Ok. So, this has been a confusion of mine for quite a while…And this thread is the closest I’ve seen my questions to be answered…I think I’m close to actually understanding what’s going on, but need some confirmations still…
I think my biggest mistake was to assume Metaphlan4 was integrated in the Humann pipeline starting from version 3.5? Do I understand it correctly that the Metaphlan used in every Humann3 version is still Metaphlan3 (which would explain why I get errors that it doesn’t recognise the newest, from Jan21 on, Metaphlan databases)?
I guess it would be this post that somewhat confused me. What does the first point under “What has changed” means exactly? Does it mean that we’re able to use Metaphlan4’s output as input in the Humann pipeline to take care of the taxonomy (but that Metaphlan should be ran separately, outside of the Humann pipeline first)? And so, not what I thought at first, that Humann >3.5 would run Metaphlan4 automatically for the taxonomy part and use this information for the functional annotation as well?