bwa aln creates 0 length sai


I appreciate your effort in porting BWA to windows. It's of great help.
I tried running "bwa aln" and it creates a zero length .sai file. I am using the index built from a linux host. Is that a valid usage ? Can I use the index built from Linux ? Am using Windows 2008 environment to run bwa.
C:\BWA>bwa.exe aln -f output.sai hg19.fa SRR062634.100.fastq
[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...
The program exits after the above without providing any error message and a 0 length output.sai file.
Thanks in advance,
Closed Jul 23, 2012 at 10:02 AM by xied75


xied75 wrote Jul 21, 2012 at 12:18 PM


Yes you can use indexed files from Linux, but you need to make sure you are using the SAME VERSION bwa. If you cross version, even on Linux it won't work. Please try to index on windows machine and see how that goes.



nmohad wrote Jul 21, 2012 at 11:13 PM

Hi Dong,

Yeah.. It works fine if I index it on the windows machine. As you pointed out, I might have been using different BWA versions between Windows and Linux. You can close the issue.


wrote Jul 23, 2012 at 10:02 AM

wrote Feb 14, 2013 at 7:35 PM

wrote May 16, 2013 at 8:44 AM