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?
•
written
by
lishen0709 •
2 answers
- Remove the
-O2fromCFLAGSin 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.
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.
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A lot of times this is an issue with the index, try rebuilding the index files and rerunning the alignment.