Question: How to deal with Segmentation fault in BWA?
0
gravatar for lishen0709
10 months ago by
lishen07090
lishen07090 wrote:

Hello everyone:

I'm now using BWA to do alignment. But when I want to calculate the SA coordinate, It report an error:

[sl2495@ruddle1 BWA_tool]$ bwa-0.7.17/bwa aln hg38.fa Project_Sc563/Sample_XD01/XD01_S1_L008_R1_001.fastq > XD01_S1_L008_R1_001.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

The verison of my BWA is 0.7.17, and I am doing this on the lab server. So does anyone know how to deal with it?

ADD COMMENTlink modified 10 months ago by Pierre Lindenbaum112k • written 10 months ago by lishen07090

A lot of times this is an issue with the index, try rebuilding the index files and rerunning the alignment.

ADD REPLYlink written 10 months ago by skbrimer500
0
gravatar for kloetzl
10 months ago by
kloetzl960
European Union
kloetzl960 wrote:

So does anyone know how to deal with it?

File a bug. A segmentation fault is a programming error and should be fixed by the authors.

ADD COMMENTlink written 10 months ago by kloetzl960
0
gravatar for Pierre Lindenbaum
10 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum112k wrote:
$ gdb  bwa-0.7.17/bwa 
> run aln -f XD01_S1_L008_R1_001.sai hg38.fa Project_Sc563/Sample_XD01/XD01_S1_L008_R1_001.fastq 

on error, print the backtrace:

bt

flll a bug report with the backtrace.

ADD COMMENTlink modified 10 months ago • written 10 months ago by Pierre Lindenbaum112k
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