Got this error when my machine didn't have enough free memory.
Hope this helps someone
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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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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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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?
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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.
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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.
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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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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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Getting the same error
Hi ,
I am getting the exact error of
[bwa_aln_core] calculate SA coordinate... Segmentation fault
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Originally posted by golharam View PostI 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.
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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.
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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.
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.
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resolution?
I'm seeing this as well. Has there been any resolution to this? I'm running BWA 64-bit v0.5.7
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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
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...
Code:Program: bwa (alignment via Burrows-Wheeler transformation) Version: 0.5.8 (r1442)
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