Welcome, @paul_daly
Hopefully you found this already but if not, this is what to try instead.
I used that tool at UseGalaxy.org a month ago, and it worked fine with several genomes (how to choose a genome). But if you have trouble, we can follow up more. The server where you are working will matter along with the format of the input GFF3 and the target reference genome. You can post screenshots or share your history to clarify those details and we’ll help to sort out what is going on.
How to do that is in the banner at this forum, or see directly here → How to get faster help with your question
Please let us know how this works out! 