Thank you for your handy detective work Matt. I am sorry that I am keeping you so busy with all of my questions!
I deleted those extra rows and resaved the metadata file and tried running the emperor plat command again and I got another error message saying that I had 17 values in the "Exper.Day" column that were non-numeric but this isn't true. This was true several steps back but I deleted those rows so that all of the data was numeric and saved the file as "metadataonlymesocosm2.txt". The bray_curtis_pcoa_results.qza file was not dependent on any previous metadata files right? So why I am I getting this error message:
(qiime2-2017.8) Helps-MacBook-Pro:Qiime2data lisacrummett$ qiime emperor plot \
--i-pcoa core-metrics-result/bray_curtis_pcoa_results.qza
--m-metadata-file metadataonlymesocosm2.txt
--p-custom-axis Exper.Day
--o-visualization core-metrics-result/bray-curtis-emperor-Exper.Day.qzv
Plugin error from emperor:
All values in a custom axis must be numeric, this summary shows the
invalid values and the number of times they were found in column
'Exper.Day': NaN 17
Please advise... you should still have my metadata file if you want to look at it.