I have a script in Python which do some computations. When I run this script in console it takes about 7 minutes to complete but when I run it thought Java shell it takes three times longer. I use following code to execute the script in Java:

this.p = Runtime.getRuntime().exec("script.py --batch", envp);

this.input = new BufferedReader(new InputStreamReader(p.getInputStream()));
this.output = new BufferedWriter(new OutputStreamWriter(p.getOutputStream()));
this.error = new BufferedReader(new InputStreamReader(p.getErrorStream()));

Do you have any suggestion why the Python script runs three time longer in Java than in a console?

update

The computation goes as follow:

1. Java sends data to the Python.
2. Python reads the data.
3. Python generates a decision tree --- this is a long operation.
4. Python sends a confirmation that the tree is ready.
5. Java receives the confirmation.

Later there is a series of communications between Java and Python but it takes only several second.