No, I didn't make any modifications.
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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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Hi,
i get seg fault like this one in my bwa-0.6.1-r104:
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[bwa_aln_core] refine gapped alignments... sh: line 1: 12337 Segmentation fault
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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.
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Originally posted by GenoMax View PostWe 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?
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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 PostYes, the index structure is new. Unfortunately, the indexes do not have a header with a versioning scheme, so seg faults would be expected.
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