Hi @alburse,
Weird. Everything looks okay.
Can you do one more thing:
Edit cryosparc2_worker/bin/cryosparcw to add the following lines right before activate_conda_env() (line 51):
conda deactivate || echo "No conda env to deactivate"
unset CONDA_SHLVL
unset CONDA_PROMPT_MODIFIER
unset _CE_CONDA
unset CONDA_EXE
unset CONDA_PREFIX
unset CONDA_PYTHON_EXE
unset CONDA_DEFAULT_ENV
unset PYTHONPATH
Save the file and try running the job again.