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BWA Alignment Segmentation Fault

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  • #16
    No, I didn't make any modifications.

    Comment


    • #17
      Getting the same error

      Hi ,
      I am getting the exact error of
      [bwa_aln_core] calculate SA coordinate... Segmentation fault

      Comment


      • #18
        I am getting the same error, any new ideas???
        bwa aln Mito.fa TpNoDotStd.fastq > alnTpNoDotStd.sai
        [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... 3.00 sec
        [bwa_aln_core] write to the disk... 0.01 sec
        [bwa_aln_core] 262144 sequences have been processed.
        [bwa_aln_core] calculate SA coordinate... 3.00 sec
        [bwa_aln_core] write to the disk... 0.02 sec
        [bwa_aln_core] 524288 sequences have been processed.
        [bwa_aln_core] calculate SA coordinate... 3.01 sec
        [bwa_aln_core] write to the disk... 0.02 sec
        [bwa_aln_core] 786432 sequences have been processed.
        [bwa_aln_core] calculate SA coordinate... 2.96 sec
        [bwa_aln_core] write to the disk... 0.02 sec
        [bwa_aln_core] 1048576 sequences have been processed.
        [bwa_aln_core] calculate SA coordinate... 2.97 sec
        [bwa_aln_core] write to the disk... 0.02 sec
        [bwa_aln_core] 1310720 sequences have been processed.
        [bwa_aln_core] calculate SA coordinate... 2.99 sec
        [bwa_aln_core] write to the disk... 0.02 sec
        [bwa_aln_core] 1572864 sequences have been processed.
        [bwa_aln_core] calculate SA coordinate... 2.98 sec
        [bwa_aln_core] write to the disk... 0.02 sec
        [bwa_aln_core] 1835008 sequences have been processed.
        [bwa_aln_core] calculate SA coordinate... 2.99 sec
        [bwa_aln_core] write to the disk... 0.02 sec
        [bwa_aln_core] 2097152 sequences have been processed.
        [bwa_aln_core] calculate SA coordinate... 2.98 sec
        [bwa_aln_core] write to the disk... 0.02 sec
        [bwa_aln_core] 2359296 sequences have been processed.
        [bwa_aln_core] calculate SA coordinate... zsh: segmentation fault bwa aln MitoNC_012920.fa TeopNoDotStd.fastq > alnTeopNoDotStd.sai

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        • #19
          Hi,
          i get seg fault like this one in my bwa-0.6.1-r104:
          ------------------
          [bwa_aln_core] refine gapped alignments... sh: line 1: 12337 Segmentation fault
          -------------------

          It happens when i modify the '-l' switch. When i set it to something below 19 is produces the error. I got it when aligning SOLID reads.

          Should i rebuild bwa as per dp05yk suggestion(modify line 82 of bwtaln.c? Any ideas are appreciated.

          thank you.

          Comment


          • #20
            Hi again,
            just rebuild bwa as suggested but got the same error.

            Now im out of ideas and i have to stick to -l 19 or larger.

            Comment


            • #21
              Yesterday found that BWA-0.6.1 cant be used for SOLID as color space is switched off. Not nice. Now using 0.5.9 and waiting for the new version where all will be all right for SOLID again.

              Comment


              • #22
                We had a problem with seg faults after switching to bwa (0.6.1).

                It appears that the problem can be fixed by re-indexing the genomes with new bwa.

                Has anyone else seen this?

                Comment


                • #23
                  Originally posted by GenoMax View Post
                  We had a problem with seg faults after switching to bwa (0.6.1).

                  It appears that the problem can be fixed by re-indexing the genomes with new bwa.

                  Has anyone else seen this?
                  Yes, the index structure is new. Unfortunately, the indexes do not have a header with a versioning scheme, so seg faults would be expected.

                  Comment


                  • #24
                    I asked my sys admin to update without looking at release notes.

                    This is going to trip some folks like me who do not always read release notes (for minor version revisions at least).

                    Originally posted by nilshomer View Post
                    Yes, the index structure is new. Unfortunately, the indexes do not have a header with a versioning scheme, so seg faults would be expected.

                    Comment


                    • #25
                      Got this error when my machine didn't have enough free memory.

                      Hope this helps someone

                      Comment

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