Error running ShortBRED tutorial example

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?


I think you should use the old version muscle, the new version muscle is change the options.

MUSCLE v3.8.1551 by Robert C. Edgar is ok