There were a number of bugs fixed in the beta2 and beta3 release and now they are on the beta5.

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    • #3
      I am using beta 5.

      bowtie2 --version
      /research/software/Bowtie2/bowtie2-2.0.0-beta5/bowtie2-align version 2.0.0-beta5
      64-bit
      Built on compute-0-38.local
      Thu Dec 15 01:02:29 EST 2011
      Compiler: gcc version 4.1.2 20080704 (Red Hat 4.1.2-46)
      Options: -O3 -m64 -msse2 -funroll-loops -g3
      Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}
      Kamalakar Gulukota,
      Director,
      Center for Bioinformatics and Computational Biology
      NorthShore University Health System, [email protected]

      Comment


      • #4
        has worked well

        I have run bowtie2 on two datasets of RNA-Seq (Illumina PE, 100x2) with each ~70million reads.
        It did fine I think though I havn't assembled the transcripts yet. I aligned on hg19 and used 12 threads.

        Specifically, I used the following options:
        --local
        -M 5

        Both of the time bowtie2 took around 13 hours to complete. Reported ~99% ('proper' paired end ~88%) alignment in each. Insert size summarized from the BAM file was around 175 which is okay.
        version 2.0.0-beta5, 64bit (compiled)

        EDIT -

        /home/amitm/bin/bowtie2-align version 2.0.0-beta5
        64-bit
        Built on atlas
        Fri Feb 3 11:17:37 IST 2012
        Compiler: gcc version 4.4.6 20110731 (Red Hat 4.4.6-3) (GCC)
        Options: -O3 -m64 -msse2 -funroll-loops -g3
        Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}
        Last edited by amitm; 02-14-2012, 10:08 AM.

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        • #5
          I haven't really switched to it because I thought it was a) unstable and b) my reads are still pretty short.

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          • #6
            A satisfactory resolution:

            I have been in private correspondence with Ben Langmead. There might be something about my sequence file that is causing great bowtie2 inefficiency. The offending option appears to be "--reorder".

            Since I can reorder my reads in many other ways, I removed that flag and all my processes ran to completion.

            Thank you Ben!
            Kamalakar Gulukota,
            Director,
            Center for Bioinformatics and Computational Biology
            NorthShore University Health System, [email protected]

            Comment

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