diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/P2PathMergeOutputFormat.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/P2PathMergeOutputFormat.java
new file mode 100644
index 0000000..0308913
--- /dev/null
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/P2PathMergeOutputFormat.java
@@ -0,0 +1,44 @@
+package edu.uci.ics.genomix.pregelix.format;
+
+import java.io.IOException;
+
+import org.apache.hadoop.io.NullWritable;
+import org.apache.hadoop.mapreduce.RecordWriter;
+import org.apache.hadoop.mapreduce.TaskAttemptContext;
+
+import edu.uci.ics.genomix.pregelix.api.io.binary.BinaryDataCleanVertexOutputFormat;
+import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
+import edu.uci.ics.genomix.pregelix.io.VertexValueWritable.State;
+import edu.uci.ics.genomix.type.KmerBytesWritable;
+import edu.uci.ics.pregelix.api.graph.Vertex;
+import edu.uci.ics.pregelix.api.io.VertexWriter;
+
+public class P2PathMergeOutputFormat extends
+    BinaryDataCleanVertexOutputFormat<KmerBytesWritable, VertexValueWritable, NullWritable> {
+
+    @Override
+    public VertexWriter<KmerBytesWritable, VertexValueWritable, NullWritable> createVertexWriter(
+            TaskAttemptContext context) throws IOException, InterruptedException {
+        @SuppressWarnings("unchecked")
+        RecordWriter<KmerBytesWritable, VertexValueWritable> recordWriter = binaryOutputFormat.getRecordWriter(context);
+        return new BinaryLoadGraphVertexWriter(recordWriter);
+    }
+
+    /**
+     * Simple VertexWriter that supports {@link BinaryLoadGraphVertex}
+     */
+    public static class BinaryLoadGraphVertexWriter extends
+            BinaryVertexWriter<KmerBytesWritable, VertexValueWritable, NullWritable> {
+        public BinaryLoadGraphVertexWriter(RecordWriter<KmerBytesWritable, VertexValueWritable> lineRecordWriter) {
+            super(lineRecordWriter);
+        }
+
+        @Override
+        public void writeVertex(Vertex<KmerBytesWritable, VertexValueWritable, NullWritable, ?> vertex)
+                throws IOException, InterruptedException {
+            byte selfFlag = (byte)(vertex.getVertexValue().getState() & State.VERTEX_MASK);
+            if(selfFlag == State.IS_FINAL)
+                getRecordWriter().write(vertex.getVertexId(), vertex.getVertexValue());
+        }
+    }
+}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/MessageWritable.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/MessageWritable.java
index 1c5f325..6356715 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/MessageWritable.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/MessageWritable.java
@@ -22,6 +22,7 @@
     private byte flag;
     private boolean isFlip;
     private int kmerlength = 0;
+    private boolean updateMsg = false;
 
     private byte checkMessage;
 
@@ -61,6 +62,7 @@
         }
         checkMessage |= CheckMessage.ADJMSG;
         this.flag = msg.getFlag();
+        updateMsg = msg.isUpdateMsg();
     }
 
     public void set(int kmerlength, KmerBytesWritable sourceVertexId, KmerBytesWritable chainVertexId, AdjacencyListWritable neighberNode, byte message) {
@@ -82,17 +84,16 @@
     }
 
     public void reset() {
-        checkMessage = 0;
-        kmer.reset(1);
-        neighberNode.reset();
-        flag = Message.NON;
+        reset(0);
     }
     
     public void reset(int kmerSize) {
-        checkMessage = 0;
+        checkMessage = (byte) 0;
+        kmerlength = kmerSize;
         kmer.reset(1);
         neighberNode.reset(kmerSize);
         flag = Message.NON;
+        isFlip = false;
     }
 
     public KmerBytesWritable getSourceVertexId() {
@@ -148,6 +149,15 @@
         this.isFlip = isFlip;
     }
 
+    
+    public boolean isUpdateMsg() {
+        return updateMsg;
+    }
+
+    public void setUpdateMsg(boolean updateMsg) {
+        this.updateMsg = updateMsg;
+    }
+
     @Override
     public void write(DataOutput out) throws IOException {
         out.writeInt(kmerlength);
@@ -160,6 +170,7 @@
             neighberNode.write(out);
         out.writeBoolean(isFlip);
         out.writeByte(flag); 
+        out.writeBoolean(updateMsg);
     }
 
