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?
We are working on a more elegant approach to this for the future, but a short-term (hacky) solution would be to copy an appropriate MetaPhlAn header (including the MetaPhlAn version number) onto the Kraken-produced file to trick HUMAnN into thinking it was made by an appropriate version of MetaPhlAn.
An upcoming HUMAnN release will have a flag to disable the sort of warnings that prevent running with mismatched databases/profiles. This is what I was alluding to above. I’ll comment on it in the corresponding release notes.
I managed to find a solution as hinted above just took a while to work out what header to use. But for Humann3.9 and metaphlan4.0.6 the header was #mpa_vJun23_CHOCOPhlAnSGB_202307
I’m also running Kraken2/Bracken with HUMAnN 3.9 and encountered the same issue: 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.
May I check if you added the header #mpa_vJun23_CHOCOPhlAnSGB_202307 to the Kraken report that was reformatted to MetaPhlAn-style using KrakenTools?
I’m using MetaPhlAn version 4.1.1 (11 Mar 2024) and humann v3.9, not sure why it does not work
Attached is the taxonomic-profile input to run HUMAnN
