running checkm2 issue

[chanyuk]

i installed CheckM2 via mambaforge but when i try to run it in the command line it gives the error message as follows:

(checkm2) cyu@ip:~/mambaforge$ checkm2 Traceback (most recent call last): File "/home/mambaforge/envs/checkm2/bin/checkm2", line 27, in <module> from checkm2 import predictQuality File "/home/mambaforge/envs/checkm2/lib/python3.6/site-packages/checkm2/predictQuality.py", line 1, in <module> from checkm2 import modelProcessing File "/home/mambaforge/envs/checkm2/lib/python3.6/site-packages/checkm2/modelProcessing.py", line 17, in <module> from tensorflow import keras File "/home/mambaforge/envs/checkm2/lib/python3.6/site-packages/tensorflow/__init__.py", line 41, in <module> from tensorflow.python.tools import module_util as _module_util File "/home/mambaforge/envs/checkm2/lib/python3.6/site-packages/tensorflow/python/__init__.py", line 41, in <module> from tensorflow.python.eager import context File "/home/mambaforge/envs/checkm2/lib/python3.6/site-packages/tensorflow/python/eager/context.py", line 28, in <module> from absl import logging File "/home/mambaforge/envs/checkm2/lib/python3.6/site-packages/absl/logging/__init__.py", line 97, in <module> from absl import flags File "/home/mambaforge/envs/checkm2/lib/python3.6/site-packages/absl/flags/__init__.py", line 35, in <module> from absl.flags import _argument_parser File "/home/mambaforge/envs/checkm2/lib/python3.6/site-packages/absl/flags/_argument_parser.py", line 82, in <module> class ArgumentParser(Generic[_T], metaclass=_ArgumentParserCache): TypeError: metaclass conflict: the metaclass of a derived class must be a (non-strict) subclass of the metaclasses of all its bases

[javiercnav]

Hello there, having the same issue here. I had to reinstall checkm2 today. Previously, I had a run that went smoothly

[ac-simpson]

I'm having the same problem too - just installed checkm2 via mamba, and got this exact error.

[ilnamkang]

I'm having the same error too.

[microbial-cookie]

I have the same error, too. see below:

[sklucas]

I solved this by including the specific version of python, since it was the only thing my environment created by mamba create -n checkm2 -c bioconda -c conda-forge checkm2 that differed from the yaml in this repo. New code: mamba create -n checkm2 -c bioconda -c conda-forge checkm2 'python>=3.7, <3.9'

[ac-simpson]

@sklucas , awesome, thank you, I now have checkm2 running properly!

[danchurch]

Also had this issue. Constraining the python version as per @sklucas worked for me.

[jsgounot]

Thanks, this should be in the readme file.