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Files with the .py extension are linked to your default Windows Python installation. One way of using your virtualenv python executable instead is by typing python manage.py <command> instead.
Please also see the accepted answer of a question I posted on this matter before.
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You don’t specify which version of virtualenv you’re using. Recently, they’ve made --no-site-packages default, but if you’re using a version before this change was instituted, you need to specify that switch to prevent the main site-packages from loading in.
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Source:stackexchange.com