Hey @alexkrohn ,
It looks like the taxonomy that you are importing has an extra semicolon at the end of each row, e.g.,
This is creating an empty 8th level after importing. Compare closely to the NCBI taxonomy generated by RESCRIPt and you will see that this hanging punctuation is not there.
The Taxon column should be a single semicolon-delimited string.
Let us know if that does the trick!