I see here you are using as input a metagenome produced using long reads. MetaPhlAn is supposed to work with short read, however you can try using a local alignment instead the default end-to-end by running it with --bt2_ps very-sensitive-local.
We made available in the bioBakery tutorial a couple of subsampled HMP metagenomes for testing purposes, you can find it at metaphlan3 · biobakery/biobakery Wiki (github.com)