Feature Request: Clear error message for duplicated file names

[nickp60]

Hi,
Just a small request: I had a large dataset that (unknown to me) contained a few .gff files with the same basename. When executing, I kept getting the "Could not extract any protein sequences" error, asking me to check whether or not my files actually had a sequence in them. After renaming the files, the error went away. I may be the only one to have this issue, but would it be difficult to add a earlier error. something to the effect of "error! basenames of gff files must be unique"?

Thanks for writing Roary!

[katrielalex]

+1 to this feature request. In particular, running Prokka with --outdir foo makes it generate output files of the form foo/PROKKA_MMDDYYYY.gff, so if you directly invoke roary on the results you get this error.