How to deal with Segmentation fault in BWA?

Question

[lishen0709]

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?

[skbrimer]

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

Answer 1

[Pierre Lindenbaum]

• Remove the -O2 from CFLAGS in https://github.com/lh3/bwa/blob/master/Makefile#L3
• recompile bwa with make -B
• run bwa with gdb

$ 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.

Answer 2

[kloetzl]

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.