diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/client/Client.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/client/Client.java
index 6c93433..aaa7e53 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/client/Client.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/client/Client.java
@@ -45,8 +45,8 @@
         @Option(name = "-runtime-profiling", usage = "whether to do runtime profifling", required = false)
         public String profiling = "false";
         
-        @Option(name = "-filter-kmer", usage = "whether to do runtime profifling", required = false)
-        public String filterKmer = "";
+        //@Option(name = "-filter-kmer", usage = "whether to do runtime profifling", required = false)
+        //public String filterKmer = "";
     }
 
     public static void run(String[] args, PregelixJob job) throws Exception {
@@ -73,7 +73,7 @@
             job.getConfiguration().setInt(TwoStepLogAlgorithmForPathMergeVertex.ITERATIONS, options.numIteration);
             job.getConfiguration().setInt(ThreeStepLogAlgorithmForPathMergeVertex.ITERATIONS, options.numIteration);
         }
-        job.getConfiguration().set(NaiveFilterVertex.FILTERKMER, options.filterKmer);
+        //job.getConfiguration().set(NaiveFilterVertex.FILTERKMER, options.filterKmer);
         return options;
     }
 
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/NaiveAlgorithmForPathMergeOutputFormat.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/NaiveAlgorithmForPathMergeOutputFormat.java
index 3dd0f2f..e3f14a4 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/NaiveAlgorithmForPathMergeOutputFormat.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/NaiveAlgorithmForPathMergeOutputFormat.java
@@ -8,7 +8,6 @@
 
 import edu.uci.ics.genomix.pregelix.api.io.binary.BinaryVertexOutputFormat;
 import edu.uci.ics.genomix.pregelix.io.ValueStateWritable;
-import edu.uci.ics.genomix.pregelix.type.State;
 import edu.uci.ics.genomix.type.KmerBytesWritable;
 import edu.uci.ics.pregelix.api.graph.Vertex;
 import edu.uci.ics.pregelix.api.io.VertexWriter;
@@ -37,9 +36,9 @@
             @Override
             public void writeVertex(Vertex<KmerBytesWritable, ValueStateWritable, NullWritable, ?> vertex) throws IOException,
                     InterruptedException {
-            	if(vertex.getVertexValue().getState() == State.FILTER
-            			|| vertex.getVertexValue().getState() == State.FINAL_VERTEX)
-            		getRecordWriter().write(vertex.getVertexId(),vertex.getVertexValue());
+            	//if(vertex.getVertexValue().getState() == State.FILTER
+            	//		|| vertex.getVertexValue().getState() == State.FINAL_VERTEX)
+            	getRecordWriter().write(vertex.getVertexId(),vertex.getVertexValue());
             }
         }
 }
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/NaiveAlgorithmForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/NaiveAlgorithmForPathMergeVertex.java
index b20d6ea..ac52e0d 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/NaiveAlgorithmForPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/NaiveAlgorithmForPathMergeVertex.java
@@ -52,7 +52,7 @@
  * Naive Algorithm for path merge graph
  */
 public class NaiveAlgorithmForPathMergeVertex extends Vertex<KmerBytesWritable, ValueStateWritable, NullWritable, NaiveAlgorithmMessageWritable>{
-	public static Logger logger = Logger.getLogger(NaiveAlgorithmForPathMergeVertex.class.getName()); 
+	//public static Logger logger = Logger.getLogger(NaiveAlgorithmForPathMergeVertex.class.getName()); 
 
 	
 	public static final String KMER_SIZE = "NaiveAlgorithmForPathMergeVertex.kmerSize";
@@ -186,12 +186,12 @@
 				responseMsgToHeadVertex();
 			}
 		}
-		String log = "Iterator:" + getSuperstep();
+		/*String log = "Iterator:" + getSuperstep();
 		log += getVertexId().toString() + "\t";
 		log += getVertexValue().getMergeChain().toString() + "\t";
 		log += GeneCode.getSymbolFromBitMap(getVertexValue().getAdjMap()) + "\t";
 		log += getVertexValue().getState();
-		logger.info(log);
+		logger.info(log);*/
 		voteToHalt();
 	}
 
