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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,