     @Override
@@ -175,6 +186,7 @@
             neighberNode.readFields(in);
         isFlip = in.readBoolean();
         flag = in.readByte();
+        updateMsg = in.readBoolean();
     }
 
     @Override
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/VertexValueWritable.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/VertexValueWritable.java
index 5d06234..6d4f683 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/VertexValueWritable.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/VertexValueWritable.java
@@ -237,6 +237,26 @@
     }
     
     /*
+     * Delete the corresponding edge
+     */
+    public void processDelete(byte neighborToDeleteDir, KmerBytesWritable nodeToDelete){
+        switch (neighborToDeleteDir & MessageFlag.DIR_MASK) {
+            case MessageFlag.DIR_FF:
+                this.getFFList().remove(nodeToDelete);
+                break;
+            case MessageFlag.DIR_FR:
+                this.getFRList().remove(nodeToDelete);
+                break;
+            case MessageFlag.DIR_RF:
+                this.getRFList().remove(nodeToDelete);
+                break;
+            case MessageFlag.DIR_RR:
+                this.getRRList().remove(nodeToDelete);
+                break;
+        }
+    }
+    
+    /*
      * Process any changes to value.  This is for edge updates
      */
     public void processUpdates(byte neighborToDeleteDir, KmerBytesWritable nodeToDelete,
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicPathMergeVertex.java
index 937fa42..8907491 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicPathMergeVertex.java
@@ -25,8 +25,8 @@
     public static int kmerSize = -1;
     protected int maxIteration = -1;
     
-    protected MessageWritable incomingMsg = null; // = new MessageWritable();
-    protected MessageWritable outgoingMsg = null; // = new MessageWritable();
+    protected MessageWritable incomingMsg = null; 
+    protected MessageWritable outgoingMsg = null; 
     protected KmerBytesWritable destVertexId = new KmerBytesWritable();
     protected Iterator<KmerBytesWritable> posIterator;
     private KmerBytesWritable kmer = new KmerBytesWritable();
@@ -96,10 +96,12 @@
     public KmerBytesWritable getNextDestVertexIdAndSetFlag(VertexValueWritable value) {
         if (value.getFFList().getCountOfPosition() > 0){ // #FFList() > 0
             posIterator = value.getFFList().iterator();
+            outFlag &= MessageFlag.DIR_CLEAR;
             outFlag |= MessageFlag.DIR_FF;
             return posIterator.next();
         } else if (value.getFRList().getCountOfPosition() > 0){ // #FRList() > 0
             posIterator = value.getFRList().iterator();
+            outFlag &= MessageFlag.DIR_CLEAR;
             outFlag |= MessageFlag.DIR_FR;
             return posIterator.next();
         } else {
@@ -111,10 +113,12 @@
     public KmerBytesWritable getPreDestVertexIdAndSetFlag(VertexValueWritable value) {
         if (value.getRFList().getCountOfPosition() > 0){ // #RFList() > 0
             posIterator = value.getRFList().iterator();
+            outFlag &= MessageFlag.DIR_CLEAR;
             outFlag |= MessageFlag.DIR_RF;
             return posIterator.next();
         } else if (value.getRRList().getCountOfPosition() > 0){ // #RRList() > 0
             posIterator = value.getRRList().iterator();
+            outFlag &= MessageFlag.DIR_CLEAR;
             outFlag |= MessageFlag.DIR_RR;
             return posIterator.next();
         } else {
@@ -290,6 +294,7 @@
      * set adjMessage to successor(from predecessor)
      */
     public void setSuccessorAdjMsg(){
+        outFlag &= MessageFlag.DIR_CLEAR;
         if(getVertexValue().getFFList().getLength() > 0)
             outFlag |= MessageFlag.DIR_FF;
         else if(getVertexValue().getFRList().getLength() > 0)
@@ -302,6 +307,7 @@
      * set adjMessage to predecessor(from successor)
      */
     public void setPredecessorAdjMsg(){
+        outFlag &= MessageFlag.DIR_CLEAR;
         if(getVertexValue().getRFList().getLength() > 0)
             outFlag |= MessageFlag.DIR_RF;
         else if(getVertexValue().getRRList().getLength() > 0)
@@ -342,18 +348,38 @@
     }
     
