You need to "drain" both Streams associated with the Process, not only the input stream. The ProcessBuilder class makes that a little easier in Java5, but you can get all sorts of problems with Processes if you don't start a parallel thread. For details look for Michael Daconta's classic article "When Runtime.exec() won't"
When running a Process, you should provide for consuming both std out and std err streams. Your code waits for the Process to end, but does not consume the output while the process is running. This is a recipe for disaster since the process may hang trying to output to std out or std err.