Hi @Faeze_Darbaniyan ,
Apologies for the delay. anadama2 does not provide a standalone CLI command that reliably reports its version (unlike humann --version or metaphlan --version). In fact, anadama2 --help or anadama2 --version often won’t work because AnADAMA2 is primarily a Python package/library rather than an executable.
Following command will confirm the anadama2 installation.
pip show anadama2
Please confirm the usage of metaphlan v4 without explictily providing databases as showing in the example here: MetaPhlAn 4.1 · biobakery/biobakery Wiki · GitHub
Regards,
Sagun