I am using PROKKA with the following set of arguments:

$ prokka myorganism.fa --cdsrnaolap ON --rfam 1 --rawproduct

While my gbk and gff seems okay, I obtain an error file of 1.2Mb saying that all my features have inconsistent gene locations and "DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist".

I though that maybe because my genome is new the IDs are not recognized. Is that right?