query_pan_genome -a difference is not working

[kenken86]

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.

[tseemann]

@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)

[mauribra]

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

[cabrerad]

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'