MetaPhlAn 4 + HUMAnN 4 compatibility

Microbial community profiling HUMAnN
11

Thanks for sharing your setup steps, @jtrachsel! :+1:

I wanted to add a note about step 3: the MetaPhlAn database installation. In my environment, the command you suggested:

metaphlan --install --db_dir metaphlan_databases/vOct22 --index mpa_vOct22_CHOCOPhlAnSGB_202403

didn’t work as expected. Instead, I had to use --bowtie2db instead of --db_dir:

metaphlan --install --bowtie2db data/databases/metaphlan/vOct22_CHOCOPhlAnSGB_202403 --index mpa_vOct22_CHOCOPhlAnSGB_202403

This might be version-specific behavior or environment-dependent, but I thought it worth mentioning for others who might encounter the same issue.

Also, the root issue I was originally referring to relates to the utility_mapping database: the file mpa_vOct22_CHOCOPhlAnSGB_202403.tsv appears to be missing from the full_mapping_v4_alpha.tar.gz archive. I’ve opened a separate thread to discuss this issue in detail, as it affects compatibility with MetaPhlAn v4.1.1 and the mpa_vOct22_CHOCOPhlAnSGB_202403 database.

Thanks again for documenting your working setup; it’s been very helpful!

Best,
Fran
:man_technologist: