Do Recent Versions Of Bwa Not Run On A Mac?

Question

[ajc8]

Hi,

Several months ago, I was not able to align my ngs reads with bwa because it kept telling me "fail to locate the index files". Indexing worked fine. I poked around on-line and found some posts saying that newer versions of bwa do not work on a mac. I downloaded an older version and the problem was solved.

I'm now taking a class and I just downloaded the newest version and I'm having the same problem - indexing is fine but alignment (using mem or alb) gives me the same error message.

Is it true that more recent versions of bwa do not run on a mac? I was fine with this conclusion several months ago, but now that I am in a room surrounded by people using macs and running bwa for the first time, and this issue has not come up (although we are doing cloud computing), I'm thinking there is something else going on.

Is there a resolution to this problem that is separate from using an older version?

Thanks! Allison

Answer 1

[Istvan Albert]

works just fine. Make sure that you have xcode and gcc installed then just download and make it instead of downloading binaries.

Answer 2

[Ido Tamir]

1. for OSX there is the heavily NGS orientated homebrew science project on github
2. I think you have are referencing an older index in your analysis and there was a change of index format/naming in some bwa versions. Make sure that the you really reference the index you just created with the bwa version that you used for creating this index.