Hi @Tawny_Bolinas, are you able to share your input data? If so, I can try to reproduce the error. Could you let me know the results of running conda list? In the mean time I'll see if I can replicate it with other datasets.
In the past this has happened when someone's dataset has a sample where, after merging, there are no reads left.If that's the case we can potentially add some better error handling for the edge case.