I'll do my best to clarify in the tutorial how to specify various optional parameters in admixr. Right now this is not obvious at all. :/
I will also make a separate note about this too-many-contigs issue for people working with this sort of data. You're definitely not the first person who works with non-human species and encountered a problem related to many contigs in the data (although this one was unknown to me)...
As explained here: