Hi-
Thanks for your responses! I ultimately decided to use the original files from QIIME2 and the re-process them in the same way that I had it in phyloseq. (I also managed to export the phyloseq OTU table to a .biom format using this information: Importing dada2 and Phyloseq objects to QIIME 2 - #4 by ChristianEdwardson).
I’m wondering where you are getting this estimate?
The tutorial says that the full PICRUSt2 pipeline takes about "~15 min and 3.8 GB of RAM". Perhaps this is just for the mammal data. Mine took about an hour, even though I allocated 10GB to the virtual box- could just be that my computer is slow, or that I have more samples.
Any suggestions for additional downstream tools? I imported my pathways & ko back into R to do some ordination and PERMANOVA testing. I also read that some people like to use the STAMP software, but I've also seen some instances of differential abundance testing for the metagenomes and pathways. However, I haven't been able to figure out if this is kosher or not.
Thanks again.