Question: Do Recent Versions Of Bwa Not Run On A Mac?
1
gravatar for ajc8
7.6 years ago by
ajc8120
University of Iowa
ajc8120 wrote:

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

bwa • 2.7k views
ADD COMMENTlink modified 7.6 years ago by Ido Tamir5.1k • written 7.6 years ago by ajc8120
2
gravatar for Istvan Albert
7.6 years ago by
Istvan Albert ♦♦ 86k
University Park, USA
Istvan Albert ♦♦ 86k wrote:

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

ADD COMMENTlink written 7.6 years ago by Istvan Albert ♦♦ 86k
0
gravatar for Ido Tamir
7.6 years ago by
Ido Tamir5.1k
Austria
Ido Tamir5.1k wrote:
  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.
ADD COMMENTlink written 7.6 years ago by Ido Tamir5.1k
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