Sorry for the delay. That does feel very slow - can you clarify what options you’re using for the run? The simplest speedup in HUMAnN 2.0 (that doesn’t alter the final results) is to use more threads, which will speed-up the various mapping steps (esp. translated search). Another options is
--bypass-translated-search, but this is only advisable if you’re working with a very well-studied community (with lots of reference genomes / pangenome coverage).
I don’t think splitting up the input file would be any more effective than working with multiple threads, and there are some steps that wouldn’t translate well with this approach (e.g. coverage filtering, which benefits from “seeing” all the sample reads in the same run).