it means you are doing something wrong, for example input and output file are the same and it's read-only.
without viewing the command you used it's impossible to know what could be the problem.
as alternative you can use quickbms and the relative script:
http://aluigi.org/papers.htm#quickbmshttp://aluigi.org/papers/bms/quakelive.bmsquickbms works also with the double-click on the executable so it's a joke to use