There’s a lot going on here. From the first part, it looks like you’re using a very old HUMAnN (v3.6). HUMAnN 3.5-3.9 were released for compatibility with different versions of MetaPhlAn 4, and they have to be paired with the right version. If you want to stick with HUMAnN 3, I would use v3.9 and install alongside MetaPhlAn following these release notes:
The other option is to upgrade to HUMAnN 4.0 alpha:
Which is the latest release and works with MetaPhlAn 4 using its mpa_vOct22_CHOCOPhlAnSGB_202403 index.
In general, when debugging MetaPhlAn-HUMAnN communication, it’s helpful to make sure you can analyze your sample / a demo file with MetaPhlAn outside of HUMAnN, as this can sometimes reveal installation / runtime issues that are not related to the HUMAnN run itself.