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  • davidblaney
    replied
    Got this error when my machine didn't have enough free memory.

    Hope this helps someone

    Leave a comment:


  • GenoMax
    replied
    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.

    Leave a comment:


  • nilshomer
    replied
    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.

    Leave a comment:


  • GenoMax
    replied
    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?

    Leave a comment:


  • kenietz
    replied
    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.

    Leave a comment:


  • kenietz
    replied
    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.

    Leave a comment:


  • kenietz
    replied
    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.

    Leave a comment:


  • pepperoni
    replied
    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

    Leave a comment:


  • aishsk
    replied
    Getting the same error

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

    Leave a comment:


  • golharam
    replied
    No, I didn't make any modifications.

    Leave a comment:


  • oiiio
    replied
    Originally posted by golharam View Post
    I upgraded bwa to 0.5.9. I rebuilt the index with the latest version and re-aligned with the latest version and everything seems okay.
    Did you need to modify bwtaln.c as suggested? I am having similar segfault errors like this, even though I am using the latest bersion of BWA.

    Leave a comment:


  • golharam
    replied
    solved

    I upgraded bwa to 0.5.9. I rebuilt the index with the latest version and re-aligned with the latest version and everything seems okay.

    Leave a comment:


  • dp05yk
    replied
    Hi golharam,

    Try upgrading to the most recent version. If that doesn't help, here's a reply I made on another thread:

    Lately I had been encountering inexplicable segmentation faults during the 'aln' command for SOLiD reads. The problem occurs when the first read of a 262144 block has a length of zero. This is why it's so rare and so hard to reproduce. I was able to fix this by initializing the max_l variable at the beginning of the bwa_cal_sa_reg_gap function to -1 instead of 0.
    It makes sense that it would occur more often with threading enabled, since the chances are multiplied by the number of threads running.

    I'd recommend:

    1. Upgrading to BWA 0.5.9.
    2. If you are still getting segmentation faults, modify line 82 of bwtaln.c: change "max_l = 0", to "max_l = -1", and recompile. This is what fixed it for me.

    Leave a comment:


  • golharam
    replied
    resolution?

    I'm seeing this as well. Has there been any resolution to this? I'm running BWA 64-bit v0.5.7

    Leave a comment:


  • dawe
    replied
    Hi all, I've got now a segfault error with bwa. Apparently this happens only if I enable threaded alignment on a NFS file system.
    Code:
    $ bwa aln -t 2 /db/bwa/hg19/hg19.fa s_1_2.fastq > s_1_2.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... Segmentation fault
    while

    Code:
    $ bwa aln  /db/bwa/hg19/hg19.fa s_1_1.fastq > s_1_1.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... 114.28 sec
    [bwa_aln_core] write to the disk... 0.08 sec
    [bwa_aln_core] 262144 sequences have been processed.
    [bwa_aln_core] calculate SA coordinate... 118.51 sec
    [bwa_aln_core] write to the disk... 0.07 sec
    [bwa_aln_core] 524288 sequences have been processed.
    [bwa_aln_core] calculate SA coordinate...
    works

    Code:
    Program: bwa (alignment via Burrows-Wheeler transformation)
    Version: 0.5.8 (r1442)

    Leave a comment:

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