     /**
+     * send update message to neighber for P2
+     * @throws IOException 
+     */
+    public void sendUpdateMsg(){
+        outgoingMsg.setUpdateMsg(true);
+        byte meToNeighborDir = (byte) (incomingMsg.getFlag() & MessageFlag.DIR_MASK);
+        switch(meToNeighborDir){
+            case MessageFlag.DIR_FF:
+            case MessageFlag.DIR_FR:
+                sendUpdateMsgToPredecessor();
+                break;
+            case MessageFlag.DIR_RF:
+            case MessageFlag.DIR_RR: 
+                sendUpdateMsgToSuccessor();
+                break;
+        }
+    }
+    
+    /**
      * send merge message to neighber for P2
      * @throws IOException 
      */
     public void sendMergeMsg(){
-        if(selfFlag == MessageFlag.IS_HEAD){
+        outgoingMsg.setUpdateMsg(false);
+        if(selfFlag == State.IS_HEAD){
             byte newState = getVertexValue().getState(); 
             newState &= ~State.IS_HEAD;
             newState |= State.IS_OLDHEAD;
             getVertexValue().setState(newState);
             resetSelfFlag();
-            outFlag |= MessageFlag.IS_HEAD;
-        } else if(selfFlag == MessageFlag.IS_OLDHEAD){
+            outFlag |= MessageFlag.IS_HEAD;  
+        } else if(selfFlag == State.IS_OLDHEAD){
             outFlag |= MessageFlag.IS_OLDHEAD;
             voteToHalt();
         }
@@ -387,6 +413,46 @@
                 sendMsg(incomingMsg.getSourceVertexId(), outgoingMsg); //getPreDestVertexId(getVertexValue())
                 break; 
         }
+//        if(headBecomeOldHead)
+//            getVertexValue().processDelete(neighborToMeDir, incomingMsg.getSourceVertexId());
+    }
+    
+    /**
+     * send final merge message to neighber for P2
+     * @throws IOException 
+     */
+    public void sendFinalMergeMsg(){
+        outFlag |= MessageFlag.IS_FINAL;
+        byte meToNeighborDir = (byte) (incomingMsg.getFlag() & MessageFlag.DIR_MASK);
+        byte neighborToMeDir = mirrorDirection(meToNeighborDir);
+        switch(neighborToMeDir){
+            case MessageFlag.DIR_FF:
+            case MessageFlag.DIR_FR:
+                setSuccessorAdjMsg();
+                if(ifFlipWithPredecessor())
+                    outgoingMsg.setFlip(true);
+                else
+                    outgoingMsg.setFlip(false);
+                outgoingMsg.setFlag(outFlag);
+                outgoingMsg.setNeighberNode(getVertexValue().getIncomingList());
+                outgoingMsg.setSourceVertexId(getVertexId());
+                outgoingMsg.setChainVertexId(getVertexValue().getKmer());
+                sendMsg(incomingMsg.getSourceVertexId(), outgoingMsg); //getNextDestVertexId(getVertexValue())
+                break;
+            case MessageFlag.DIR_RF:
+            case MessageFlag.DIR_RR:
+                setPredecessorAdjMsg();
+                if(ifFilpWithSuccessor())
+                    outgoingMsg.setFlip(true);
+                else
+                    outgoingMsg.setFlip(false);
+                outgoingMsg.setFlag(outFlag);
+                outgoingMsg.setNeighberNode(getVertexValue().getOutgoingList());
+                outgoingMsg.setSourceVertexId(getVertexId());
+                outgoingMsg.setChainVertexId(getVertexValue().getKmer());
+                sendMsg(incomingMsg.getSourceVertexId(), outgoingMsg); //getPreDestVertexId(getVertexValue())
+                break; 
+        }
     }
     
     /**
@@ -551,7 +617,7 @@
         byte meToNeighborDir = (byte) (msg.getFlag() & MessageFlag.DIR_MASK);
         byte neighborToMeDir = mirrorDirection(meToNeighborDir);
 
-        byte neighborToMergeDir = flipDirection(neighborToMeDir, incomingMsg.isFlip());
+        byte neighborToMergeDir = flipDirection(neighborToMeDir, msg.isFlip());
         
         getVertexValue().processMerges(neighborToMeDir, msg.getSourceVertexId(), 
                 neighborToMergeDir, VertexUtil.getNodeIdFromAdjacencyList(msg.getNeighberNode()),
@@ -579,12 +645,12 @@
     }
     
