diff --git a/genomix/genomix-pregelix/pom.xml b/genomix/genomix-pregelix/pom.xml
index cb74294..ebed72c 100644
--- a/genomix/genomix-pregelix/pom.xml
+++ b/genomix/genomix-pregelix/pom.xml
@@ -111,6 +111,13 @@
                 	<type>jar</type>
                 	<scope>compile</scope>
                 </dependency>
+                 <dependency>
+                	<groupId>edu.uci.ics.hyracks</groupId>
+                	<artifactId>genomix-data</artifactId>
+                	<version>0.2.4-SNAPSHOT</version>
+                	<type>jar</type>
+                	<scope>compile</scope>
+                </dependency>
         </dependencies>
 
   <scm>
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/BinaryLoadGraphInputFormat.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/BinaryLoadGraphInputFormat.java
index f203297..82fe3d9 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/BinaryLoadGraphInputFormat.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/BinaryLoadGraphInputFormat.java
@@ -15,7 +15,7 @@
 import edu.uci.ics.pregelix.api.util.BspUtils;
 import edu.uci.ics.pregelix.bitwise.BitwiseOperation;
 import edu.uci.ics.pregelix.example.io.MessageWritable;
-import edu.uci.ics.pregelix.type.KmerCountValue;
+import edu.uci.ics.genomix.type.KmerCountValue;
 
 public class BinaryLoadGraphInputFormat extends
 	BinaryVertexInputFormat<BytesWritable, ByteWritable, NullWritable, MessageWritable>{
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/GraphVertexOperation.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/GraphVertexOperation.java
index 8197ea8..37f348c 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/GraphVertexOperation.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/GraphVertexOperation.java
@@ -24,7 +24,7 @@
 import edu.uci.ics.pregelix.type.KmerCountValue;
 
 public class GraphVertexOperation {
-	public static final int k = 3; //kmer, k: the length of kmer
+	public static final int k = 15; //kmer, k: the length of kmer
 	static private final Path TMP_DIR = new Path(
 			GenerateSequenceFile.class.getSimpleName() + "_INTERIM");
 	/**
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/LogAlgorithmForMergeGraphInputFormat.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/LogAlgorithmForMergeGraphInputFormat.java
index a6e4a6c..4044a06 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/LogAlgorithmForMergeGraphInputFormat.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/LogAlgorithmForMergeGraphInputFormat.java
@@ -15,7 +15,7 @@
 import edu.uci.ics.pregelix.bitwise.BitwiseOperation;
 import edu.uci.ics.pregelix.example.io.LogAlgorithmMessageWritable;
 import edu.uci.ics.pregelix.example.io.ValueStateWritable;
-import edu.uci.ics.pregelix.type.KmerCountValue;
+import edu.uci.ics.genomix.type.KmerCountValue;
 import edu.uci.ics.pregelix.type.State;
 
 public class LogAlgorithmForMergeGraphInputFormat extends
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/LogAlgorithmForMergeGraphVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/LogAlgorithmForMergeGraphVertex.java
index c341e0d..a3d5e3f 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/LogAlgorithmForMergeGraphVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/LogAlgorithmForMergeGraphVertex.java
@@ -55,6 +55,7 @@
  */
 public class LogAlgorithmForMergeGraphVertex extends Vertex<BytesWritable, ValueStateWritable, NullWritable, LogAlgorithmMessageWritable>{
 	
