The migrate sub-command was not introduced to Django until the 1.7 release. The first thing I would do is to make sure the correct version of Django is being installed in your container. The best way to do this is to specify a specific version in your requirements.txt file. E.g:

Django==1.9.8

You'll also want to make sure that your project structure is correct. As Dokku uses a lot of best practices from Heroku, the easiest way to do that might be to use Heroku's Django Starter Template for a new projects.

You can start a new Django project using that template, by running:

django-admin.py startproject --template=https://github.com/heroku/heroku-django-template/archive/master.zip --name=Procfile myproject