Make use of AudioSystem.write() method. It is much easier
targetDataLine.open(format);
targetDataLine.start();
AudioInputStream ais=new AudioInputStream(targetDataLine);
AudioFileFormat.Type fileformat=AudioFileFormat.Type.WAVE;
/*
Other Audio file formats supported:
AudioFileFormat.Type.AU
AudioFileFormat.Type.AIFF
AudioFileFormat.Type.AIFC
AudioFileFormat.Type.SND
*/
File audoutputfile=new File('myfile');
//adjust extension according to AudioFileFormat
AudioSystem.write(ais,fileformat, audoutputfile);