+	private byte[] tmpVertextId;
 	private byte[] tmpSourceVertextId;
 	private byte[] tmpDestVertexId;
 	private byte[] tmpChainVertexId;
@@ -74,8 +75,9 @@
 	@Override
 	public void compute(Iterator<LogAlgorithmMessageWritable> msgIterator) {
 		try {
-			writer = new OutputStreamWriter(new FileOutputStream("test/check",true));
+			writer = new OutputStreamWriter(new FileOutputStream("test/check_Log",true));
 		} catch (FileNotFoundException e1) { e1.printStackTrace();}
+		tmpVertextId = GraphVertexOperation.generateValidDataFromBytesWritable(getVertexId());
 		if (getSuperstep() == 1) {
 			tmpVal = getVertexValue();
 			tmpVertexValue = tmpVal.getValue();
@@ -83,32 +85,31 @@
 			tmpMsg.setChainVertexId(tmpChainVertexId);
 			if(GraphVertexOperation.isHead(new ByteWritable(tmpVertexValue))){
 				tmpMsg.setMessage(Message.START);
-				tmpDestVertexId = GraphVertexOperation.getDestVertexId(getVertexId().getBytes(), tmpVertexValue);
+				tmpDestVertexId = GraphVertexOperation.getDestVertexId(tmpVertextId, tmpVertexValue); 
 				sendMsg(new BytesWritable(tmpDestVertexId),tmpMsg);
 				//test
 				GraphVertexOperation.testLogMessageCommunication(writer, getSuperstep(),
-						getVertexId().getBytes(), tmpDestVertexId, tmpMsg);
-				voteToHalt();
+						tmpVertextId, tmpDestVertexId, tmpMsg);
+				//voteToHalt();
 			}
 			else if(GraphVertexOperation.isRear(new ByteWritable(tmpVertexValue))){
 				tmpMsg.setMessage(Message.END);
-				tmpDestVertexId = GraphVertexOperation.getLeftDestVertexId(getVertexId().getBytes(), tmpVertexValue);
+				tmpDestVertexId = GraphVertexOperation.getLeftDestVertexId(tmpVertextId, tmpVertexValue);
 				sendMsg(new BytesWritable(tmpDestVertexId),tmpMsg);
 				//test
 				GraphVertexOperation.testSetVertexState(writer, getSuperstep(), getVertexId().getBytes(), 
 						tmpDestVertexId, tmpMsg, tmpVal);
-				voteToHalt();
+				//voteToHalt();
 			}
 			else if(GraphVertexOperation.isPathVertex(new ByteWritable(tmpVertexValue))){
 				tmpVal = getVertexValue();
 				tmpVal.setState(State.MID_VERTEX);
 				setVertexValue(tmpVal);
 				//test
-				GraphVertexOperation.testSetVertexState(writer, getSuperstep(), getVertexId().getBytes(), 
-						null, null, tmpVal);
+				GraphVertexOperation.testSetVertexState(writer, getSuperstep(),tmpVertextId , 
+						null, null, tmpVal); 
 			}
-			else
-				voteToHalt();
+			voteToHalt();
 		}
 		else if(getSuperstep() == 2){
 			if(msgIterator.hasNext()){
@@ -120,16 +121,17 @@
 					tmpVal.setState(State.START_VERTEX);
 					setVertexValue(tmpVal);
 					//test
-					GraphVertexOperation.testSetVertexState(writer, getSuperstep(), getVertexId().getBytes(), 
+					GraphVertexOperation.testSetVertexState(writer, getSuperstep(), tmpVertextId, 
