Gitlab repositories not migrating to omnibus version

I am having trouble migrating gitlab repositories from manual version to omnibus version.

When I run:
sudo -u git -H bundle exec rake gitlab:backup:create RAILS_ENV=production
I get empty repositories!!

I even tried to copy them manually:

sudo cp -r /home/git/repositories/* /var/opt/gitlab/git-data/repositories/ sudo chown -R git:git /var/opt/gitlab/git-data/repositories/* sudo gitlab-rake gitlab:import:repos

But still no luck, the files are there, but in the admin interface it says the repo is empty.

Thanks for your help,