MetaPhlAn version 4.1.0 (23 Aug 2023)
metaphlan --install --index mpa_vJun23_CHOCOPhlAnSGB_202403 --bowtie2db metaphlan_db/
After downloading the db, command quit because I hadn’t installed bowtie2 in the conda env. Fixed and now it’s re-downloading the db. Would be cool if it checked for the download and checked md5, then move to next step if already downloaded.