I have run roary on 1277 gff files (as a collection) and everything seemed to work fine. I got all green output blocks but when I go to the “Core gene alignment”, I see that is empty. The other outputs as summary statistics or Rtab files have something in them. Is there an explanation for this?
Based on previous errors, I have checked the names of the input files and they don’t seem to have spaces in them or any weird symbols.
Thanks for the help!
Just an update, I found out what was going on, the maximum number of clusters is set by default to 50000. The tool produces a green output for everything but, as described above, an empty “Core gene alignment”. This is quite confusing. The solution is to increase the default maximum number of clusters and roary will run smoothly.
Please note that this is alright to do in case you have made sure you don’t have any unwanted species as a contamination or if you’re working with a species that has a known wide pangenome like E. coli.