Hi @Biancabrown! Which release of QIIME 2 do you have installed? You can find that info by running qiime info. My guess is that you're running into a bug with MAFFT that we fixed in the 2017.8 release:
Hi @Biancabrown! Which release of QIIME 2 do you have installed? You can find that info by running qiime info. My guess is that you're running into a bug with MAFFT that we fixed in the 2017.8 release: