nevermind, I figured it out. Don't specify your mod directory as the same directory core and base are in.

Setting up a headless linux server on CentOS 7. Everything looks basically good to go, until I try to generate a new map.

The command I'm using to create the map is:
# sudo /opt/factorio/bin/x64/factorio --create /opt/factorio/saves/1.zip --mod-directory /opt/factorio/data/ --map-gen-settings /opt ...