picrust-users

I'm currently running a large dataset through PICRUSt2, but the process has been extremely slow—

Hey everyone, I wanted to open a discussion about NSTI values, since I think it's a bit unclear

Thanks Robyn! I tried setting the chunk_size and still received an error. The exact command input/

Hi Robyn, Thank you for your reply and for the very helpful advice! I also appreciate your decision

Hi everyone, I have a question about the pathway_pipeline.py outputs in PICRUSt2. After running the

Hmm OK. Can you post your commands that you ran to get to this point? Was there a reason that you

Hello, Apologies for my delayed reply. Can you please confirm whether you have followed the

It won't make a difference whether you run PICRUSt2 separately for each of the groups or together

Hi David, You will be able to run PICRUSt2 exactly the same way with full-length 16S sequences as

Hi again, I'm just coming back to this since updating PICRUSt2 on bioconda. I think that for Mac

Hi there, I finally had a chance to properly look into this and it was an issue with the automatic

OK great. Just an FYI that if you used conda/mamba to install before today, some of the default

Hi there, I think this could be an issue with your sequence names being only numbers, and one of the

Rscript /home/tools/picrust2-2.6.2/picrust2/Rscripts/castor_nsti.R qiime_realsc/arc.tre /tmp/

Hi there, What are you using to open these files? That definitely does sound a bit weird! Can you use

Hi there, Does the paid version of KEGG allow you to annotate genomes with it? If not, then no - you

Hello Robyn, I wanted to follow up as I reran the data using the same command. Interestingly, KO was

Hello Robyn, These are great ideas for validating taxonomic classifications/picrust2 outputs that I

Hi there, You're correct, COG and TIGRFAM are not available in the latest version - I've used

Help On Thu, 27 Mar 2025, 11:00 pm Robyn Wright, <roby...@gmail.com> wrote: I already said -

Thanks for clarifying. As this is a single function and not an entire database of organisms, I'd

Hi there, Unfortunately there isn't really any way around this. This means that there was nothing

Thanks so much! I appreciate it. Best, Anandi On Thursday, 27 February 2025 at 08:13:04 UTC-5 roby...

Thank you so much for the clarification, I got it! All the best! вт, 18 мар. 2025 г. в 17:06, Robyn

Hi, Could you give details on how you installed PICRUSt2 please? Thanks, Robyn On Tuesday, 25

Hi there, Could you give some more information on where you're running this - how much memory do

Hi there, Thank you so much for noticing this and pointing it out. I've now replaced the files in

Hi there, Could you please attach (as a text file, ideally) the full output that you get? And can you

Hi Jay, I'm actually not familiar with the biom-validate command, but you don't mention

I am so glad that this (finally) worked for you, and thanks for sharing the steps that worked -