 							null, null, tmpVal);
 				}
 				else if(tmpMessage == Message.END && tmpVertexState == State.MID_VERTEX){
 					tmpVal.setState(State.END_VERTEX);
 					setVertexValue(tmpVal);
 					//test
-					GraphVertexOperation.testSetVertexState(writer, getSuperstep(), getVertexId().getBytes(), 
+					GraphVertexOperation.testSetVertexState(writer, getSuperstep(), tmpVertextId, 
 							null, null, tmpVal);
 				}
+				voteToHalt();
 			}
 		}
 		//head node sends message to path node
@@ -148,7 +150,7 @@
 					tmpMsg.setSourceVertexId(tmpSourceVertextId);
 					sendMsg(new BytesWritable(tmpDestVertexId),tmpMsg);
 					//test
-					GraphVertexOperation.testMessageCommunication2(writer, getSuperstep(), getVertexId().getBytes(),
+					GraphVertexOperation.testMessageCommunication2(writer, getSuperstep(), tmpVertextId,
 							tmpDestVertexId, tmpMsg, null);
 				}
 				else if(tmpVertexState != State.END_VERTEX){
@@ -156,7 +158,7 @@
 					tmpMsg.setSourceVertexId(tmpSourceVertextId);
 					sendMsg(new BytesWritable(tmpDestVertexId),tmpMsg);
 					//test
-					GraphVertexOperation.testMessageCommunication2(writer, getSuperstep(), getVertexId().getBytes(),
+					GraphVertexOperation.testMessageCommunication2(writer, getSuperstep(), tmpVertextId,
 							tmpDestVertexId, tmpMsg, null);
 				}
 			}
@@ -174,7 +176,7 @@
 						tmpMsg.setSourceVertexId(tmpSourceVertextId);
 						sendMsg(new BytesWritable(tmpDestVertexId),tmpMsg);
 						//test
-						GraphVertexOperation.testMessageCommunication2(writer, getSuperstep(), getVertexId().getBytes(),
+						GraphVertexOperation.testMessageCommunication2(writer, getSuperstep(), tmpVertextId,
 								tmpDestVertexId, tmpMsg, null);
 					}
 					else if(tmpVertexState != State.END_VERTEX){
@@ -182,13 +184,14 @@
 						tmpMsg.setSourceVertexId(tmpSourceVertextId);
 						sendMsg(new BytesWritable(tmpDestVertexId),tmpMsg);
 						//test
-						GraphVertexOperation.testMessageCommunication2(writer, getSuperstep(), getVertexId().getBytes(),
+						GraphVertexOperation.testMessageCommunication2(writer, getSuperstep(), tmpVertextId,
 								tmpDestVertexId, tmpMsg, null);
 					}
 				}
 				else
 					voteToHalt();
 			}
+			voteToHalt();
 		}
 		//path node sends message back to head node
 		else if(getSuperstep()%3 == 1){
@@ -199,7 +202,7 @@
 				tmpSourceVertextId = tmpMsg.getSourceVertexId();
 				if(tmpVal.getLengthOfMergeChain() == 0){
 					tmpVal.setLengthOfMergeChain(GraphVertexOperation.k);
-					tmpVal.setMergeChain(getVertexId().getBytes());
+					tmpVal.setMergeChain(tmpVertextId);
 					setVertexValue(tmpVal);
 				}
 				tmpMsg.setLengthOfChain(tmpVal.getLengthOfMergeChain());
@@ -214,7 +217,7 @@
 
