Thank you Mike for your response!
I looked through the links, and from the first link I have found that the only difference in my problem code segment:
biom convert -i DADA2/ExportedRaw/Fungi-Table-With-Taxonomy.biom -o DADA2/ExportedRaw/Fungi-Table-With-Taxonomy.tsv -m Fungal-Metadata-BLM.tsv --to-tsv --header-key taxonomy
is the addition of my metadata with -m Fungal-Metadata-BLM.tsv. The rest of the code generates the needed files except for this last chunk of code. So I checked the second link. Sadly this is the same attempted fix I did before posting from that other post, Biom add metadata problem, and it didn’t fix the issue either.
Again thank you so much for your help, I am still relatively new to all this so I am likely overlooking something obvious.