Good questions. The program works on small files, i.e. smaller annotation files of just a few lines that I used to test. They are the same format as the full files. When using the full files however, the program would not exit, even after I started it just prior to leaving on Friday, to come back to it early this morning (didn't think it would take that long :p). I did get information printed in the output file however. The program can find the end of the files, and is designed to annotate just one file at a time.