I am attempting to create a core genome alignment of a set of Corynebacterium diphtheriae genomes, and on the advice of collaborators have asked Roary to not split paralogs and include the paralogs in the core alignment output using the following command:

roary -e -s -ap *.gff

The csv, newick tree and all other outputs have been completed successfully, but the alignment produced is 3.2 KB, having only the genome names and nothing else at all.

Any advice would be really appreciated as to what I'm doing wrong!