Roary pan genome analysis: where can I find 'clustered_proteins' for the command Roary query_pan_genome -a union -g clustered_proteins *.gff

Question

[daniel.knight]

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

Answer 1

[mah2002]

Hi Dan, What system did you install to? I used ubuntu 14.04 and I had this problem too. It turned out to be a problem with my path, I re installed and finished with PATH=$PATH:$(pwd), problem solved. Meg