java filewriter write incomplete data of instance

I had an input file having 45311 instance. After applying my programing task, when I write it back in a new file, it actually writes 43371 instances only. It runs successfully, but where are my remaining instances?

package kmean;

import java.io.IOException;

import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.FileWriter;

import weka.clusterers.SimpleKMeans;
import weka.core.Instances;

public class Kmean {

    public static BufferedReader readDataFile(String filename) {
        BufferedReader inputReader = null;

        try {
            inputReader = new BufferedReader(new FileReader(filename));
        } catch (FileNotFoundException ex) {
            System.err.println("File not found: " + filename);
        }

        return inputReader;
    }

    /**
     * @param args the command line arguments
     */
    public static void main(String[] args) throws IOException, Exception {
        BufferedWriter writer = null;

        try {
            writer = new BufferedWriter(new FileWriter("perturbed1.csv"));
        }
        catch (IOException e) {
        }
        SimpleKMeans kmeans = new SimpleKMeans();

        kmeans.setSeed(10);

        //important parameter to set: preserver order, number of cluster.
        kmeans.setPreserveInstancesOrder(true);
        kmeans.setNumClusters(5);

        BufferedReader datafile = readDataFile("elecNormNew.arff"); 
        // BufferedReader datafile = readDataFile("perturbed.csv"); 
        Instances data = new Instances(datafile);

        kmeans.buildClusterer(data);

        // This array returns the cluster number (starting with 0) for each instance
        // The array has as many elements as the number of instances
        int[] assignments = kmeans.getAssignments();
        StringBuilder sb = new StringBuilder();
        int i=0;
        for(int clusterNum : assignments) {
           // System.out.printf("Instance %d -> Cluster %d \n", i, clusterNum);
            sb.append(i);
            sb.append(";");
            sb.append(clusterNum);
            sb.append("\n");
            //System.out.printf("\n");
            i++;
        }
        System.out.println(sb.toString());           
        writer.write(sb.toString()+"\n");
        // TODO code application logic here
    }
}

You should call writer.close() at the end after writing all data.