I cannot get humann4 to work. simply using --input --ouput does not work. My metaphlan options dont work with humann. I have metaphlan 4 and the Jan25 database. Humann wants vOct22. I downloaded it. Humann wanted bt2 not bt21 files. I created those. It didnt work. The metaphlan.tsv files from metaphlan 4 output using the Jan25 db does not work with Humann 4 either. The format is not accepted. I simply cannot run humann 4 with anything.This goes back to the biobakery workshop week where I upgraded metaphlan and humann. I just want humann 4 to work so i can get some tables like the ones I experienced at the workshop. HELP,
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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.
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