I am analysing a group of bacterial genomes with Roary. The core and pan genome estimates are working great. However, when I try and use the query_pan_genome command for union, complement and intersection of groups of genomes I can't locate the file required for passing the -g flag e.g. 'clustered_proteins'.

The manual says it is a Groups file. Not sure what that is and cant locate anything that resembles it.

Anyone else come across this?

Cheers

Dan