Last I checked, the SHOGUN plugin seemed like it needed some updates - it may or may not work at the moment, but you can find some documentation of it here.
While it won't help at the moment, there is a suite of plugins to support shotgun analysis in progress, so this may be ready to go for your next analysis. In the meantime, another option is that you can generate pathway/gene family/taxonomy tables with HUMANn and MetaPhlan, and import those tables for analysis with QIIME 2 using the new q2-sapienns plugin. I expect to put some documentation together on installing q2-sapienns in a QIIME 2 2022.8 environment in the next few days, and will post it to Community Contributions when I do.