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sudoku-64 -f%#xc puzz.txt > patt.txt prints the minlex pattern from a 81 char text string puzzle
or
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sudoku-64 -f%#xc 1...7..2..7.2....3..2..51...3.9....46....78....7.2..9...9.6.5..5....8..9.1.5...6.
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..X..X..X.X..X..X.X..X..X....X..X..X.X..X.X..X..X...X...X.X...X.X.X...X.X....XX..
Not sure why its not working for you. but sometimes the command line needs two %% instead of one % when in batch mode