GOAL1 does not read the alphabet from a GFF file. Instead, after opening the automaton in a GFF file, the alphabet is collected from the symbols on the transitions. If, for example, the classical alphabet in the GFF file is {a, b, c} but only a appears in the transitions, then the alphabet of the automaton will become {a} in GOAL1. In GOAL2, the alphabet defined in the GFF file is the alphabet of the automaton.

In GOAL2 versions before 2012-04-09 (inclusive), the startup shell script changes the working directory to where the shell script is before invoking GOAL2 and then changes the working directory back after quitting GOAL2. If GOAL2 is not in the current working directory and no path is given for the GFF file (i.e., the file is in the current working directory), then the error occurs. For example, the error may be induced by the following command:

$ WHERE/GOAL/IS/goal complement FILE.gff

This error is actually that the GFF file is not found.