     /**
-     * set final state
+     * set stop flag
      */
     public void setStopFlag(){
-        byte state = incomingMsg.getFlag();
+        byte state = getVertexValue().getState();
         state &= State.VERTEX_CLEAR;
-        state |= State.IS_STOP;
+        state |= State.IS_FINAL;
         getVertexValue().setState(state);
     }
     
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/LogAlgorithmForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/LogAlgorithmForPathMergeVertex.java
index 49bca8e..e2e8933 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/LogAlgorithmForPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/LogAlgorithmForPathMergeVertex.java
@@ -4,12 +4,12 @@
 import java.util.Iterator;
 
 import edu.uci.ics.pregelix.api.job.PregelixJob;
-import edu.uci.ics.genomix.oldtype.PositionWritable;
 import edu.uci.ics.genomix.pregelix.client.Client;
-import edu.uci.ics.genomix.pregelix.format.GraphCleanOutputFormat;
 import edu.uci.ics.genomix.pregelix.format.InitialGraphCleanInputFormat;
+import edu.uci.ics.genomix.pregelix.format.P2PathMergeOutputFormat;
 import edu.uci.ics.genomix.pregelix.io.MessageWritable;
 import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
+import edu.uci.ics.genomix.pregelix.io.VertexValueWritable.State;
 import edu.uci.ics.genomix.pregelix.type.MessageFlag;
 import edu.uci.ics.genomix.pregelix.type.MessageFromHead;
 import edu.uci.ics.genomix.type.KmerBytesWritable;
@@ -45,7 +45,7 @@
     BasicPathMergeVertex {
 
     private ArrayList<MessageWritable> receivedMsgList = new ArrayList<MessageWritable>();
-    KmerBytesWritable tempPostition = new KmerBytesWritable();
+    KmerBytesWritable tmpKmer = new KmerBytesWritable();
 
     /**
      * initiate kmerSize, maxIteration
@@ -55,9 +55,14 @@
             kmerSize = getContext().getConfiguration().getInt(KMER_SIZE, 5);
         if (maxIteration < 0)
             maxIteration = getContext().getConfiguration().getInt(ITERATIONS, 1000000);
-        headFlag = (byte)(getVertexValue().getState() & MessageFlag.IS_HEAD);
-        selfFlag =(byte)(getVertexValue().getState() & MessageFlag.VERTEX_MASK);
-        outgoingMsg.reset();
+        headFlag = (byte)(getVertexValue().getState() & State.IS_HEAD);
+        selfFlag = (byte)(getVertexValue().getState() & State.VERTEX_MASK);
+        if(incomingMsg == null)
+            incomingMsg = new MessageWritable(kmerSize);
+        if(outgoingMsg == null)
+            outgoingMsg = new MessageWritable(kmerSize);
+        else
+            outgoingMsg.reset(kmerSize);
         receivedMsgList.clear();
     }
 
@@ -66,18 +71,18 @@
      */
     public void sendOutMsg() {
         //send wantToMerge to next
-        tempPostition = getNextDestVertexIdAndSetFlag(getVertexValue());
-        if(tempPostition != null){
-            destVertexId.set(tempPostition);
+        tmpKmer = getNextDestVertexIdAndSetFlag(getVertexValue());
+        if(tmpKmer != null){
+            destVertexId.set(tmpKmer);
             outgoingMsg.setFlag(outFlag);
             outgoingMsg.setSourceVertexId(getVertexId());
             sendMsg(destVertexId, outgoingMsg);
         }
         
