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This was solved by using the correct settings in the passenger_wsgi.py:
import sys, os
cwd = os.getcwd()
sys.path.append(cwd)
project_location = cwd + '/my_project'
sys.path.insert(0,project_location)
INTERP = os.path.expanduser("/home/user/python/Python-3.4.3/venv/bin/python")
if sys.executable != INTERP: os.execl(INTERP, INTERP, *sys.argv)
sys.path.insert(0,'$HOME/python/Python-3.4.3/venv/bin')
sys.path.insert(0,'$HOME/python/Python-3.4.3/venv/lib/python3.4/site-packages/django')
sys.path.insert(0,'$HOME/python/Python-3.4.3/venv/lib/python3.4/site-packages')
os.environ['DJANGO_SETTINGS_MODULE'] = "my_project.settings"
from django.core.wsgi import get_wsgi_application
application = get_wsgi_application()
Source:stackexchange.com