I’ve tried running metaphlan 3 on our data multiple times, but I keep getting repeated errors like this one. Clearing the metaphlan database directory as instructed doesn’t fix the problem.
Downloading MetaPhlAn database
Please note due to the size this might take a few minutes
File /opt/anaconda/lib/python3.7/site-packages/metaphlan/metaphlan_databases/file_list.txt already present!
File /opt/anaconda/lib/python3.7/site-packages/metaphlan/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901.tar already present!
File /opt/anaconda/lib/python3.7/site-packages/metaphlan/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901.md5 already present!
MD5 checksums do not correspond! If this happens again, you should remove the database files and rerun MetaPhlAn so they are re-downloaded