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  • BWA crashes in Fedora

    Lately I changed OS from Ubuntu to Fedora (KDE) (both 64bit).
    While in Ubuntu BWA worked perfectly it now crashes while trying to align a 7.4GB Illumina fastQ file which I could align perfectly in Ubuntu.

    The output is

    Code:
    [bwa_aln] 17bp reads: max_diff = 2
    [bwa_aln] 38bp reads: max_diff = 3
    [bwa_aln] 64bp reads: max_diff = 4
    [bwa_aln] 93bp reads: max_diff = 5
    [bwa_aln] 124bp reads: max_diff = 6
    [bwa_aln] 157bp reads: max_diff = 7
    [bwa_aln] 190bp reads: max_diff = 8
    [bwa_aln] 225bp reads: max_diff = 9
    [bwa_aln_core] calculate SA coordinate... Segmentation fault (core dumped)
    I use 16GB quadcore 64bit Fedora 14 and I tried every bwa version from 0.5.6 to 0.5.9.

    The command was:
    Code:
    bwa aln ~/RefSeq/hg19_070510/Chromosomes/hg19.fa test.fq > test.aln
    Any help appreciated (looking in your direction lh3...)

  • #2
    I had the same problem (BWA on Fedora 13) and gave up on it for a long time. Then someone passed me a BLOG link:

    Here's what I use for bwa alignment (without removing PCR dups). You can replace the paths with your own and put into a bash script for au...


    My problem seemed to be i was using a solid2fastq script from a different program (BFAST i think. Why was i doing this, because it is C-compiled therefore much faster!). Once i used solid2fast from the BWA package it started working.

    I hope this helps!

    Comment


    • #3
      Thank you for your help.
      I was just too stupid for reading the manual. I did new indexing of the genome with the -a is argument which is not recommended for large genomes. After applying the -a bwt option in indexing, alignment worked.

      Comment


      • #4
        Dear all,

        I got this error message, too, when running bwa samse (bwa-0.5.9rc1):

        Code:
        [bwa_aln_core] refine gapped alignments... Segmentation fault (core dumped)
        however, the difference to the previous posts is that
        1. my original SOLiD reads were reformatted using bwa's solid2fastq.pl alright, and
        2. I ran a batch of 12 samples that were processed all the same way. Only 7 gave this error, 5 were processed without error.

        Any ideas why this happens will be appreciated.

        thanks,
        Sophia

        Comment


        • #5
          Let me reply to my own question:

          What happened is that the solid2fastq script obviously did not process the reads completely (as a part of the batch process).
          Funnily enough, the last read of the fastq file being incomplete did not prevent bwa aln to run and generate a .sai file.
          Only in the bwa samse step, this caused trouble and led to said error message.

          Hope this helps.

          cheers,
          Sophia

          Comment

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