Execute spark-submit programmatically from java

I am trying to execute it via:

Process process = Runtime.getRuntime().exec(spark_cmd);

with no luck. The command ran via shell starts my application which succeeds. Running it via exec start a process which dies shortly after and does nothing. When I try

process.waitFor();

it hangs and waits forever. Real magic begins when I try to read something from the process:

 InputStreamReader isr = new InputStreamReader(process.getErrorStream());
 BufferedReader br = new BufferedReader(isr);

To do so I start a thread that reads from the stream in a while loop:

class ReadingThread extends Thread {

   BufferedReader reader;
   Wontekk(BufferedReader reader) {
      this.reader = reader;

   }

   @Override
   public void run() {
      String line;
      try {
         while ((line = reader.readLine()) != null) {
            System.out.println(line);
         }
      } catch (IOException e) {
         // TODO Auto-generated catch block
         e.printStackTrace();
      }
   }
}

Application starts, does some stuff, and hangs. When I abort my application, spark application wakes up (??????????) and completes remaining work. Does anyone have reasonable explanation of what is happening?

thanks