Plugin error from aldex2, An error was encountered while running ALDEx2 in R (return code 1)

Sorry for posting the same problem again.
I'm having ALDEx2 plugin error.

I tried the following code,

conda install bioconductor-aldex2 -c defaults -c bioconda -c conda-forge
conda install -c dgiguere q2-aldex2

But the error showing is,

I was able to install ALDEx2 in R but the above code is not working in "qiime2-2022.11" environment.
And as this is not working I'm also not able to run the following command for my analysis.

qiime aldex2 aldex2 \
    --i-table gut-table.qza \
    --m-metadata-file sample-metadata.tsv \
    --m-metadata-column subject \
    --output-dir gut-test

As expected the error showing is,

For your kind information I'm trying to use the qiime2R tutorial. But I'm stuck in the "Volcano Plot" in this tutorial because of this ALDEx2 plugin error.

I'm currently using qiime2-2022.11 and fondue installed in qiime2 environment.

Can anyone help me?
@lizgehret, @adamova @Mehrbod_Estaki please... :pleading_face:

I think the issue you are running into is because ALDex2 is not tested in 2022.11.
On this plugin's q2-library page, it says that its only tested on 2019.7 :qiime2:. I would recommend downloading qiime2-2019.7 and running the ALDex2 command there. This will probably fix the weird errors that you are running into.

If that doesn't work please run your command with the --verbose tag, so that we can get more info on the error:

qiime aldex2 aldex2 \
    --i-table gut-table.qza \
    --m-metadata-file sample-metadata.tsv \
    --m-metadata-column subject \
    --output-dir gut-test


1 Like

Dear @cherman2,

Can I install downgrade qiime2 like q2-2019.7 as an separate environment and use this to install ALDEx2?
And if "Yes", How can I install downgrade qiime2 version as a separate environment? without changing anything in my present qiime2-2022.11 environment? I don't want to change it because I have done all my previous analysis in 2022.11 version.

Hi @turtle,
You will want to conda deactivate so that you are no longer in your qiime2-2022.11 environment. As long as you are not in your qiime2-2022.11 environment, making another env should not effect your old one.
Then you will just follow the Natively installing QIIME 2 — QIIME 2 2019.7.0 documentation . Make sure to Click "Show Me the content on this page", q2-docs tries to redirect to the newest version.


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