The command line tools (obomerge, obo2obo, obo2flat, obodiff) do not use the same memory management settings as OBO-Edit. Their memory settings are configured independently by passing options directly to the Java interpreter.
This is done through the use of a .vmoptions file. Each command-line utility may have a file named <utility name>.vmoptions in the same directory as the utility. Each line of this file should contain a single option to be passed directly to the Java virtual machine. The last line of this file MUST BE BLANK! Otherwise the options file will not be read correctly.
To run obomerge with 1024M of memory, create a text file named obomerge.vmoptions in the same directory as the obomerge utility with the following contents:
-Xmx1024M
Note the blank line at the end of the file.