bwa aln fails on mac

[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

[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]

I have not. Works fine on Linux.

[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.

[quincymo]

I did build the index on Mac
bwa index -a bwtsw genome.fa
which produced the following files:
genome.fa.ann genome.fa.pac genome.fa.amb genome.fa.bwt genome.fa.sa

bwa failed to calculate SA coordinate. Note it only took 0.75 sec.

Software/bwa-0.6.2/bwa aln Genome/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.6.2/genome.fa ERR001014_1.fastq > ERR001014_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... 0.75 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 250000 sequences have been processed.
[main] Version: 0.6.2-r126
[main] CMD:Software/bwa-0.6.2/bwa aln Genome/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.6.2/genome.fa ERR001014_1.fastq
[main] Real time: 1.118 sec; CPU: 1.114 sec

[GenoMax]

I did build the index on Mac
bwa index -a bwtsw genome.fa
which produced the following files:
genome.fa.ann genome.fa.pac genome.fa.amb genome.fa.bwt genome.fa.sa

File sizes for the index files look ok?
e.g. .sa file should be about 1.5G and .bwt 2.9G.

[quincymo]

I think it looks OK.

2.9G genome.fa
8.0K genome.fa.amb
4.0K genome.fa.ann
2.9G genome.fa.bwt
738M genome.fa.pac
1.4G genome.fa.sa
8.0G total

[quincymo]

bwa 0.5.9 works fine on my Mac, but 0.6.x do not work.

[GenoMax]

I think it looks OK.

2.9G genome.fa
8.0K genome.fa.amb
4.0K genome.fa.ann
2.9G genome.fa.bwt
738M genome.fa.pac
1.4G genome.fa.sa
8.0G total

That looks good.

Is the alignment failing for all files or just one file?

[quincymo]

It failed for all the files I tested. But bwa 0.5.9 worked fine on the same files.

[GenoMax]

It failed for all the files I tested. But bwa 0.5.9 worked fine on the same files.

Perhaps someone else on the forum can chime in (do not have a Mac handy to test now) if they are successfully using bwa (v.0.6.2) on OS X. Please indicate exact OS X version.

[quincymo]

Thanks for your replies.

My Mac OS version is Mac OS X Lion 10.7.5.

[cboustred]

I am also having the same problem running the current bwa release (0.6.2) on Mac OSX Moutain Lion (10.8.2). All indexes were made on the Mac using bwa.

Using the older version of bwa (0.5.9) everything works fine

[TabeaK]

Uhm, by the way, I have started running the latest bwa on my Macbook (Mac OSX 10.7.4; Lion) yesterday.

Runs fine - the first round of paired end alignment is complete, the program ran right through and processed my 60million odd reads.

The only issues I encountered were with bwa having problems to infer the insert size, but I suspect that is due to either a problem with my fastq files or my ineptitude at selecting the right settings.

The program itself works and is lightning-fast even on my crappy machine!

Edit: I actually had problems with directing bwa to the file directories. No idea why, but even though the path to the files WAS DEFINITELY right, bwa failed to open the files. So, I have copied everything to my home directory and run from there --> no more problems.

[cboustred]

It 'worked' lightening fast for me too, except when I looked at the resulting BAM files none of the reads were aligned properly

Try running samtools flagstat to check the number of mapped reads