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.
qiime alignment mafft \
I have these errors:
(1/3?) no such option: --o-masked-alignment
(2/3?) no such option: --o-tree
(3/3?) no such option: --o-rooted-tree
Any suggests would be appreciated (btw, I am a new qiime2 user).