-        ////send wantToMerge to prev
-        tempPostition = getPreDestVertexIdAndSetFlag(getVertexValue());
-        if(tempPostition != null){
-            destVertexId.set(tempPostition);
+        //send wantToMerge to prev
+        tmpKmer = getPreDestVertexIdAndSetFlag(getVertexValue());
+        if(tmpKmer != null){
+            destVertexId.set(tmpKmer);
             outgoingMsg.setFlag(outFlag);
             outgoingMsg.setSourceVertexId(getVertexId());
             sendMsg(destVertexId, outgoingMsg);
@@ -118,7 +123,7 @@
      */
     public void sendMsgToPathVertex(Iterator<MessageWritable> msgIterator) {
         //send out wantToMerge msg
-        if(selfFlag != MessageFlag.IS_HEAD){
+        if(selfFlag != State.IS_HEAD && selfFlag != State.IS_OLDHEAD){
                 sendOutMsg();
         }
     }
@@ -127,17 +132,19 @@
      * path response message to head
      */
     public void responseMsgToHeadVertex(Iterator<MessageWritable> msgIterator) {
-        if(!msgIterator.hasNext() && selfFlag == MessageFlag.IS_HEAD){
-            getVertexValue().setState(MessageFlag.IS_STOP);
+        if(!msgIterator.hasNext() && selfFlag == State.IS_HEAD){
+            outFlag |= MessageFlag.IS_FINAL;
             sendOutMsg();
         }
         while (msgIterator.hasNext()) {
             incomingMsg = msgIterator.next();
             if(getMsgFlag() == MessageFlag.IS_FINAL){
                 processMerge(incomingMsg);
-                getVertexValue().setState(MessageFlag.IS_FINAL);
-            }else
+                getVertexValue().setState(State.IS_FINAL);
+            }else{
+                sendUpdateMsg();
                 sendMergeMsg();
+            }
         }
     }
 
@@ -149,11 +156,13 @@
         while (msgIterator.hasNext()) {
             incomingMsg = msgIterator.next();
             if(getMsgFlag() == MessageFlag.IS_FINAL){
-                setStopFlag();
-                sendMergeMsg();
+                sendFinalMergeMsg();
                 break;
             }
-            receivedMsgList.add(incomingMsg);
+            if(incomingMsg.isUpdateMsg() && selfFlag == State.IS_OLDHEAD)
+                processUpdate();
+            else if(!incomingMsg.isUpdateMsg())
+                receivedMsgList.add(incomingMsg);
         }
         if(receivedMsgList.size() != 0){
             byte numOfMsgsFromHead = checkNumOfMsgsFromHead();
@@ -162,13 +171,13 @@
                 case MessageFromHead.OneMsgFromOldHeadAndOneFromHead:
                     for(int i = 0; i < 2; i++)
                         processMerge(receivedMsgList.get(i));
-                    getVertexValue().setState(MessageFlag.IS_FINAL);
+                    getVertexValue().setState(State.IS_FINAL);
                     voteToHalt();
                     break;
                 case MessageFromHead.OneMsgFromHeadAndOneFromNonHead:
                     for(int i = 0; i < 2; i++)
                         processMerge(receivedMsgList.get(i));
-                    getVertexValue().setState(MessageFlag.IS_HEAD);
+                    getVertexValue().setState(State .IS_HEAD);
                     break;
                 case MessageFromHead.BothMsgsFromNonHead:
                     for(int i = 0; i < 2; i++)
@@ -189,12 +198,21 @@
         else if (getSuperstep() == 2)
             initState(msgIterator);
         else if (getSuperstep() % 3 == 0 && getSuperstep() <= maxIteration) {
-            sendMsgToPathVertex(msgIterator);
-            if(selfFlag != MessageFlag.IS_HEAD)
-                voteToHalt();
+            if(msgIterator.hasNext()){ //for processing final merge
+                incomingMsg = msgIterator.next();
+                if(getMsgFlag() == MessageFlag.IS_FINAL){
+                    setFinalState();
+                    processMerge(incomingMsg);
+                }
+            }
+            else{
+                sendMsgToPathVertex(msgIterator);
+                if(selfFlag != State.IS_HEAD)
+                    voteToHalt();
+            }
         } else if (getSuperstep() % 3 == 1 && getSuperstep() <= maxIteration) {
             responseMsgToHeadVertex(msgIterator);
-            if(selfFlag != MessageFlag.IS_HEAD)
+            if(selfFlag != State.IS_HEAD)
                 voteToHalt();
         } else if (getSuperstep() % 3 == 2 && getSuperstep() <= maxIteration){
             processMergeInHeadVertex(msgIterator);
@@ -209,8 +227,8 @@
          * BinaryInput and BinaryOutput~/
          */
         job.setVertexInputFormatClass(InitialGraphCleanInputFormat.class);
-        job.setVertexOutputFormatClass(GraphCleanOutputFormat.class);
-        job.setOutputKeyClass(PositionWritable.class);
+        job.setVertexOutputFormatClass(P2PathMergeOutputFormat.class);
+        job.setOutputKeyClass(KmerBytesWritable.class);
         job.setOutputValueClass(VertexValueWritable.class);
         job.setDynamicVertexValueSize(true);
         Client.run(args, job);
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P4ForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P4ForPathMergeVertex.java
index 94428ca..c473867 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P4ForPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P4ForPathMergeVertex.java
@@ -78,8 +78,8 @@
             incomingMsg = new MessageWritable(kmerSize);
         if(outgoingMsg == null)
             outgoingMsg = new MessageWritable(kmerSize);
-        //if (randSeed < 0)
-        //    randSeed = getContext().getConfiguration().getLong("randomSeed", 0);
+        else
+            outgoingMsg.reset(kmerSize);
         randSeed = getSuperstep();
         randGenerator = new Random(randSeed);
         if (probBeingRandomHead < 0)
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/type/DirectionFlag.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/type/DirectionFlag.java
index 6e1bc4b..bee1dd8 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/type/DirectionFlag.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/type/DirectionFlag.java
@@ -9,4 +9,5 @@
     public static final byte DIR_RF = 0b011 << 0;
     public static final byte DIR_RR = 0b100 << 0;
     public static final byte DIR_MASK = 0b111 << 0;
+    public static final byte DIR_CLEAR = 0b1111000 << 0;
 }
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobGen/JobGenerator.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobGen/JobGenerator.java
index 0e798fe..e18c31b 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobGen/JobGenerator.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobGen/JobGenerator.java
@@ -7,6 +7,7 @@
 import edu.uci.ics.genomix.pregelix.format.GraphCleanInputFormat;
 import edu.uci.ics.genomix.pregelix.format.GraphCleanOutputFormat;
 import edu.uci.ics.genomix.pregelix.format.InitialGraphCleanInputFormat;
+import edu.uci.ics.genomix.pregelix.format.P2PathMergeOutputFormat;
 import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
 import edu.uci.ics.genomix.pregelix.operator.bridgeremove.BridgeAddVertex;
 import edu.uci.ics.genomix.pregelix.operator.bridgeremove.BridgeRemoveVertex;
@@ -42,21 +43,21 @@
 //                + "NaiveAlgorithmForMergeGraph.xml");
 //    }
 
