Dear all, thank you for using PhyloPhlAn and reporting this.
I’m afraid I’m experiencing the same issue but this is a bit independent from PhyloPhlAn. In particular if the mapping step is carried out by diamond. It is very likely you have installed diamond version >=2 and in comparison to the first version, it is much slower. However, this is likely due also to a bug present in the first version that was recently discovered, you can read more about this here: Announcing HUMAnN 3.6 (Critical Update).
Apologies for not being more helpful in this case.
Many thanks,
Francesco