I installed miniconda 3 and then Qiime2 without problems, however when I try to run qiime2 with the command:
conda activate qiime2-2021.8
I get this error:
ImportError: cannot import name '_errors' from partially initialized module 'h5py' (most likely due to a circular import) (/opt/apps/intel19/impi19_0/python3/3.7.0/lib/python3.7/site-packages/h5py/init.py)
Can anyone advise? Should I try another version of python? I am using 3.9 currently.
Thank you,
Keir Macartney
Hi @kjm1049!
This error is actually an indication that either your PATH or PYTHONPATH env vars are configured in a way that is causing all kinds of "mixing" of your isolated python environments. In particular, I see that the error is referencing a Python 3.7 deployment, however QIIME 2 ships in a Python 3.8 environment.
Go ahead and run env, then copy and paste the results here and we can lend a hand.
Awesome thank you! I ran env but got quite a lot of output so I piped it into a text file. Please let me know if you need anything else.
kjm1049_env_output.txt (25.7 KB)
Hi @kjm1049!
The offending env var is here:
PYTHONPATH=/opt/apps/intel19/impi19_0/python3/3.7.0/lib/python3.7/site-packages
Take a look at the conda FAQ for some details on why PYTHONPATH cannot be set inside an active conda env:
Managed to sort the issue! Thank you very much!
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