New Biobakery Install Causing Issues with MetaPhlAn

Good afternoon,

I have been using this program for a while now, I am trying to set up a local Biobakery install, I am testing it using the same samples I have run before and now I am getting 100% unknown on samples where previously I got taxonomic classifications, I checked and I am using the same database and same version of Bowtie2. Do you have any idea what could be causing the issue?

Thank you in advance for the help