HuManN v4 output are different

[franzosa]

Sorry I’m not following your question. You want to use the newest MetaPhlAn with the newest MetaPhlAn database? If so, that is discussed here:

Announcing MetaPhlAn 4.1.1 release

Announcement: We are pleased to share that MetaPhlAn 4.1.1 is now available, which provides fixed and consistent taxonomic identification at high taxonomic ranks, allowing accurate relative abundance estimation also at high taxonomic levels. This is enabled by a new version of the MetaPhlAn database (vJun23_202403) containing the taxonomic updates. It is also possible to fix taxonomic profiles generated with previous versions of the MetaPhlAn database (i.e., vJun23_202307 and earlier) by running…