QIIME 2 has no plugin/command named 'metadata'.

[turtle]

I run the command bellow......

qiime metadata tabulate
--m-input-file fondue-output/metadata.qza
--o-visualization fondue-output/metadata.qzv

but it's showing error, (Error: QIIME 2 has no plugin/command named 'metadata'.)

I also run this command,
qiime info

and the result is,
System versions
Python version: 3.8.15
QIIME 2 release: 2022.8
QIIME 2 version: 2022.8.3
q2cli version: 2022.8.0

Installed plugins
fondue: 2022.4.0.dev0+12.g5afa120
types: 2022.8.0

Application config directory
/home/nihad/miniconda3/envs/fondue/var/q2cli

Getting help
To get help with QIIME 2, visit https://qiime2.org

What to do now?

[Oddant1]

Hello @turtle, how did you install QIIME 2, and what environment did you install it in? It looks like the installation didn't go correctly. Official installation instructions can be found here

[turtle]

I install it in conda environment. Do I neet to activate conda first? and then activate fondue?
or Do I need to uninstall qiime2 and reinstall again?

actually I was doing the fondue tutorial and this error is happening.

[adamova (Anja Adamov)]

Hi @turtle, It's nice to see you are using q2-fondue. In the tutorial you are going through, there is a note there mentioning that to run qiime metadata tabulate you have to ensure that you have q2-metadata installed in your conda environment. You can do this with this command: conda install -c qiime2 q2-metadata. Let me know if this solves your error.

For background information: When installing q2-fondue according to the installation instructions, you are not installing the full QIIME2 ecosystem but only the packages needed to get q2-fondue running. q2-metadata is not part of this crucial set of packages. Therefore, we have to install it additionally if needed.

[turtle]

@adamova I didn't see the Note for installing metadata, thank you so much.
As I'm following the fondue tutorial there is Downstream analysis in QIIME 2. And it has "demux" & "dada2" command. I solved the same error for demux with "conda install -c qiime2 q2-demux" but the I think the same isn't working for "dada2".

Here I uploaded the image.

[adamova (Anja Adamov)]

Hi @turtle,
To install q2-dada2 in this conda environment, you have to specify a few more channels. When running this with conda it is a lot slower than when using mamba install with the same parameters. Hence, I would suggest you run:
mamba install -c qiime2 -c conda-forge -c bioconda -c defaults q2-dada2. Let me know if this works.

We are planning to give more instructions on setting up the environment for running the complete q2-fondue tutorial soon .

[turtle]

I don't know. Is it not working? or I'm running the code wrong?

I just entered the folder where all the file is and run "conda activate fondue" then tried to run the suggested code "mamba install -c qiime2 -c conda-forge -c bioconda -c defaults q2-dada2".

but the following happens...

[adamova (Anja Adamov)]

hm, what is the output of the commands conda env list and conda info --envs?

If this error persists maybe it is worth first removing the existing fondue environment and then creating a new one with:

1. Deactivate current conda env & remove former fondue env:

conda deactivate
conda remove -n fondue --all -y

2. Install & activate new basic fondue environment:

mamba create -y -n fondue \
   -c https://packages.qiime2.org/qiime2/2022.8/tested/ \
   -c conda-forge -c bioconda -c defaults \
   q2cli q2-fondue

conda activate fondue

3. install the required dependencies for the tutorial

mamba install -c qiime2 -c conda-forge -c bioconda -c defaults q2-metadata q2-demux q2-dada2
qiime dev refresh-cache

[turtle]

@adamova
It helps, the code you suggest to install q2-dada2. But not in the process I mentioned above. I did the whole process from installing mamba and fondue from the stating code "conda install mamba -n base -c conda-forge" described in the "fondue tutorial". Can you please why I need to do the whole process?

and after the dada2 step I also failed to run the next command,

qiime feature-table summarize
--i-table fondue-output/dada2_table.qza
--m-sample-metadata-file fondue-output/metadata.qza
--o-visualization fondue-output/dada2_table.qzv

the error showing is....

[adamova (Anja Adamov)]

Sure, I suggested to reinstall all the plugins because it seemed there was something broken in your former conda environment and with the information provided so far I could not pinpoint what was broken.

Yes, as before you would need to install feature-table in your conda environment with the command:
mamba install -c qiime2 q2-feature-table

[turtle]

Thank you so much, @adamova

It really helped!!! I've been able to complete till the dada2 step.
But I just practiced this tutorial using these tsv files given in this tutorial. Now, if I want to do this for my own project where I have a list of project IDs in a csv or other format, how could I convert them into tsv format in qiime2? Like these provided in the tutorial folder of q2-fondue.....

metadata_files.tsv

metadata_files_runs.tsv

And again, Thanks for all the suggestions above.

[adamova (Anja Adamov)]

Hi @turtle, I'm happy to hear that my suggestions were helpful.

QIIME2 is not the tool to use for converting csv (comma-separated value fields) to tsv (tab-separated value fields) files. You can:

• either directly save the respective project IDs in a tsv instead of saving them in a csv file
  or
• you can do this transformation in a tool of your choice (e.g. Excel, TextEditor, R, Python - a simple "Tools to convert CSV to TSV" search in Google will give you more suggestions).

Good luck with your project!