Hi @sjohnson
If you are doing a fresh installation (no previous metaphlan or humann installation in your conda environment) humann3.6 recipe should automatically install metaphlan 4 (if this is not the case, please report it into the humann subforum HUMAnN - The bioBakery help forum). In case you are upgrading your previous installation, metaphlan should also be manually upgraded. Please have a look at the following guide (it is for 3.5 but works the same for 3.6): Announcing HUMAnN 3.5