bwa aln fails on mac

[GenoMax]

Are you using indexes that were built on the Mac? If not, it may be useful to try and recreate the indexes on the Mac to see if that helps.

[Jnome]

I have not. Works fine on Linux.

[quincymo]

I experienced the same problem. BWA 0.6.2 works on our Linux cluster, but not on my Mac Pro. Have you solved the problem?

[Jnome]

Has anyone had problems running bwa on a mac? Building from source using make compiles fine. Running aln gives no errors either. But the .sai file ends up being full of 0's.

./bwa aln ~/data_files/reference/ucsc.hg19.fasta ~/data_files/test/test_1.fastq > ~/data_files/test/tmp/test_1.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... 0.19 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 36921 sequences have been processed.
[main] Version: 0.6.2-r131
[main] CMD: ./bwa aln /Users/jason/data_files/reference/ucsc.hg19.fasta /Users/jason/data_files/test/test_1.fastq
[main] Real time: 0.310 sec; CPU: 0.312 sec