From here I quote @XiaoshanShao:
We built MHCnuggets mostly on python2 instead of python3. Although we built it to be indifferent to python versions, it could be one aspect of your problem (probably not the main issue here).
Because Python2 is in its last version, I suggest to move to Python 3 and drop support to Python 2, so MHCnuggets can still be used everywhere.
From here I quote @XiaoshanShao:
Because Python2 is in its last version, I suggest to move to Python 3 and drop support to Python 2, so MHCnuggets can still be used everywhere.