Welcome @bburnes
The error message is probably referring to the other inputs.
Tutorial step Hands-on: 16S Microbial Analysis with mothur (extended) / 16S Microbial Analysis with mothur (extended) / Microbiome
Screenshot
Did you source both the fasta and tax datasets from the tutorial? Then, are both the fasta and count table inputs from the prior Remove.seqs step?
I can let you know that the taxonomy dataset has a special format. It is important to load this up to Galaxy using all defaults in the Upload tool. Then, allow Galaxy to perform the implicit format conversion during runtime – there will be another copy of the file in your history nested inside of the original file (same data, different format). Try to not disturb that data. If you already did, try loading the data again this way to see if it can resolve the current problem.
Then, tools in this protocol are used a few times, so it is pretty easy to mix up the datasets! Later on you can use a workflow that will do the data sorting for you.
Finally, I just started up the tutorial’s workflow at UseGalaxy.org to see what happens! This is the shared workflow invocation.
Please let us know if you are able to resolve this or not! You are also welcome to share back your history for a closer review. 
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