Trying to run both hadoop MapReduce commands and linux commands in shell script

I have a shell script like this.

#!/bin/sh
/home/hduser/Downloads/hadoop/bin/stop-all.sh
echo "RUNNING HADOOP PROGRAM"
cd /home/hduser/Downloads/hadoop
sudo rm -R /tmp/*
sudo rm -R /app/*
cd
sudo mkdir -p /app/hadoop/tmp
sudo chown hduser:hadoop /app/hadoop/tmp
sudo chmod 750 /app/hadoop/tmp
hadoop namenode -format
/home/hduser/Downloads/hadoop/bin/start-all.sh
jps
hadoop dfs -mkdir -p ~/Downloads/hadoop/input
hadoop dfs -copyFromLocal /home/hduser/Desktop/iris.arff ~/Downloads/hadoop/input
hadoop jar ~/Desktop/try.jar 2 weka.classifiers.trees.J48  ~/Downloads/hadoop/input ~/Downloads/hadoop/output
/home/hduser/Downloads/hadoop/bin/stop-all.sh

I am invoking this script in my java program like this

    public class UIinput 
    {
        public static void main(String[] args) throws IOException
        {

    //      Runtime.getRuntime().exec("/home/hduser/Desktop/initial.sh");
    new ProcessBuilder("/home/hduser/Desktop/initial.sh");
            ProcessBuilder pb = new ProcessBuilder("/home/hduser/Desktop/initial.sh");
               Process process=pb.start();      
               InputStream is = process.getInputStream();
               InputStreamReader isr = new InputStreamReader(is);
               BufferedReader br = new BufferedReader(isr);

               String line;

               System.out.printf("Output of running %s is:", 
                  Arrays.toString(args));

               while ((line = br.readLine()) != null)
               {
                 System.out.println(line);
               }
    }
}

My start-all.sh,stop-all.sh and echo commands That are getting executed present in the script are getting executed but other commands are not.My output is like

Output of running [] is:no jobtracker to stop
localhost: no tasktracker to stop
no namenode to stop
localhost: no datanode to stop
localhost: no secondarynamenode to stop
RUNNING HADOOP PROGRAM
starting namenode, logging to /home/hduser/Downloads/hadoop/libexec/../logs/hadoop-hduser-namenode-ubuntu.out
localhost: starting datanode, logging to /home/hduser/Downloads/hadoop/libexec/../logs/hadoop-hduser-datanode-ubuntu.out
localhost: starting secondarynamenode, logging to /home/hduser/Downloads/hadoop/libexec/../logs/hadoop-hduser-secondarynamenode-ubuntu.out
starting jobtracker, logging to /home/hduser/Downloads/hadoop/libexec/../logs/hadoop-hduser-jobtracker-ubuntu.out
localhost: starting tasktracker, logging to /home/hduser/Downloads/hadoop/libexec/../logs/hadoop-hduser-tasktracker-ubuntu.out
stopping jobtracker
localhost: stopping tasktracker
no namenode to stop

Can anyone help me?I when I run my java code i want all of the commands to be executed in the shell script. Thank you