Function Profile (COG) for individual replicons/scaffolds from a mutli-scaffold genome

[Talitha Rogers]

Hi All

I am trying to create function profiles for each replicon in my multi-replicon genome (Paraburkholderia sprentiae WSM5005). My attempts have resulted in the grouping of all 5 scaffolds together and I can't figure out how to just get the profile for each individually. 

Does anyone have any tips?

Thanks