BWA Segmantation fault

[jyli]

Dear all,

I have recently encountered a weird error with BWA (0.4.5)alignment. It runs fine to generate .sai file, but when I ran "bwa samse", I got "segmentation fault". The weird thing is though, it was OK with MAQ 0.7.1, and OK with tophat (1.0.12)

A few lines from the log are like the following:

[bwa_aln_core] 4718592 sequences have been processed.
[bwa_aln_core] convert to sequence coordinate... 1.14 sec
[bwa_aln_core] refine gapped alignments... 0.21 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_aln_core] convert to sequence coordinate... 1.13 sec
[bwa_aln_core] refine gapped alignments... Segmentation fault

Any help is highly appreciated.

Jianying Li

[lh3]

0.4.5 is over 10 releases or a year behind the latest 0.5.7. You should try the latest version in the first place.

[jyli]

Thanks for your attention! And, it solved the problem that I have.