-//    private static void generateLogAlgorithmForMergeGraphJob(String jobName, String outputPath) throws IOException {
-//        PregelixJob job = new PregelixJob(jobName);
-//        job.setVertexClass(LogAlgorithmForPathMergeVertex.class);
-//        job.setVertexInputFormatClass(LogAlgorithmForPathMergeInputFormat.class);
-//        job.setVertexOutputFormatClass(GraphCleanOutputFormat.class); //LogAlgorithmForPathMergeOutputFormat
-//        job.setDynamicVertexValueSize(true);
-//        job.setOutputKeyClass(PositionWritable.class);
-//        job.setOutputValueClass(VertexValueWritable.class);
-//        job.getConfiguration().setInt(LogAlgorithmForPathMergeVertex.KMER_SIZE, 3);
-//        job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
-//    }
-//
-//    private static void genLogAlgorithmForMergeGraph() throws IOException {
-//        generateLogAlgorithmForMergeGraphJob("LogAlgorithmForMergeGraph", outputBase + "LogAlgorithmForMergeGraph.xml");
-//    }
+    private static void generateLogAlgorithmForMergeGraphJob(String jobName, String outputPath) throws IOException {
+        PregelixJob job = new PregelixJob(jobName);
+        job.setVertexClass(LogAlgorithmForPathMergeVertex.class);
+        job.setVertexInputFormatClass(InitialGraphCleanInputFormat.class);
+        job.setVertexOutputFormatClass(P2PathMergeOutputFormat.class); 
+        job.setDynamicVertexValueSize(true);
+        job.setOutputKeyClass(KmerBytesWritable.class);
+        job.setOutputValueClass(VertexValueWritable.class);
+        job.getConfiguration().setInt(LogAlgorithmForPathMergeVertex.KMER_SIZE, 3);
+        job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
+    }
+
+    private static void genLogAlgorithmForMergeGraph() throws IOException {
+        generateLogAlgorithmForMergeGraphJob("LogAlgorithmForMergeGraph", outputBase + "LogAlgorithmForMergeGraph.xml");
+    }
 //    
 //    private static void generateP3ForMergeGraphJob(String jobName, String outputPath) throws IOException {
 //        PregelixJob job = new PregelixJob(jobName);
@@ -77,22 +78,22 @@
 //                + "P3ForMergeGraph.xml");
 //    }
     
