Java IOException: Permission denied on linux while running as owner
===

I need to create some directories and files and all of them should have permission 0600.  
When I Run from NetBeans:
After creating directory when i try to store some files there I get `IOException` with "Permission Denied" message while both directories and files are created with same application at the same time with the same user so I think 0600 (owner read/write) should work.  
And When Running Jar file chmod doesn't work at all!
My code is:  

    if(!Dest.exists()){
       boolean res=dirs.mkdirs();
       if(res){
          Runtime.getRuntime().exec("chmod -R 600 '"+dirs.getAbsolutePath()+"'");                
        }
    }
    File Destination=new File(Dest, source.getName());
    documentManager.copyFile(source, Destination);
    
and the copyFile is:  

    public static void copyFile(File sourceFile, File destFile) throws FileNotFoundException,IOException {
        if(!destFile.exists()) {
            destFile.createNewFile();
        }

        FileChannel source = null;
        FileChannel destination = null;
        try {
            source = new FileInputStream(sourceFile).getChannel();
            destination = new FileOutputStream(destFile).getChannel();
            destination.transferFrom(source, 0, source.size());
        }
        finally {
            if(source != null) {
                source.close();
            }
            if(destination != null) {
                Runtime.getRuntime().exec("chmod 600 '"+destFile.getAbsolutePath()+"'");
                destination.close();
            }
        }
    }

What's the problem?

Thanks