Were you able to solve your --parttree problem? I am running into the identical problem as the number of sequences in my feature table is larger than 1 million.
I have tried to run this, but received the error below.
Type qiime phylogeny align-to-tree-mafft-fasttree --help to see the available parameters. I recommend reading through the q2-phylogeny tutorial. Other tutorials can be found here.