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
Thanks in advance
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