[galaxy-dev] BWA empty output and failed alignment

Hi, 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 Praveen