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    “Warning: No structures processed. Existing output files may have been skipped, did you mean to delete them or to use the -overwrite flag?”

    This almost certainly means you already had done the run once and thus had the results already in the directory (probably named ????_0001.pdb, or with a 0001 tag in a silent file). (It may ship with a copy of the results already present.). Either deleting the pre-existing result, or using -overwrite, should fix this.