I was having great difficulties with this but I have solved my issue. I am on Windows 10 using Vagrant ssh in my virtualenv environment, the box I have installed is ubuntu/xenial64, Django version 2.1, python==3.6.
When I was installing packages I was using pip3 but most importantly I was using sudo and the -H
flag to install these packages. When I ran sudo pip3 freeze
my packages would come up, but when I ran a plain pip3 freeze
there would be no packages.
Then I tried the python3 manage.py startapp <YOUR APP NAME>
and it did not work same error as you.
I finally thought to try sudo python3 manage.py startapp <YOUR APP NAME>
it finally worked!
Hope this was help :)