I think there are a few things going on here. Firstly, that first thread you referred to discusses how to run PICRUSt1 with QIIME2-outputted files. This is no longer required since you can use the PICRUSt2 plugin with QIIME2 (i.e. there’s no need to do closed reference OTU picking).
If the error you got was related to reference.fna.qza and reference.tre.qza missing then indeed you will need to acquire these files. You’ll need to download these files, which is done during the q2-picrust2 tutorial.
Also, this page seems to reference the first QIIME, so I used instructions from the support forum thread for the files above (from Gil Sharon)
I’m not sure what page you’re referring to here - would you mind clarifying?
Hi Gavin - I had assumed that the tutorial files were all relevant just for the tutorial, so I moved the files from the test folder to my working folder and all has been smooth from there. Thank you so much for your help and work!