PICRUSt2 for Mac M2

[Kaitlin Ingram]

Hello all!

I have seemingly tried all the workaround to get my Mac to run PICRUSt2. I have tried Rosetta, Mamba, even installing a Docker. All of these failed miserably. I tried removing all of the old environments/data/folders to start completely over multiple times. No matter what I do, I get some kind of error (mostly that after each installation my computer still can't identify PICRUSt anywhere).

Does anyone have any thoughts?

I then went to Galaxy (the European version, of course) but I've been having different issues there. I'm out of luck so far other than literally buying a PC which is ridiculous. Any thoughts appreciated!

[Salvador EJ]

Hi,

Your problem is very common on Mac computers with Apple ARM chips.

You could try the Picrust2 which is available on NIH-Nephele. It is an open access platform. https://nephele.niaid.nih.gov/ 

The paper is here: Nephele: a cloud platform for simplified, standardised and reproducible microbiome data analysis. Bioinformatics, 34(8), 1411-1413. https://pubmed.ncbi.nlm.nih.gov/29028892/

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[Robyn Wright]

Hi there,

Could you give some details on what exactly you've tried please, and maybe a text file with the terminal output? I have an M1 Mac and specifying the platform when creating the environment as well as installing r-essentials worked for me (like here). 

If you won't want to run anything aside from the default pipeline, you could try running the PICRUSt2 plugin for QIIME2 - I'm currently in the process of trying to update that, but currently it still uses PICRUSt2-v2.5.3. I think some of the documentation has been moved around with the updates currently going on with the QIIME2 website, but you can see the old installation instructions here.

Robyn

[Kajal Kumari]

Hey .. finally I installed qiime2 in my system ... I have Raw data ...how I upload it in qiime2 ... I need biom and fasta file which I run in picrust2 for functional potential

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[Robyn Wright]

Please follow the instructions for using QIIME2 on their website: https://amplicon-docs.readthedocs.io/en/latest/

They also have a forum where you can get help on running QIIME2. 

We also have a standard operating procedure for QIIME2 for steps that you need to run before you can run PICRUSt2: https://github.com/LangilleLab/microbiome_helper/wiki/Amplicon-SOP-v2-(qiime2%E2%80%902024.5)

If you are new to microbiome analysis, we have some lecture recordings from a workshop last year on this page. 

[Kajal Kumari]

Hello everyone
How to interpret picrust2 output

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[Robyn Wright]

Hello,

What are you trying to get from the PICRUSt2 output: which functions are you interested in for your research project? What is your research project about, what are your hypotheses? How are you hoping to use PICRUSt2 to test your hypotheses?

The output from PICRUSt2 gives you predictions for the functional content of the microbes in your samples. We give this as EC numbers, KEGG orthologs and MetaCyc pathways by default. You can see some suggestions for next steps for visualisation of analysis in our FAQ page here, and ggpicrust2 offers a lot of potentially useful analyses, but ultimately we don't know what your research project is, why you've run PICRUSt2, or what you want to get from your data by running PICRUSt2 (and this isn't for us to decide, either). These are some possible next steps, but part of scientific research is coming up with your own questions and hypotheses, and we can't do that for you.

Best wishes,

Robyn

[Kajal Kumari]

Functional prediction

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[Robyn Wright]

Hi again,

I'm just coming back to this since updating PICRUSt2 on bioconda. I think that for Mac the best option currently is probably installation from source - I think that there are potentially a few dependency issues that seem to come up with updating Macs, to do with Python versions, arm-64 vs osx-64, etc. The instructions here for installing on a Mac have worked for me this morning - could you try running those?

Best wishes,

Robyn