Hi @willowblade! I just ran the command you reported above, using the files you provided to @mortonjt in QIIME 2 2018.2 and everything appeared to work as expected. One minor change I had to make was to your sample metadata file - we added all new metadata handling in QIIME 2 2018.2, and one of the new rules has to do with the sample id column header (you have #Sample_ID, which is invalid, I replaced it with sample-id and that fixed the problem). To be clear, the issue wasn’t about your metadata file’s sample id label, but, if you run this in 2018.2 you will have an issue unless you rename that. Also related to that metadata change, the parameter --m-metadata-category was renamed to --pm-metadata-column.
I also ran this in 2017.12, just to double-check, and also was unable to reproduce the error you reported above. Long story short, give this a shot again (preferably using QIIME 2 2018.2) and let us know how it goes! 