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  • bwa mem segmentation fault aligning 454 reads alignment to reference sequences

    Hi!
    I need to align 454 reads to a set of 17 reference sequences.
    I thought to use bra with the men algorithm.

    I built the index, then I tried:

    bwa mem -t 5 -k 50 -r 1 -M poxE_bwa_db seqs.fna

    It gave me this error:
    [M::bwa_idx_load_from_disk] read 0 ALT contigs
    [M:rocess] read 2805 sequences (1947633 bp)...
    Segmentation fault: 11

    However, I have only 2800 sees to map, so I don't think it could be a memory problem.

    Any suggestions?

  • #2
    Are you using the newest bwa available?

    Comment


    • #3
      Try to run using one thread. More threads uses more memory.

      Comment


      • #4
        I'm using bwa-0.7.12.

        The same error occurs also with -t 1.

        Comment


        • #5
          I had the same error.

          I used a newer version of BWA with a genome reference index created by an older version of BWA. I just had to re-index the genome again with current BWA (v0.7.12) and this fixed it.

          Comment

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