Dear bioBakery team,
first many thanks for the magnificent work on MetaPhlAn 4.0.5, and the publication. Bravo to all the team!
As far as I can follow the commits on HUMAnN, it seems that HUMAnN (even v3.6) is compatible with MetaPhlAn versions that use database version “vJan21” or older, but not the brand new “vOct22” used by MetaPhlAn v4.0.5. My question is then: is my interpretation correct? And then what is the latest version of MetaPhlAn compatible with HUMAnN? And, if I may, are you cooking us some nice surprise for HUMAnN ?
for GMT, Raynald
Your interpretation is correct. HUMAnN 3.6 includes compatibility files to associate MetaPhlAn 4 profiles from the Jan21 database with the HUMAnN 3 pangenome collection. We are working on a HUMAnN 3.7 release that will add compatibility with the new database. In the meantime you can add
--metaphlan-options="--index mpa_vJan21_CHOCOPhlAnSGB_202103" to your HUMAnN 3.6 command to tell MetaPhlAn 4 to get/use the previous index.
We are continuing to work on the HUMAnN 4.0 release which will avoid these extra v3-v4 compatibility steps. Once we have an alpha that’s ready for testing we’ll announce it here for folks to try. Stay tuned!
@franzosa Many thanks for the clarification and insights!