I am trying to customize a GFF3 file containing features from two distinct genomes. I created the lines:
##sequence-region custom 1 278541
The length of the feature is the combination of the two individual genomes. I set each genome as a different region, thus I have the lines (3 and 436, respectively):
NC_<something> Genebank region 1 147589 . + . ID=<custom>;Name=<something>
NC_<something_else> Genebank region 147590 278541 . + . ID=<custom>;Name=<something_else>
I then ran gff3validator from the gt package but I got:
$ gt gff3validator <file>.gff3
gt gff3validator: error: the multi-feature with ID "<custom>" on line 436 in file "<file>.gff3" has a different sequence id than its counterpart on line 3
Since the ID is <custom> in both cases, the difference is in the names not the IDs. Or should the NC_<something> and NC_<something_else> be the same?
What I am missing?