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ffmpeg video comparison using java

I am working on ffmpeg video comparison. I call ffmpeg video comparison command from java. After execute the command. The comparison process was stopped. If i kill the javaw.exe the command resume and working and result file was created. Am using following code to execute the command:

String command2CompareVideos = "D:\\bin\\ffmpeg -y -i D:\\postVideo_16.mp4 -i D:\\postVideo_16.mp4 -filter_complex \"[1:v]format=yuva444p,lut=c3=128,negate[video2withAlpha],[0:v][video2withAlpha]overlay[out]\" -map [out] D:\\ResultVideo.mp4"

    String[] processCommand = { "cmd", "/c","CALL",  command2CompareVideos};
    Process imgComProcess = Runtime.getRuntime().exec(processCommand);  
    imgComProcess.waitFor();
    BufferedReader ouPiutReader = new BufferedReader(new InputStreamReader(imgComProcess.getInputStream()));
                String outPut = ouPiutReader.readLine();
                while(outPut != null){
                    outPut = ouPiutReader.readLine();
                    System.out.println("Output: "+outPut);
                }

Not sure, but just go through the link and it may help you to understand about JAVAW.EXE.

http://javapapers.com/core-java/java-vs-javaw-vs-javaws/

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