-    private static void generateP4ForMergeGraphJob(String jobName, String outputPath) throws IOException {
-        PregelixJob job = new PregelixJob(jobName);
-        job.setVertexClass(P4ForPathMergeVertex.class);
-        job.setVertexInputFormatClass(InitialGraphCleanInputFormat.class);
-        job.setVertexOutputFormatClass(GraphCleanOutputFormat.class);
-        job.setDynamicVertexValueSize(true);
-        job.setOutputKeyClass(KmerBytesWritable.class);
-        job.setOutputValueClass(VertexValueWritable.class);
-        job.getConfiguration().setInt(P4ForPathMergeVertex.KMER_SIZE, 3);
-        job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
-    }
-
-    private static void genP4ForMergeGraph() throws IOException {
-        generateP4ForMergeGraphJob("P4ForMergeGraph", outputBase
-                + "P4ForMergeGraph.xml");
-    }
+//    private static void generateP4ForMergeGraphJob(String jobName, String outputPath) throws IOException {
+//        PregelixJob job = new PregelixJob(jobName);
+//        job.setVertexClass(P4ForPathMergeVertex.class);
+//        job.setVertexInputFormatClass(InitialGraphCleanInputFormat.class);
+//        job.setVertexOutputFormatClass(GraphCleanOutputFormat.class);
+//        job.setDynamicVertexValueSize(true);
+//        job.setOutputKeyClass(KmerBytesWritable.class);
+//        job.setOutputValueClass(VertexValueWritable.class);
+//        job.getConfiguration().setInt(P4ForPathMergeVertex.KMER_SIZE, 3);
+//        job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
+//    }
+//
+//    private static void genP4ForMergeGraph() throws IOException {
+//        generateP4ForMergeGraphJob("P4ForMergeGraph", outputBase
+//                + "P4ForMergeGraph.xml");
+//    }
     
 //    private static void generateTipAddGraphJob(String jobName, String outputPath) throws IOException {
 //        PregelixJob job = new PregelixJob(jobName);
@@ -198,7 +199,7 @@
     
     public static void main(String[] args) throws IOException {
         //genNaiveAlgorithmForMergeGraph();
-        //genLogAlgorithmForMergeGraph();
+        genLogAlgorithmForMergeGraph();
         //genP3ForMergeGraph();
         //genTipAddGraph();
 //        genTipRemoveGraph();
@@ -206,7 +207,7 @@
 //        genBridgeRemoveGraph();
 //        genBubbleAddGraph();
 //        genBubbleMergeGraph();
-        genP4ForMergeGraph();
+//        genP4ForMergeGraph();
     }
 
 }
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/PathMergeSmallTestSuite.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/PathMergeSmallTestSuite.java
index 115f090..5aedeb7 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/PathMergeSmallTestSuite.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/PathMergeSmallTestSuite.java
@@ -45,14 +45,14 @@
 
