MSG: Got a sequence without letters. Could not guess alphabet

[hallkyl6]

I am running Roary on 83 Shigella isolates (should not be an issue of similarity), with 83 .gff files from Prokka.
It seems to run fine, and most of the output files are generated. However, the error shown in the attached image then gets thrown, and the core_gene_alignment.aln file is generated but empty (no sequences). Any recommendations on how to fix this?