Running QIIME 2 tutorials via R .

Technical Support
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1

Hi all,

I am trying to work through the the CMI Tutorial, and run QIIME 2 via the proposed R commands.

However, I am unable to get past the first step. I've not been able to find any tutorials that explicitly discuss how this would work... So, here is what I've tried:

I activated my environment and then ran R:

(base)$ conda activate qiime2-amplicon-2025.4

(qiime2-amplicon-2025.4)$  R

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> library(reticulate)
> Metadata <- import("qiime2")$Metadata
Error in py_module_import(module, convert = convert) : 
  ModuleNotFoundError: No module named 'qiime2'
Run `reticulate::py_last_error()` for details.

What is the preferred way to run QIIME 2 via R? Are there other commands or packages I need to load, install, or fix?

2

Looks like this is an old issue with reticulate

Try telling it exactly what conda env to use, even if you are using R within the correct conda env already

# Before loading library(reticulate) or as the very first reticulate command
reticulate::use_condaenv("qiime2-amplicon-2025.4", required = TRUE)
library(reticulate)

# then
qiime2 <- import("qiime2")
Metadata <- qiime2$Metadata
1 Like
3

Thanks @colinbrislawn! That worked!

But wow... that is quite an important missing step!

There are some other R command errors too... I assume the R-based tutorials are still being tweaked...

4

Apparently this is fixed in reticulate v1.31 and the amplicon env yaml file claims 1.36 so I'm not sure what's going on.

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5

Oh that part I was having issue with works now thanks to your help... I am referring to later steps in the tutorial... like this step, e.g. zipfile <- import("zipfile"). I get an error stating how I should specify 'QIIME' or other method... nothing seems to work.

I do not have an immediate need for this R functionality to work. It's just that some of my colleagues here like to use R, and was hoping to show them how they can to use QIIME 2 via R...

6

Hello @SoilRotifer,

Could you post the full error you get? We certainly want the R api to work for people.

1 Like
7

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