I have written code in Java to read the content of a file. But it is working for small line of file only not for more than 1000 line of file. Please tell me me what error I have made in the below program.

program:

import java.io.DataInputStream;
import java.io.DataOutputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

    public class aaru

    {


        public static void main(String args[]) throws FileNotFoundException
        {

            File sourceFile = new File("E:\\parser\\parse3.txt");
            File destinationFile = new File("E:\\parser\\new.txt");
            FileInputStream fileIn = new FileInputStream(sourceFile);
            FileOutputStream fileOut = new FileOutputStream(destinationFile);
            DataInputStream dataIn = new DataInputStream(fileIn);
            DataOutputStream dataOut = new DataOutputStream(fileOut);

            String str="";
            String[] st;
            String sub[]=null;
            String word="";
            String contents="";
            String total="";

String stri="";;
  try
  {
      while((contents=dataIn.readLine())!=null)

      {

        total = contents.replaceAll(",","");
        String  str1=total.replaceAll("--","");
        String str2=str1.replaceAll(";","" );
        String str3=str2.replaceAll("&","" );
        String str4=str3.replaceAll("^","" );
        String str5=str4.replaceAll("#","" );
        String str6=str5.replaceAll("!","" );
        String str7=str6.replaceAll("/","" );
        String str8=str7.replaceAll(":","" );
        String str9=str8.replaceAll("]","" );
        String str10=str9.replaceAll("\\?","");
        String str11=str10.replaceAll("\\*","");
        String str12=str11.replaceAll("\\'","");



          Pattern pattern = Pattern.compile("\\s+", Pattern.CASE_INSENSITIVE | Pattern.DOTALL | Pattern.MULTILINE);
          Matcher matcher = pattern.matcher(str12);
          //boolean check = matcher.find();
        String  result=str12;
Pattern p=Pattern.compile("^www\\.|\\@");
Matcher m=p.matcher(result);
           stri = m.replaceAll(" ");




         int i;
          int j;



st=stri.split("\\.");

    for(i=0;i<st.length;i++)
    {
        st[i]=st[i].trim();
        /*if(st[i].startsWith(" "))
        st[i]=st[i].substring(1,st[i].length);*/
    sub=st[i].split(" ");

    if(sub.length>1)
    {
    for(j=0;j<sub.length-1;j++)
    {
        word = word+sub[j]+","+sub[j+1]+"\r\n";



    }
    }
    else
    {
        word = word+st[i]+"\r\n";
    }




    }

      }







      System.out.println(word);
      dataOut.writeBytes(word+"\r\n");




  fileIn.close();
    fileOut.close();
    dataIn.close();
    dataOut.close();
  }
    catch(Exception e)
    {
    System.out.print(e);
    }
    }
    }