The file pointer is set to the end of the file when the 1st while is executed. try this:
Scanner in = new Scanner(file);
while(in.hasNext())
{
in.next();
words++;
}
in = new Scanner(file);
while(in.hasNextLine())
{
in.nextLine();
lines++;
}
in = new Scanner(file);
while(in.hasNextByte())
{
in.nextByte();
chars++;
}