Dear users,
I had the same error [MD5 checksums do not correspond!] but I think I made it work.
First, I took (transferred) humann databases from another machine and relinked them to my installation with humann_config.
humann_config --update database_folders utility_mapping databases/utility_mapping/
humann_config --update database_folders nucleotide databases/chocophlan
humann_config --update database_folders protein databases/uniref
I manually downloaded the MPA databases and I passed metaphlan options and strictly pointed to a that folder.
humann --input demo.fastq --output OUT --threads 6 --metaphlan-options "--bowtie2db /home/andrespara/HUMANN/nowmetaphlan"
BTW, I have humann v3.8 + MetaPhlAn version 4.0.6 (1 Mar 2023), both installed through mamba.
Cheers
Edited to add: I removed the database from this folder ~/mambaforge/envs/humano/lib/python3.10/site-packages/metaphlan/metaphlan_databases/ as @sachiwije mentioned below
A