I have been trying to run ShortBRED with python (2.7), but I am getting an error with one of the protein clusters with the following error:
Invalid command line
Unknown option in
subprocess.CalledProcessError: Command ‘[‘muscle’, ‘-in’, ‘example_identify/clust/fams/tonB_EGT66731.faa’, ‘-out’, ‘example_identify/clust/fams/tonB_EGT66731.faa.aln’]’ returned non-zero exit status 1
It worked well for other protein clusters:
tonB_ABS46221.faa tonB_AIE04533.faa tonB_CAE16995.faa tonB_CDO13422.faa
BUT, for tonB_EGT66731.faa, it returned the above error. Does anyone know how to handle this?