 				sendMsg(new BytesWritable(tmpSourceVertextId),tmpMsg);
 				//test
-				GraphVertexOperation.testMessageCommunication2(writer, getSuperstep(), getVertexId().getBytes(),
+				GraphVertexOperation.testMessageCommunication2(writer, getSuperstep(), tmpVertextId,
 						tmpSourceVertextId, tmpMsg, tmpSourceVertextId);
 				//kill Message because it has been merged by the head
 				if(tmpMessage == Message.START){
@@ -227,7 +230,7 @@
 						&& getVertexValue().getState() != State.END_VERTEX
 						&& tmpMessage != Message.END && tmpMessage != Message.START){
 					
-					GraphVertexOperation.testDeleteVertexInfo(writer, getSuperstep(), getVertexId().getBytes(), "not receive any message");
+					GraphVertexOperation.testDeleteVertexInfo(writer, getSuperstep(), tmpVertextId, "not receive any message");
 					deleteVertex(getVertexId()); //killSelf because it doesn't receive any message
 				}
 			}
@@ -237,7 +240,7 @@
 				tmpMsg = msgIterator.next();
 				tmpVal = getVertexValue();
 				tmpVertexState = tmpVal.getState();
-				tmpSourceVertextId = getVertexId().getBytes();
+				tmpSourceVertextId = tmpVertextId;
 				if(tmpVertexState == State.TODELETE){
 					GraphVertexOperation.testDeleteVertexInfo(writer, getSuperstep(),
 							tmpSourceVertextId, "already merged by head");
@@ -254,7 +257,7 @@
 					tmpVal.setState(tmpVertexState);
 					if(getSuperstep() == 5){
 						lengthOfMergeChainVertex = GraphVertexOperation.k;
-						mergeChainVertexId = getVertexId().getBytes();
+						mergeChainVertexId = tmpVertextId;
 					}
 					else{
 						lengthOfMergeChainVertex = tmpVal.getLengthOfMergeChain(); 
@@ -280,20 +283,20 @@
 						sendMsg(getVertexId(),tmpMsg);
 						//test
 						GraphVertexOperation.testMessageCommunication2(writer, getSuperstep(), getVertexId().getBytes(),
-								getVertexId().getBytes(), tmpMsg, null);
+								tmpVertextId, tmpMsg, null);
 					}
 				}
 				if(tmpVertexState == State.END_VERTEX){
 					voteToHalt();
 					//test
-					GraphVertexOperation.testVoteVertexInfo(writer, getSuperstep(), getVertexId().getBytes(),
+					GraphVertexOperation.testVoteVertexInfo(writer, getSuperstep(), tmpVertextId,
 							" it is the rear!");
 				}
 				if(tmpVertexState == State.FINAL_VERTEX){
 					voteToHalt();
 					try {
 						GraphVertexOperation.flushChainToFile(tmpVal.getMergeChain(), 
-								tmpVal.getLengthOfMergeChain(),getVertexId().getBytes());
+								tmpVal.getLengthOfMergeChain(),tmpVertextId);
 			    		writer.write("Step: " + getSuperstep() + "\r\n");
 			    		writer.write("Flush! " + "\r\n");
 					} catch (IOException e) { e.printStackTrace(); }
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/MergeGraphVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/MergeGraphVertex.java
index 3e02d2f..5d8d199 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/MergeGraphVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/MergeGraphVertex.java
@@ -67,7 +67,7 @@
 	@Override
 	public void compute(Iterator<MessageWritable> msgIterator) {
 		try {
-			writer = new OutputStreamWriter(new FileOutputStream("test/check",true));
+			writer = new OutputStreamWriter(new FileOutputStream("test/check_Naive",true));
 		} catch (FileNotFoundException e1) { e1.printStackTrace();}
 		tmpVertextId = GraphVertexOperation.generateValidDataFromBytesWritable(getVertexId());
 		if (getSuperstep() == 1) {
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/SequenceFile/GenerateSequenceFile.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/SequenceFile/GenerateSequenceFile.java
index e2f7b19..9cae8b2 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/SequenceFile/GenerateSequenceFile.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/SequenceFile/GenerateSequenceFile.java
@@ -13,7 +13,7 @@
 
 import edu.uci.ics.pregelix.GraphVertexOperation;
 import edu.uci.ics.pregelix.bitwise.BitwiseOperation;
-import edu.uci.ics.pregelix.type.KmerCountValue;
+import edu.uci.ics.genomix.type.KmerCountValue;
 
 public class GenerateSequenceFile {
 	
@@ -349,7 +349,10 @@
 	public static void generateNumOfLinesFromBigFile(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);
+	    
+		ClassLoader ctxLoader = Thread.currentThread().getContextClassLoader();
+		Thread.currentThread().setContextClassLoader(GenerateSequenceFile.class.getClassLoader());
+		SequenceFile.Reader reader = new SequenceFile.Reader(fileSys, inFile, conf);
 	    SequenceFile.Writer writer = SequenceFile.createWriter(fileSys, conf,
 	         outFile, BytesWritable.class, KmerCountValue.class, 
 	         CompressionType.NONE);
@@ -364,13 +367,14 @@
 	    }
 	    writer.close();
 	    reader.close();
+	    Thread.currentThread().setContextClassLoader(ctxLoader);
 	}
 	
