Parsing owl to ntriples and store them in separate files

Question

Trying To-Do:

1) Execute Rapper functionality for each file in 'data' folder to get ntriples out of owl files.

2) Copy the resultant ntriples into another file as 'ntriples/output_file.ntriples'

3) Command : rapper -o ntriple ./data/file1.owl > ./ntriples/file2.ntriple

Tools used:

1) Rapper Redland libraries

2) System command executor code from Devdaily

3) Eclipse IDE

Issues:

1)No issues when I execute the following code:

        /* Running Commands for Multiple Files
     * for each file in the 'data' folder, call the rapper command
     * */
    List<String> commands = new ArrayList<String>();
    StringBuilder parsedTriples= new StringBuilder();
    final File folder = new File("./data/");

    //add commands
    commands.add("rapper");
    commands.add("-o");
    commands.add("ntriples");

    //walk the whole folder and retrieve the file path
    for (final File fileEntry : folder.listFiles()) {
        commands.add(fileEntry.getPath());
        parsedTriples.append(getTriples(commands));
        //System.out.println(parsedTriples.length());
        commands.remove(3);
    }
public static StringBuilder getTriples(List<String> commands) throws IOException, InterruptedException
{

    SystemCommandExecutor commandExecutor = new SystemCommandExecutor(commands);
    int result = commandExecutor.executeCommand();

    // stdout and stderr of the command are returned as StringBuilder objects
    StringBuilder stdout = commandExecutor.getStandardOutputFromCommand();
    StringBuilder stderr = commandExecutor.getStandardErrorFromCommand();

    return stdout;
}

The code just tries to execute rapper command for each file within 'data' folder and store it in parsedTriples variable. This works fine

2)When I try to copy the result to a file instead of keeping it in just a variable, it doesn't work but provides no error !!

Code: (definition for getTriples() remains the same)

List<String> commands = new ArrayList<String>();
    StringBuilder parsedTriples= new StringBuilder();
    final File folder = new File("./data/");

    //add commands
    commands.add("rapper");
    commands.add("-o");
    commands.add("ntriples");

    //walk the whole folder and retrieve the file path
    for (final File fileEntry : folder.listFiles()) {

        commands.add(fileEntry.getPath());
        commands.add(">");
        String filePath="../ntriples/"+FilenameUtils.removeExtension(fileEntry.getName())+".ntriples";
        commands.add(filePath);
        parsedTriples.append(getTriples(commands));
        System.out.println(parsedTriples.length());
        //System.out.println(commands.get(0)+commands.get(1)+commands.get(2)+commands.get(3)+commands.get(4)+commands.get(5));
        commands.remove(5);
        commands.remove(4);
        commands.remove(3);
    }

Project Structure:

Also, i have tried giving path "./ntriples/" instead of "../ntriples/". I am not sure why this is happening and need some pointers !! Thanks in advance !!