Update: I was finally able to successfully run transrate within transfuse for the two assemblies I want to "fuse". (I discovered that it was always the second assembly that snap stalled on, so switched the order of the assembly fastas and got one good run for each.) Unfortunately, snap has stalled again at the end of running the alignment on transfused_assembly_cons.fa. I also notice that the number of transcript contigs only decreased by 0.7% between the "all*.fa" and the transfused_assembly_cons.fa, so not much of an improvement. I will try running transrate on the transfused assembly to get the "good" and "bad" contigs and assembly score.