 	 public static void main(String[] argv) throws Exception {
 		 //createTestDat();
 		 //createMergeTest();
 		 //createTestDat();
-		/* Path dir = new Path("data/webmap");
+		 /*Path dir = new Path("data/webmap");
 		 Path inFile = new Path(dir, "part-1");
 		 Path outFile = new Path(dir, "part-1-out-100");
 		 generateNumOfLinesFromBigFile(inFile,outFile,100);*/
@@ -410,11 +414,12 @@
 		  *  AGCATGCTAT
 		  */ 
 		 
-		 generateSequenceFileFromGeneCode3("AGCATGGCCTGCTAT");//GTCGATT  //before T: GGACG
+		 //generateSequenceFileFromGeneCode3("AGCATGCTAT");//GTCGATT  //before T: GGACG
+		 generateSequenceFileFromGeneCode15("AAAAAAAAAAAAAGCATGCTATAAAAAAAAAAAA");
 	 }
 	 public static void generateSequenceFileFromGeneCode3(String s) throws IOException{
 		 Configuration conf = new Configuration();
-	     Path outFile = new Path(outDir, "11");//sequenceShortFileMergeTest
+	     Path outFile = new Path(outDir, "sequenceShortFileMergeTest");//sequenceShortFileMergeTest
 	     FileSystem fileSys = FileSystem.get(conf);
 	     SequenceFile.Writer writer = SequenceFile.createWriter(fileSys, conf,
 	         outFile, BytesWritable.class, KmerCountValue.class, 
@@ -562,7 +567,7 @@
 	 }
 	 public static void generateSequenceFileFromGeneCode5(String s) throws IOException{
 		 Configuration conf = new Configuration();
-	     Path outFile = new Path(outDir, "sequenceFileMergeTest4");
+	     Path outFile = new Path(outDir, "sequenceFileMergeTest5");
 	     FileSystem fileSys = FileSystem.get(conf);
 	     SequenceFile.Writer writer = SequenceFile.createWriter(fileSys, conf,
 	         outFile, BytesWritable.class, KmerCountValue.class, 
@@ -626,7 +631,7 @@
 	     writer.close();
 	     
 	     //read outputs
-	     Path inFile = new Path(outDir, "sequenceFileMergeTest4");
+	     Path inFile = new Path(outDir, "sequenceFileMergeTest5");
 	     outKey = new BytesWritable();
 	     outValue = new KmerCountValue();
 	     SequenceFile.Reader reader = new SequenceFile.Reader(fileSys, inFile, conf);
@@ -645,10 +650,9 @@
 	       reader.close();
 	     }
 	 }
-	 
 	 public static void generateSequenceFileFromGeneCode8(String s) throws IOException{
 		 Configuration conf = new Configuration();
-	     Path outFile = new Path(outDir, "sequenceFileMergeTest4");
+	     Path outFile = new Path(outDir, "sequenceFileMergeTest8");
 	     FileSystem fileSys = FileSystem.get(conf);
 	     SequenceFile.Writer writer = SequenceFile.createWriter(fileSys, conf,
 	         outFile, BytesWritable.class, KmerCountValue.class, 
@@ -712,7 +716,7 @@
 	     writer.close();
 	     
