Odd. It seems like a problem with the Python installation/environment rather than with bigwigAverage specifically. How did you install deepTools? Have you changed the codebase at all? Have you mixed packages from different installation methods? Have you installed additional packages in a single environment since installing deepTools, potentially perturbing deepTools’ dependencies?

To avoid issues like this, I recommend installing deepTools in its own clean environment or container (or perhaps a separate environment/container just for these kinds of programs—after making sure there aren’t dependency/package conflicts).

For example, a straightforward way to do this is with miniforge (if needed, see the link for installation instructions and more details):

conda create -n deeptools -c conda-forge -c bioconda deeptools  # Using 'mamba' rather than 'conda' here is faster; you may need to install it first, e.g., in your base environment or another one that you use to run env installations (e.g., 'conda install conda-forge::mamba')
conda activate deeptools                                        # Activate the newly created env 'deeptools' to use it; depending on how your system is set up, you could do 'source activate deeptools' too

If the environment already exists and it’s activated, then run

conda activate environment_to_put_deeptools_in  # Run if not already activated
conda install -c conda-forge -c bioconda deeptools