I have metagenome shotgunning data that I am running through metaphlan2. As per advice from other posts, I made sure to remove human contamination using kneaddata and trimmed based upon kit recommendations. However, the issue is removing the human data yields no results whatsoever from metaphlan2 (or even humann2.) The results are either "unclassified" or empty.
I'm trying to troubleshoot, and the only thing I can think of is perhaps that knneaddata is removing too many reads that might not be contamination.
Any ideas or thoughts would be much appreciative!