I tried to convert Kraken2 report with " Krakentools: Convert kraken report file to MetaPhlAn-style" (and bypassed the taxonomy profiling step) and provide it, but Humann3 outputed:
ERROR: The MetaPhlAn taxonomic profile provided was not generated with the expected database version. Please update your version of MetaPhlAn to at least v3.0.
Do you know how to use Humann2 with Kraken2 classification? or at least use/run Humann2 regardless taxonomy just to profile the community as a whole (regardless of the metaphlan classification)? My problem is that MetaPhlan is doing very poorly on my dataset. So I prefer to stay with Kraken2 classification?