Either, increase the disk size or lower the threshold in the UI.
On the GUI: Manager » System settings » General settings (at the very botton reduce to 500, or whatever you like)
For reference, here are instructions for setting these limits via the GUI, CLI, and configuration files.
In latest version it is changed
from version 6.3.3
on GUI : Settings>>Server Settings >> general settings >> Pause indexing if free disk space (in MB) falls below * (make the size whatever you want here)