@bimbam23 I'm not sure how pacbio reads work with transrate, we've not tested that. Given that works ok then it is possible, although not with the current version. I have some updates that haven't been pushed out yet that will allow you to have a different read set for each assembly.
@monicabritton I'm sorry you're having so many problems with snap. It is strange where it fails and seems to be architecture dependent. We are working on an update that will remove snap entirely and should speed up transrate and make it much more reliable.