 	     //read outputs
-	     Path inFile = new Path(outDir, "sequenceFileMergeTest4");
+	     Path inFile = new Path(outDir, "sequenceFileMergeTest8");
 	     outKey = new BytesWritable();
 	     outValue = new KmerCountValue();
 	     SequenceFile.Reader reader = new SequenceFile.Reader(fileSys, inFile, conf);
@@ -731,7 +735,91 @@
 	       reader.close();
 	     }
 	 }
-	 
+	 public static void generateSequenceFileFromGeneCode15(String s) throws IOException{
+		 Configuration conf = new Configuration();
+	     Path outFile = new Path(outDir, "sequenceFileMergeTest15");
+	     FileSystem fileSys = FileSystem.get(conf);
+	     SequenceFile.Writer writer = SequenceFile.createWriter(fileSys, conf,
+	         outFile, BytesWritable.class, KmerCountValue.class, 
+	         CompressionType.NONE);
+		 BytesWritable outKey = null;
+	     KmerCountValue outValue;
+	     byte adjBitMap; 
+	     ArrayList<String> lists = new ArrayList<String>();
+
+	     lists.add("000000000000000000000000001001"); //AAAAAAAAAAAAAGC
+	     lists.add("110011000000000000000000000000"); //TATAAAAAAAAAAAA
+	     String binaryString = "";
+		 for(int i = 1; i < s.length()-GraphVertexOperation.k; i++){
+			 binaryString = GraphVertexOperation.convertGeneCodeToBinaryString(s.substring(i,i+GraphVertexOperation.k));
+			 if(lists.contains(binaryString)){
+				 System.out.println("error: " + binaryString);
+				 return;
+			 }
+			 lists.add(binaryString);
+			 outKey = new BytesWritable(BitwiseOperation.convertBinaryStringToBytes(binaryString));
+			 outValue = new KmerCountValue();
+			 adjBitMap = GraphVertexOperation.getPrecursorFromGeneCode((byte)0, s.charAt(i-1));
+			 adjBitMap = GraphVertexOperation.getSucceedFromGeneCode(adjBitMap, s.charAt(i+GraphVertexOperation.k));
+			 outValue.setAdjBitMap(adjBitMap);
+			 writer.append(outKey, outValue);
+		 }
+		 /**
+		  *  CAG - AGC ------ TAT - ATA
+		  *  GAG 					ATC
+		  */
+		 // AGC
+	     String tmpKey = "000000000000000000000000001001";
+		 byte[] key = BitwiseOperation.convertBinaryStringToBytes(tmpKey);
+		 String tmpValue = "00000001";
+		 byte value = BitwiseOperation.convertBinaryStringToByte(tmpValue);
+		 BytesWritable keyWritable = new BytesWritable(key);
+		 ByteWritable valueWritable = new ByteWritable(value);
+	     
+	     ArrayList<BytesWritable> arrayOfKeys = new ArrayList<BytesWritable>();
+	     arrayOfKeys.add(keyWritable);
+	     ArrayList<ByteWritable> arrayOfValues = new ArrayList<ByteWritable>();
+	     arrayOfValues.add(valueWritable);
+	     
+	     // TAT
+	     tmpKey = "110011000000000000000000000000";
+	     key = BitwiseOperation.convertBinaryStringToBytes(tmpKey);
+	     tmpValue = "00100000";
+	     value = BitwiseOperation.convertBinaryStringToByte(tmpValue);
+	     keyWritable = new BytesWritable(key);
+	     valueWritable = new ByteWritable(value);
+	     arrayOfKeys.add(keyWritable);
+	     arrayOfValues.add(valueWritable);
+
+	     KmerCountValue kmerCountValue = null;
+	     //wirte to sequence file
+	     for(int i = 0; i < arrayOfKeys.size(); i++){
+	    	 kmerCountValue = new KmerCountValue();
+	    	 kmerCountValue.setAdjBitMap(arrayOfValues.get(i).get());
+	    	 writer.append(arrayOfKeys.get(i), kmerCountValue);
+	     }
+	     writer.close();
+	     
+	     //read outputs
+	     Path inFile = new Path(outDir, "sequenceFileMergeTest15");
+	     outKey = new BytesWritable();
