Hi @rlhughes,
If you tried the code here with any version of QIIME2 after 2018.8 it won’t work. I just added an update to the post, but basically you have to change “–source-format” to “–input-format” in the QIIME2 commands.
The phyloseq2qiime2.R code creates a BIOMV100Format biom file, so that may be the issue there.