You can run SEQUENCE without displaying a screen. In this mode it reads an input file provided on the command line and writes out a file containing an image of the resulting sequence diagram in .png format. You need to supply the --headless command line option and follow it by the name of the file containing the text describing the diagram. The name of the output file is formed by stripping the last extension off the input file name and then appending .png.

java -jar sequence.jar --headless my_sequence_diagram.txt