Open kenken86 opened 6 years ago
@kenken86 is there are clustered_proteins
file in the test
folder you are running this from?
(it comes from the output of roary
I think)
I had the same issue, finally found out it was because you need all Roary output within the same folder as the .gff files so query_pan_genome works
I still have the same problem even though all files are in the same folder, query_pan_genome doesn't work. ' -bash: query_pan_genome: command not found'
When ran "query_pan_genome -a difference" it came up with
MacBook-Pro:test kenken$ query_pan_genome -a difference -o difference --input_set_one CAS988.gff,D14_15_08Ph.gff --input_set_two E09_10_13Ph.gff,E13_14_10sub.gff Error: Cant access the groups file: clustered_proteins Usage: query_pan_genome [options] *.gff Perform set operations on the pan genome to see the gene differences between groups of isolates.
I used the same files as I used with roary command which is working very well.