Error when conda-installed qiime2-2019.7

Technical Support
1

I have already successfully installed a qiime2-2019.4 enviroment using miniconda3 (python version 3.6).
But when I install qiime2-2019.7 with same way
(command “conda env create -n qiime2-2019.7 --file qiime2-2019.7-py36-linux-conda.yml”)
I got some error informention

Collecting package metadata (repodata.json): done
Solving environment: done
Preparing transaction: done
Verifying transaction: done
Executing transaction: / Killed

This “qiime2-2019.7” enviroment seems fine because I can still activate it and use command such as “qiime --help” or other plugins

However i cannot install scikit-learn

$conda install --override-channels -c defaults scikit-learn=0.21.2

DirectoryNotACondaEnvironmentError: The target directory exists, but it is not a conda environment.
Use ‘conda create’ to convert the directory to a conda environment.
target directory: /home/ubuntu/miniconda3/envs/qiime2-2019.7

I also remove the enviroment qiime2-2019.7 and reinstalled again.Still the same killed error.
Should I also remove the packages in ~/miniconda3/pkg3 ?

Need some help guys

2

Sounds like the installation is not completing, so you are not just missing some packages, you are also not making a fully fledged conda environment. Strange that you can activate and run some QIIME 2 commands then — you have a frankenstein environment.

Yes maybe try updating conda and use conda clean --all then reinstall as a first pass at fixing. If that does not work, it’s time to roll up our sleeves.

3

I do follow this advise but it still has some error.I donot think it is a Qiime2 issue but a server issue because i switch to another server and it did well.Maybe a memory issue.I can still use it with a frankenstein environment!
Thx u.

4

Oh very interesting — could also be a permissions issue? You may want to discuss with the server administrator to see how you can resolve.

I wouldn’t be so sure — a few plugins use scikit-learn (or other plugins that do), so you will run into roadblocks. I suppose frankenstein is the wrong analogy… more like you built a robot that is missing several parts! I would personally be a bit nervous — what else is missing?