Hi @slh277! It looks like maybe you ran into this error - can you take a look at the workaround suggested there and see if that works for you? Sorry you lost your progress after so much time spent on it. Also, don’t forget to experiment with --p-n-threads - you can experience a pretty significant speed-up by tuning this parameter to something makes sense for the system you are running QIIME 2 on. Let us know how it goes - thanks! 
The parent issue for this TMP bug can be found here.