You can also write a shell script file and invoke that file from the java code. as shown below

{
   Process proc = Runtime.getRuntime().exec("./your_script.sh");                        
   proc.waitFor();
}

Write the linux commands in the script file, once the execution is over you can read the diff file in Java.

The advantage with this approach is you can change the commands with out changing java code.

Use ProcessBuilder to separate commands and arguments instead of spaces. This should work regardless of shell used:

import java.io.BufferedReader;
import java.io.File;
import java.io.IOException;
import java.io.InputStreamReader;
import java.util.ArrayList;
import java.util.List;

public class Test {

    public static void main(final String[] args) throws IOException, InterruptedException {
        //Build command 
        List<String> commands = new ArrayList<String>();
        commands.add("/bin/cat");
        //Add arguments
        commands.add("/home/narek/pk.txt");
        System.out.println(commands);

        //Run macro on target
        ProcessBuilder pb = new ProcessBuilder(commands);
        pb.directory(new File("/home/narek"));
        pb.redirectErrorStream(true);
        Process process = pb.start();

        //Read output
        StringBuilder out = new StringBuilder();
        BufferedReader br = new BufferedReader(new InputStreamReader(process.getInputStream()));
        String line = null, previous = null;
        while ((line = br.readLine()) != null)
            if (!line.equals(previous)) {
                previous = line;
                out.append(line).append('\n');
                System.out.println(line);
            }

        //Check result
        if (process.waitFor() == 0) {
            System.out.println("Success!");
            System.exit(0);
        }

        //Abnormal termination: Log command parameters and output and throw ExecutionException
        System.err.println(commands);
        System.err.println(out.toString());
        System.exit(1);
    }
}

Change the final line of your program from

Process pp=Runtime.getRuntime().exec(arr);

to:

 for (String cmdLine: arr) {
    Process pp=Runtime.getRuntime().exec(cmdLine);

and you will execute each line separately, according to RunTime documentation.