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/TwoStepLogAlgorithmForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/TwoStepLogAlgorithmForPathMergeVertex.java
index 2ef2932..eb5edc3 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/TwoStepLogAlgorithmForPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/TwoStepLogAlgorithmForPathMergeVertex.java
@@ -49,7 +49,7 @@
  * The details about message are in edu.uci.ics.pregelix.example.io.MessageWritable. 
  */
 public class TwoStepLogAlgorithmForPathMergeVertex extends Vertex<KmerBytesWritable, ValueStateWritable, NullWritable, LogAlgorithmMessageWritable>{	
-	public static Logger logger = Logger.getLogger(TwoStepLogAlgorithmForPathMergeVertex.class.getName()); 
+	//public static Logger logger = Logger.getLogger(TwoStepLogAlgorithmForPathMergeVertex.class.getName()); 
 	
 	public static final String KMER_SIZE = "TwoStepLogAlgorithmForPathMergeVertex.kmerSize";
 	public static final String ITERATIONS = "TwoStepLogAlgorithmForPathMergeVertex.iteration";
@@ -341,12 +341,12 @@
 		}
 		else
 			voteToHalt();
-		String log = "Iterator:" + getSuperstep();
+		/*String log = "Iterator:" + getSuperstep();
 		log += getVertexId().toString() + "\t";
 		log += getVertexValue().getMergeChain().toString() + "\t";
 		log += GeneCode.getSymbolFromBitMap(getVertexValue().getAdjMap()) + "\t";
 		log += getVertexValue().getState();
-		logger.info(log);
+		logger.info(log);*/
 	}
 	/**
 	 * @param args
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/GenerateSmallFile.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/GenerateSmallFile.java
index 88bec61..d9fd35f 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/GenerateSmallFile.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/GenerateSmallFile.java
@@ -1,6 +1,11 @@
 package edu.uci.ics.genomix.pregelix.sequencefile;
 
+import java.io.BufferedReader;
+import java.io.BufferedWriter;
 import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.FileWriter;
 import java.io.IOException;
 
 import org.apache.commons.io.FileUtils;
@@ -15,38 +20,81 @@
 
 public class GenerateSmallFile {
 
-	public static void generateNumOfLinesFromBigFile(Path inFile, Path outFile, int numOfLines) throws IOException{
+	public static void generateNumOfLinesFromGraphBuildResuiltBigFile(
+			Path inFile, Path outFile, int numOfLines) throws IOException {
 		Configuration conf = new Configuration();
 		FileSystem fileSys = FileSystem.get(conf);
 
-		SequenceFile.Reader reader = new SequenceFile.Reader(fileSys, inFile, conf);
-	    SequenceFile.Writer writer = SequenceFile.createWriter(fileSys, conf,
-	         outFile, KmerBytesWritable.class, KmerCountValue.class, 
-	         CompressionType.NONE);
-	    KmerBytesWritable outKey = new KmerBytesWritable(55);
-	    KmerCountValue outValue = new KmerCountValue();
-	    int i = 0;
-	    
-	    for(i = 0; i < numOfLines; i++){
-	    	 //System.out.println(i);
-	    	 reader.next(outKey, outValue);
-	    	 writer.append(outKey, outValue);
-	    }
-	    writer.close();
-	    reader.close();
+		SequenceFile.Reader reader = new SequenceFile.Reader(fileSys, inFile,
+				conf);
+		SequenceFile.Writer writer = SequenceFile.createWriter(fileSys, conf,
+				outFile, KmerBytesWritable.class, KmerCountValue.class,
+				CompressionType.NONE);
+		KmerBytesWritable outKey = new KmerBytesWritable(55);
+		KmerCountValue outValue = new KmerCountValue();
+		int i = 0;
+
+		for (i = 0; i < numOfLines; i++) {
+			// System.out.println(i);
+			reader.next(outKey, outValue);
+			writer.append(outKey, outValue);
+		}
+		writer.close();
+		reader.close();
 	}
-	/**
-	 * @param args
-	 * @throws IOException 
-	 */
+
+	public static void generateNumOfLinesFromGraphBuildResuiltBigFile(
+			String inFile, String outFile, int numOfLines) throws IOException {
+		String lines = readTextFile(inFile, numOfLines);
+		writeTextFile(outFile, lines);
+	}
+
 	public static void main(String[] args) throws IOException {
-		// TODO Auto-generated method stub
-		Path dir = new Path("data/test8m");
+		/*Path dir = new Path("data/test8m");
 		Path outDir = new Path("data/input/test");
 		FileUtils.cleanDirectory(new File("data/input/test"));
 		Path inFile = new Path(dir, "part-0");
 		Path outFile = new Path(outDir, "part-0-out-100");
-		generateNumOfLinesFromBigFile(inFile,outFile,100);
+		generateNumOfLinesFromGraphBuildResuiltBigFile(inFile, outFile, 100);*/
+		String inFile = "data/shortjump_1.head8M.fastq";
+		String outFile = "data/testGeneFile";
+		generateNumOfLinesFromGraphBuildResuiltBigFile(inFile, outFile, 100000);
 	}
 
