qiime diversity core-metrics-phylogenetic: command not found

Hi everyone

Anyone else can help me please with this error in Qiime2 2023 version.

I want to run:

qiime diversity core-metrics-phylogenetic \
--i-phylogeny 12-rooted-tree.qza \
--i-table 03-table.qza \
--p-sampling-depth 39955\
--m-metadata-file metadata.tsv
--output-dir core-metrics-phylogenetic

However, an error message appears called: "qiime diversity core-metrics-phylogenetic: command not found"
Can you help me with this issue? or guide me? I'm new in qiime2

I appreciate your help :slight_smile:


Can you run conda info to check that you have the correct conda environment for your install activated? If you do not, you will need to ensure that it is using: conda activate <name of your qiime2 environment>, and then try re-running the command.

Hi Keegan

Thanks for your help. I run conda info and the below versions were showed:

I believe the version are correct but I am not 100% sure. Also, I verified the qiime2 environment was activate too.

Hello @pau_u,
Nothing is standing out to me about your conda info.

I think something went wrong with the install and now it will activate but it wont actually run anything?

Can you run qiime info? If that doesn't run it would be a good sign that the install went bad and you should remove the conda env and re-install qiime. If it does run, can you attach a screenshot?

Hope that helps!



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