We are running Qiime2 and Picrust2 in the Winscp terminal. For this purpose, I have found the Picrust2 scripts which were already set up by someone who is no longer a part of our lab. In our terminal using Picrust2, we are unable to get the KEGG pathways including all KEGG levels. I think in our script we have some problem which I did not understand as I am not that much efficient. I am sending our script in the attachment for your reference. Kindly make changes in the part of KEGG pathways accordingly so that we would able to get all the categories of KEGG pathways. Thanks in advance
Hi @hussain,
Welcome to the forum!
Looks like you are using the stand alone PICRUSt2 tool, and not the q2-PICRUSt2 plugin. I’m pinging the developer of this tool @gmdouglas for his comments, though you may have better luck getting your question answered by recruiting helpthrough the official PICRUSt2 page.