Hi @AllieNguyen, thanks for reporting this problem. If at all possible would you mind uploading this artifact into Dropbox or alternatively sharing it through the forum?
After looking at these plots, it seems like you have found a bug. Emperor cannot display a plot where there are only two samples. More specifically (in your case) since any resulting ordination with 2 samples would have at most 2 dimensions, the code is failing because it assumes all displayed matrices will have 3 dimensions.
I would be surprised if this worked before, maybe you had included more samples before?
@AllieNguyen four samples should display with no problem. Unfortunately what is crashing is not the QIIME command but the user interface that displays the data. I’ve opened an issue here to fix this or provide a meaningful error message.
As a side note: I would suggest that you reconsider using an ordination as a display for two samples, since it might not be the best representation.