Thank you very much for your reply. I am wondering if MAFFT is even the correct alignment program to use for my data. I have a total of ~1.5 million sequences, and according to their website (MAFFT - a multiple sequence alignment program) this aligner works optimally for much lower sequences.
Will Qiime2 perhaps incorporate an aligner that can handle larger data sets?
Also, I can use a different aligner; however, I am not sure what format Qiime2 would need to use the output of an external aligner so that I may continue into alpha and beta diversity analysis w/ my data. Perhaps I can use Qiime 1? I was thinking these commands:
align_seqs.py
make_phylogeny.py
to get the .tre file, then input back into Qiime2 as a tree and continue to diversity metrics.