+	     outValue = new KmerCountValue();
+	     SequenceFile.Reader reader = new SequenceFile.Reader(fileSys, inFile, conf);
+	     int iteration = 1;
+	     try {
+	         while(reader.next(outKey, outValue)){
+	        	 System.out.println(iteration);
+	        	 String kmer = BitwiseOperation.convertBytesToBinaryStringKmer(outKey.getBytes(),GraphVertexOperation.k);
+			     System.out.println("key: " + kmer);
+			     System.out.println("code: " + GraphVertexOperation.convertBinaryStringToGenecode(kmer));
+			     System.out.println("value: " + BitwiseOperation.convertByteToBinaryString(outValue.getAdjBitMap()));
+			     System.out.println();
+			     iteration++;
+	         }
+	     } finally {
+	       reader.close();
+	     }
+	 }
 	 public static void generateSequenceFileFromTwoGeneCode3(String s, String s2) throws IOException{
 		 Configuration conf = new Configuration();
 	     Path outFile = new Path(outDir, "sequenceFileMergeTest4");
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/SequenceFile/generateSmallFile.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/SequenceFile/generateSmallFile.java
new file mode 100644
index 0000000..bde6f43
--- /dev/null
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/SequenceFile/generateSmallFile.java
@@ -0,0 +1,51 @@
+package edu.uci.ics.pregelix.SequenceFile;
+
+import java.io.IOException;
+
+import org.apache.hadoop.conf.Configuration;
+import org.apache.hadoop.fs.FileSystem;
+import org.apache.hadoop.fs.Path;
+import org.apache.hadoop.io.BytesWritable;
+import org.apache.hadoop.io.SequenceFile;
+import org.apache.hadoop.io.SequenceFile.CompressionType;
+
+import edu.uci.ics.genomix.type.KmerCountValue;
+
+public class generateSmallFile {
+
+	public static void generateNumOfLinesFromBigFile(Path inFile, Path outFile, int numOfLines) throws IOException{
+		Configuration conf = new Configuration();
+		FileSystem fileSys = FileSystem.get(conf);
+	    
+		//ClassLoader ctxLoader = Thread.currentThread().getContextClassLoader();
+		//Thread.currentThread().setContextClassLoader(GenerateSequenceFile.class.getClassLoader());
+		SequenceFile.Reader reader = new SequenceFile.Reader(fileSys, inFile, conf);
+	    SequenceFile.Writer writer = SequenceFile.createWriter(fileSys, conf,
+	         outFile, BytesWritable.class, KmerCountValue.class, 
+	         CompressionType.NONE);
+	    BytesWritable outKey = new BytesWritable();
+	    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();
+	    //Thread.currentThread().setContextClassLoader(ctxLoader);
+	}
+	/**
+	 * @param args
+	 * @throws IOException 
+	 */
+	public static void main(String[] args) throws IOException {
+		// TODO Auto-generated method stub
+		Path dir = new Path("data/webmap");
+		Path inFile = new Path(dir, "part-1");
+		Path outFile = new Path(dir, "part-1-out-200000");
+		generateNumOfLinesFromBigFile(inFile,outFile,200000);
+	}
+
+}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/api/io/binary/BinaryVertexInputFormat.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/api/io/binary/BinaryVertexInputFormat.java
index c5db334..31274ac 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/api/io/binary/BinaryVertexInputFormat.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/api/io/binary/BinaryVertexInputFormat.java
@@ -3,7 +3,6 @@
 import java.io.IOException;
 import java.util.List;
 
