Hi @Nicholas_Bokulich thank you! To try and narrow down the error I ran the following command using the default greengenes database:
qiime fragment-insertion sepp \
--i-representative-sequences rep-seqs.qza \
--o-tree insertion-tree.qza \
--o-placements insertion-placements.qza
And it seems to be working so I think the issue is my reference alignment and phylogeny
rooted_tree.qza (367.0 KB)
alignment.qza (2.5 MB)
Thanks for your help!