Usually when executing commands using ProcessBuilder, PATH variable is not taken into consideration. Your python C:/Machine_Learning/Text_Analysis/Ontology_based.py is directly working in your CMD shell because it can locate the python executable using the PATH variable. Please provide the absolute path to python command in your Java code. In below code replace <Absolute Path to Python> with the path to python command and its libraries. Usually it will something like C:\Python27\python in Windows by default

package text_clustering;

import java.io.*;

public class Similarity {

    /**
     * 
     * @param args
     * 
     */
    public static void main(String[] args){
        try{
            String pythonPath = "C:/Machine_Learning/Text_Analysis/Ontology_based.py";
            //String pythonExe = "C:/Users/AppData/Local/Continuum/Anaconda/python.exe";
            ProcessBuilder pb = new ProcessBuilder(Arrays.asList("<Absolute Path to Python>/python", pythonPath));
            Process p = pb.start();

            BufferedReader bfr = new BufferedReader(new InputStreamReader(p.getInputStream()));
            String line = "";
            System.out.println("Running Python starts: " + line);
            int exitCode = p.waitFor();
            System.out.println("Exit Code : "+exitCode);
            line = bfr.readLine();
            System.out.println("First Line: " + line);
            while ((line = bfr.readLine()) != null){
                System.out.println("Python Output: " + line);


            }

        }catch(Exception e){System.out.println(e);}
    }

}

Just give them as separate strings in the array, instead of combining the last two into "val_31 val_32":

String[] command = {"script.py", "run",
                    "-arg1", "val1", 
                    "-arg2", "val2" ,          
                    "-arg3" , "val_31", "val_32",
       };

Otherwise it will escape the space in between val_31 and val_32 because you are telling it that they're a single parameter. Incidentally, you can also use the varargs constructor and skip having to create an array, if you want:

ProcessBuilder probuilder = new ProcessBuilder( "script.py", "run",
                    "-arg1", "val1", 
                    "-arg2", "val2" ,          
                    "-arg3" , "val_31", "val_32");

I don't think reading the executable (a series of binary numbers) will do any good. Also, The class java.lang.ProcessBuilder, in Java 1.5, is used to create operating system processe. Instead you should use the jython API: http://www.jython.org/javadoc/org/python/util/PythonInterpreter.html

Particularly: PyInstance and PythonInterpreter;

Your script runs, but it does not reach "Step 2", so

gUpdate.parse("BBCOntology.rdf" )

will be the source of the problem. Possibly it is because the file BBCOntology.rdf is not in the current working directory of the Python process. Or it could be that the Python process does not have permission to open that file.

It might be worth reading the error stream from the Python process and printing that out in Java. Use p.getErrorStream() in the same manner that you use p.getInputStream().

Or, easier, add an exception handler to your Python code that catches and prints exception messages to standard out:

import traceback

try:
    gUpdate = Graph()
    print ".> Step....1"
    gUpdate.parse("BBCOntology.rdf" )
    print ".> Step....2"
    print gUpdate.serialize(format='xml')
    print ".>  Finished......."
except Exception as exc:
    traceback.print_exc()
    raise exc

Your Java process should then print the message, which might be informative.