Hi @Faeze_Darbaniyan ,
Apologies you are still running into the installing issues for baqlava and its dependencies (humann and metaphlan). I see that you are now using humann v3.9 and metaphlan v4.1 with mpa_vJun23_CHOCOPhlAnSGB_202307 database in this post which is the correct path forward for baqlava installation.
Since metaphlan v4.1 demo is running as expected and humann v3.9 demo is not, this error usually happens when HUMAnN can’t properly run metaphlan --version, often because of an environment mismatch or small formatting issues in the command.
Could you quickly run:
which humann
which metaphlan
metaphlan --version
and confirm they’re coming from the same conda environment? Also, please try retyping the HUMAnN command manually just to avoid any hidden special characters(quotes).
Let me know what you see and we’ll sort it out.
Regards,
Sagun