Hi @skw,
I'm afraid there's not much you can do right this moment. I gave a summary of the current situation in this thread here: QIIME is caching your current deployment.....Illegal instruction (core dumped) - #78 by ebolyen
Outside of attempting to update unifrac manually (which is likely not going to go very smoothly because of all of the pins QIIME 2 sets) or emulating those instructions, you'll need to wait for us to update unifrac on our end. Hopefully soon!