query_pan_genome -a difference problem

sanger-pathogens / Roary

Rapid large-scale prokaryote pan genome analysis

http://sanger-pathogens.github.io/Roary

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query_pan_genome -a difference problem #237

Open rndg20 opened 8 years ago

rndg20 commented 8 years ago

Hi,

I two sets of isolates and am trying to find the differences between them. I have run the following script; query_pan_genome -a difference --input_set_one ../path_toset1/.gff --input_set_two ../path_toset2/.gff

The script runs, but the outputs aren't correct.

set_difference_unique_set_two_statistic.csv, is a blank document except for headings. set_difference_unique_set_one_statistics.csv, only lists the genes for 1 isolate.

I am using the latest version of roary, 3.6.0

tseemann commented 8 years ago

@rndg20 your command looks broken - do you really mean ../path_to_set1/.gff ?
or *.gff ?