I am trying to use the picrust2 plug in. Here is my code and my error…I am a bit lost as what to do, am I not activating the right environment? (Source activate qiime2-2018.11). Usually, I can figure this out, but its been a few days…
Also, the output files from q2-fragment-insertion work in downstream applications. It looks like all tip states are hidden, but I don’t know what that means if it works for other things…
I am not a developer of q2-picrust, but I did just have quick peek at the official tutorial and I noticed this little tidbit:
Note that you need to place your ASVs into the PICRUSt2 reference files - if you place your ASVs into the default SEPP reference files you will get downstream errors .
It looks like you might gave used the default SEPP reference (according to your first command).
Have you tried following the steps in that tutorial? If not, maybe give that a whirl
ASV files? SEPP is still used in the tutorial, which I followed. I also used the q2 filter-insertion pipeline separately. I took the original files out of DADA2 post filter for greater than 50 features.
Should I run it without SEPP?
Thank you for your response!! Love the dinosaur emoticon! =)
I did follow the tutorial line for line…SEEP is there, so I am a bit confused and would really like some more clarification. Thank you. for your response in advance!!
Should I export to a .biom file then to q2-picrust2?
I am not a dev for this plugin, and I have never used it, so please take my advice with a grain of salt. According to the tutorial I linked to, you need to download the picrust reference phylogeny (and reference alignment) and use that as input into q2-fragment-insertion — the example command demonstrating that is about halfway down the page on that tutorial.