+	public static String readTextFile(String fileName, int numOfLines) {
+		String returnValue = "";
+		FileReader file;
+		String line = "";
+		try {
+			file = new FileReader(fileName);
+			BufferedReader reader = new BufferedReader(file);
+			try {
+				while ((numOfLines > 0) && (line = reader.readLine()) != null) {
+					returnValue += line + "\n";
+					numOfLines--;
+				}
+			} finally {
+				reader.close();
+			}
+		} catch (FileNotFoundException e) {
+			throw new RuntimeException("File not found");
+		} catch (IOException e) {
+			throw new RuntimeException("IO Error occured");
+		}
+		return returnValue;
+
+	}
+
+	public static void writeTextFile(String fileName, String s) {
+		FileWriter output;
+		try {
+			output = new FileWriter(fileName);
+			BufferedWriter writer = new BufferedWriter(output);
+			writer.write(s);
+			writer.close();
+		} catch (IOException e) {
+			e.printStackTrace();
+		}
+
+	}
 }
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/PathMergeSmallTestSuite.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/PathMergeSmallTestSuite.java
index d05fc7a..898d059 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/PathMergeSmallTestSuite.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/PathMergeSmallTestSuite.java
@@ -20,6 +20,7 @@
 import java.io.FileNotFoundException;
 import java.io.FileOutputStream;
 import java.io.FileReader;
+import java.io.FilenameFilter;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
@@ -30,6 +31,7 @@
 import junit.framework.TestSuite;
 
 import org.apache.commons.io.FileUtils;
+import org.apache.commons.io.filefilter.WildcardFileFilter;
 import org.apache.hadoop.conf.Configuration;
 import org.apache.hadoop.fs.FileSystem;
 import org.apache.hadoop.fs.Path;
@@ -44,15 +46,15 @@
 	private static final Logger LOGGER = Logger
 			.getLogger(PathMergeSmallTestSuite.class.getName());
 
-	public static final String PreFix = "data";
+	public static final String PreFix = "graphbuildresult"; //"graphbuildresult";
 	public static final String[] TestDir = { PreFix + File.separator
-		+  "test8m"};
+		+  "result"};
 		/*+ "BridgePath", PreFix + File.separator
 		+ "CyclePath", PreFix + File.separator
 		+ "SimplePath", PreFix + File.separator
 		+ "SinglePath", PreFix + File.separator
-		+ "TreePath"};*/
-		/*+ "2", PreFix + File.separator
+		+ "TreePath"};
+		+ "2"}, PreFix + File.separator
 		+ "3", PreFix + File.separator
 		+ "4", PreFix + File.separator
 		+ "5", PreFix + File.separator
@@ -60,7 +62,6 @@
 		+ "7", PreFix + File.separator
 		+ "8", PreFix + File.separator
 		+ "9", PreFix + File.separator
-		+ "10", PreFix + File.separator
 		+ "TwoKmer", PreFix + File.separator
 		+ "ThreeKmer", PreFix + File.separator
 		+ "SinglePath", PreFix + File.separator
@@ -112,6 +113,7 @@
 			File src = new File(testDir);
 			Path dest = new Path(HDFS_INPUTPATH + File.separator + src.getName());
 			dfs.mkdirs(dest);
+			//src.listFiles()
 			//src.listFiles((FilenameFilter)(new WildcardFileFilter("part*")))
 			for (File f : src.listFiles()){
 				dfs.copyFromLocalFile(new Path(f.getAbsolutePath()), dest);
diff --git a/pregelix/pregelix-core/src/main/java/edu/uci/ics/pregelix/core/driver/Driver.java b/pregelix/pregelix-core/src/main/java/edu/uci/ics/pregelix/core/driver/Driver.java
index a072b9b..05f1022 100644
--- a/pregelix/pregelix-core/src/main/java/edu/uci/ics/pregelix/core/driver/Driver.java
+++ b/pregelix/pregelix-core/src/main/java/edu/uci/ics/pregelix/core/driver/Driver.java
@@ -130,7 +130,6 @@
             do {
                 start = System.currentTimeMillis();
                 runLoopBodyIteration(deploymentId, jobGen, i);
-                runHDFSWRite(deploymentId, jobGen);
                 end = System.currentTimeMillis();
                 time = end - start;
                 LOG.info("iteration " + i + " finished " + time + "ms");