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I am using Python3.6 in my project and I have specified the same in Web tab. I have created and set a virtualenv with same python version. Then I installed all my requirements using "pip3.6 install module". After migrating for the first time it created all the tables in my db. Now the modules installed works perfectly when I call them, but if I try to migrate through console it gives my ModuleNotFound error. For instance, I use "fcm_django" in my project, I can see the module file in site packages in my virtualenv of python3.6, I receive the fcm notifications as expected, but its just not letting me migrate or do anything new through console.

Does you console have your virtualenv activated when you call the migrate?

An easy way to do this would be to click the "start a console in this virtualenv" button in your webapps tab.

or when in console use workon myvirtualenv to activate it