BWA error: [bwa_idx_build] fail to open file 'ref.fa' : No such file or directory

Question

[David]

Hi, I'm looking to leverage BWA to do some HLA typing. I can't get past the "Getting Started" code on the Github page for some reason. When running ./bwa index ref.fa I get the error below:

[bwa_idx_build] fail to open file 'ref.fa' : No such file or directory

I'm running this out of Terminal on MacOS. Please let me know if there's any more information you need from my end. Any help would be much appreciated! Thank you!

[swbarnes2]

In the future, the context of the error message is important for troubleshooting. You should quote the exact command line that generated the error. You should also show evidence that you did some troubleshooting yourself; e.g when the error says "file not found", you should put the command line that you used to determine if the file does indeed exist where you told the program it is.

Answer 1

[Mensur Dlakic]

[bwa_idx_build] fail to open file 'ref.fa' : No such file or directory

It is exactly as stated: there is no file with that name in a directory from which you are running the command. You can do one of two things: 1) copy ref.fa from wherever it is into your current directory, then repeat the command; 2) give a full location of the ref.fa file (something like /home/david/files/ref.fa).