I have a problem running BWA in my local instance of galaxy.
When I try to align the short reads in bwa, sometimes it gives empty file 
otherwise it throws the following error

BWA Version: 0.6.1-r104
The alignment failed.

The output file is empty. You may simply have no matches, or there may be an 
error with your input file or settings

But the alignment works fine in command line. Can anyone help me to resolve 
this issue.

Thanks in advance

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