On Mar 7, 2012, at 2:40 , Jackie Lighten wrote: > I am attempting to run multiple assemblies, each in a separate terminal > window. However, once the first assembly is running, I can not start another > separate instance as Mira fails to find the new unique fasta file. Ummm ... could you please expand on this? I have problems following you there. Maybe post the log of one of the runs which "fail"? > I attempted at change the working directory, containing the new project > inputs, but this did not resolve the issue. Maybe I entered the –cwd in the > wrong position within the command line? Well, you didn't say what your command line actually was, so there again I currently cannot help. > Or maybe I can only run one assembly at a time using the same executable file? Definitively not: I a regularly running several MIRA instances in parallel. B.