Hi @soung,
Thanks for the clear description of the problem.
From the paths it looks like even though cryosparc is using the correct python (/home/cryosparc/anaconda2/bin/python), modules are being preferentially loaded from a different location (/home/.local/lib/python2.7/site-packages). All the python modules installed in the cryosparc python installation should be in /home/cryosparc/anaconda2.
Can you check if your $PYTHONPATH is being set somehome? There are some python EM packages that change your shell startup files and set the $PYTHONPATH directly, which can lead to this kind of problem.
Ali