Metaphlan: error: unrecognized arguments: --bowtie2db

Microbial community profiling MetaPhlAn
1

MetaPhlAn version 4.2.2 (4 Jun 2025)

Hey,

I just installed MetaPhlan in a conda env, following the instructions on github.

When executing $ metaphlan --install --bowtie2db /home/usr/metaphlan, I receive the error metaphlan: error: unrecognized arguments: --bowtie2db.

What is the cause and what is the best workaround?

Thanks!

Best

2

Hi @mr2raccoon
In the new version of MetaPhlAn 4.2.2 some parameters have changed names, due to the fact that now MetaPhlAn also support long reads and can perform the mapping either with bowtie or minimap. The parameter --bowtie2db has been replaced with --db_dir (see here for the updated wiki: MetaPhlAn 4.2 · biobakery/MetaPhlAn Wiki · GitHub)