This sounds like a memory issue on your computer — emperor will start just fine with 33 samples but 550 cause your browser to hang when loading this visualization. You could try opening on a different computer, or just wait (it should eventually open unless if it is causing your browser to crash).
It seems there are errors caused by different metadata rows number when the emperor is loading files.
Also I have checked the log file while generating core-metrics. There are warnings like:
RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.34533786907859787 and the largest is 17.217787970350557.
Do you think these warnings are related to those different metadata rows numbers?
@katon, I think this might have to do something with your metadata. Have you been able to use your mapping file with another plugin? For example with qiime feature-table summarize? Otherwise, I think I would need to have a look at your metadata.
Hi @katon, thanks for posting these artifacts. It looks like you've found a bug in Emperor where the metadata needs to have at least one ore column (in addition to the sample identifier). I've generated a metadata file with an extra column and things seem to work just fine: