We will be adding support for MetaPhlAn 4.2 + the Jan25 SGBs in the next release of HUMAnN. Right now the HUMAnN 4 alpha does not yet support these latest versions. My recommendation would be to stick with running HUMAnN 4 with MetaPhlAn 4.1 + the Oct22 SGBs for now. If you’d like to also experiment with MetaPhlAn 4.2, you could do so in a separate conda environment.
If you would like to use MetaPhlAn 4.2 output with HUMAnN, you could run MetaPhlAn outside of HUMAnN including the following flags: -x mpa_vOct22_CHOCOPhlAnSGB_202403 -t rel_ab_w_read_stats. This will force MetaPhlAn 4.2 to 1) use the SGB catalog that HUMAnN 4 is currently built against (i.e. Oct22, but with updated taxonomy) and 2) include the additional coverage statistics in the output that HUMAnN expects. You could then pass the resulting taxonomic profile to HUMAnN using the --taxonomic-profile flag.