-import org.apache.hadoop.io.ByteWritable;
 import org.apache.hadoop.io.BytesWritable;
 import org.apache.hadoop.io.Writable;
 import org.apache.hadoop.io.WritableComparable;
@@ -15,7 +14,7 @@
 
 import edu.uci.ics.pregelix.api.io.VertexInputFormat;
 import edu.uci.ics.pregelix.api.io.VertexReader;
-import edu.uci.ics.pregelix.type.KmerCountValue;
+import edu.uci.ics.genomix.type.KmerCountValue;
 
 public class BinaryVertexInputFormat <I extends WritableComparable, V extends Writable, E extends Writable, M extends Writable>
 	extends VertexInputFormat<I, V, E, M>{
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/pregelix/JobGen/JobGenerator.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/pregelix/JobGen/JobGenerator.java
index 7affcbf..325ebdb 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/pregelix/JobGen/JobGenerator.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/pregelix/JobGen/JobGenerator.java
@@ -47,7 +47,7 @@
     
     private static void generateBinaryLoadGraphJob(String jobName, String outputPath) throws IOException {
     	PregelixJob job = new PregelixJob(jobName);
-    	job.setVertexClass(TestLoadGraphVertex.class);
+    	job.setVertexClass(MergeGraphVertex.class);
     	job.setVertexInputFormatClass(BinaryLoadGraphInputFormat.class);
         job.setVertexOutputFormatClass(BinaryLoadGraphOutputFormat.class);
         job.setOutputKeyClass(BytesWritable.class);
@@ -84,8 +84,8 @@
 	 */
 	public static void main(String[] args) throws IOException {
 		// TODO Auto-generated method stub
-		//genLogAlgorithmForMergeGraph();
 		genBinaryLoadGraph();
+		//genLogAlgorithmForMergeGraph();
 		//genSequenceLoadGraph();
 		//genBasicBinaryLoadGraph();
 	}
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/pregelix/JobRun/RunJobTestCase.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/pregelix/JobRun/RunJobTestCase.java
index e3fa41c..7af814c 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/pregelix/JobRun/RunJobTestCase.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/pregelix/JobRun/RunJobTestCase.java
@@ -1,6 +1,9 @@
 package edu.uci.ics.pregelix.JobRun;
 
 import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.OutputStreamWriter;
 
 import junit.framework.TestCase;
 
@@ -68,6 +71,7 @@
 	@Test
 	public void test() throws Exception {
 		setUp();
+		
         for (JobGen jobGen : giraphJobGens) {
             FileSystem dfs = FileSystem.get(job.getConfiguration());
             dfs.delete(new Path(HDFS_OUTPUTPAH), true);
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/pregelix/JobRun/RunJobTestSuite.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/pregelix/JobRun/RunJobTestSuite.java
index 58e4ea3..879cc20 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/pregelix/JobRun/RunJobTestSuite.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/pregelix/JobRun/RunJobTestSuite.java
@@ -7,6 +7,7 @@
 import java.io.FileOutputStream;
 import java.io.FileReader;
 import java.io.IOException;
+import java.io.OutputStreamWriter;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.logging.Logger;
@@ -40,7 +41,7 @@
 	private static final String PATH_TO_ONLY = "src/test/resources/only.txt";
 	private static final String FILE_EXTENSION_OF_RESULTS = "result";
 
-	private static final String DATA_PATH = "data/webmap/part-1-out";//sequenceFileMergeTest
+	private static final String DATA_PATH = "data/webmap/part-1-out-200000";//sequenceFileMergeTest
 	private static final String HDFS_PATH = "/webmap/";
 	
 	private static final String HYRACKS_APP_NAME = "pregelix";
@@ -144,6 +145,12 @@
 	 */
 	@Override
 	public void run(TestResult result) {
+		OutputStreamWriter writer = null;
+		try {
+			writer = new OutputStreamWriter(new FileOutputStream("test/time",true));
+		} catch (FileNotFoundException e1) { e1.printStackTrace();}
+		long startTime = System.currentTimeMillis();
+		
 		try {
 			int testCount = countTestCases();
 			for (int i = 0; i < testCount; i++) {
@@ -157,6 +164,15 @@
 		} catch (Exception e) {
 			throw new IllegalStateException(e);
 		}
+		
+		long endTime = System.currentTimeMillis();
+		long totalTime = endTime - startTime;
+		System.out.println(totalTime);
+		try {
+			writer.write("Time: " + totalTime);
+			writer.close();
+		} catch (IOException e) { // TODO Auto-generated catch block 
+			e.printStackTrace();} 
 	}
 
 	protected static List<String> getFileList(String ignorePath)