     public static final String PreFix = "data/PathMergeTestSet"; //"graphbuildresult";
     public static final String[] TestDir = { PreFix + File.separator
-    + "2", PreFix + File.separator
-    + "3", PreFix + File.separator
-    + "4", PreFix + File.separator
-    + "5", PreFix + File.separator
-    + "6", PreFix + File.separator
-    + "7", PreFix + File.separator
-    + "8", PreFix + File.separator
-    + "9"};
+//    + "2", PreFix + File.separator
+//    + "3", PreFix + File.separator
+//    + "4", PreFix + File.separator
+//    + "5", PreFix + File.separator
+//    + "6", PreFix + File.separator
+//    + "7", PreFix + File.separator
+//    + "8", PreFix + File.separator
+    + "4"};
     private static final String ACTUAL_RESULT_DIR = "data/actual/pathmerge";
     private static final String PATH_TO_HADOOP_CONF = "src/test/resources/hadoop/conf";
     private static final String PATH_TO_CLUSTER_STORE = "src/test/resources/cluster/stores.properties";
diff --git a/genomix/genomix-pregelix/src/test/resources/jobs/P4ForMergeGraph.xml b/genomix/genomix-pregelix/src/test/resources/jobs/P4ForMergeGraph.xml
deleted file mode 100644
index 597e5c3..0000000
--- a/genomix/genomix-pregelix/src/test/resources/jobs/P4ForMergeGraph.xml
+++ /dev/null
@@ -1,142 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?><configuration>
-<property><name>mapred.tasktracker.dns.nameserver</name><value>default</value></property>
-<property><name>mapred.queue.default.acl-administer-jobs</name><value>*</value></property>
-<property><name>mapred.skip.map.auto.incr.proc.count</name><value>true</value></property>
-<property><name>mapred.jobtracker.instrumentation</name><value>org.apache.hadoop.mapred.JobTrackerMetricsInst</value></property>
-<property><name>mapred.skip.reduce.auto.incr.proc.count</name><value>true</value></property>
-<property><name>fs.hsftp.impl</name><value>org.apache.hadoop.hdfs.HsftpFileSystem</value></property>
-<property><name>mapred.submit.replication</name><value>10</value></property>
-<property><name>ipc.server.tcpnodelay</name><value>false</value></property>
-<property><name>fs.checkpoint.dir</name><value>${hadoop.tmp.dir}/dfs/namesecondary</value></property>
-<property><name>mapred.output.compression.type</name><value>RECORD</value></property>
-<property><name>mapred.job.shuffle.merge.percent</name><value>0.66</value></property>
-<property><name>mapred.child.java.opts</name><value>-Xmx200m</value></property>
-<property><name>mapred.queue.default.acl-submit-job</name><value>*</value></property>
-<property><name>keep.failed.task.files</name><value>false</value></property>
-<property><name>mapred.jobtracker.job.history.block.size</name><value>3145728</value></property>
-<property><name>mapred.output.value.class</name><value>edu.uci.ics.genomix.pregelix.io.VertexValueWritable</value></property>
-<property><name>io.bytes.per.checksum</name><value>512</value></property>
-<property><name>mapred.task.tracker.report.address</name><value>127.0.0.1:0</value></property>
-<property><name>hadoop.util.hash.type</name><value>murmur</value></property>
-<property><name>fs.hdfs.impl</name><value>org.apache.hadoop.hdfs.DistributedFileSystem</value></property>
-<property><name>fs.ramfs.impl</name><value>org.apache.hadoop.fs.InMemoryFileSystem</value></property>
-<property><name>mapred.jobtracker.restart.recover</name><value>false</value></property>
-<property><name>fs.hftp.impl</name><value>org.apache.hadoop.hdfs.HftpFileSystem</value></property>
-<property><name>fs.checkpoint.period</name><value>3600</value></property>
-<property><name>mapred.child.tmp</name><value>./tmp</value></property>
-<property><name>mapred.local.dir.minspacekill</name><value>0</value></property>
-<property><name>map.sort.class</name><value>org.apache.hadoop.util.QuickSort</value></property>
-<property><name>hadoop.logfile.count</name><value>10</value></property>
-<property><name>ipc.client.connection.maxidletime</name><value>10000</value></property>
-<property><name>io.map.index.skip</name><value>0</value></property>
-<property><name>mapred.tasktracker.expiry.interval</name><value>600000</value></property>
-<property><name>mapred.output.compress</name><value>false</value></property>
-<property><name>io.seqfile.lazydecompress</name><value>true</value></property>
-<property><name>mapred.reduce.parallel.copies</name><value>5</value></property>
-<property><name>fs.checkpoint.size</name><value>67108864</value></property>
-<property><name>mapred.job.reduce.input.buffer.percent</name><value>0.0</value></property>
-<property><name>mapred.job.name</name><value>P4ForMergeGraph</value></property>
-<property><name>local.cache.size</name><value>10737418240</value></property>
-<property><name>fs.s3n.impl</name><value>org.apache.hadoop.fs.s3native.NativeS3FileSystem</value></property>
-<property><name>mapred.userlog.limit.kb</name><value>0</value></property>
-<property><name>fs.file.impl</name><value>org.apache.hadoop.fs.LocalFileSystem</value></property>
-<property><name>mapred.task.tracker.http.address</name><value>0.0.0.0:50060</value></property>
-<property><name>mapred.task.timeout</name><value>600000</value></property>
-<property><name>fs.kfs.impl</name><value>org.apache.hadoop.fs.kfs.KosmosFileSystem</value></property>
-<property><name>mapred.max.tracker.blacklists</name><value>4</value></property>
-<property><name>fs.s3.buffer.dir</name><value>${hadoop.tmp.dir}/s3</value></property>
-<property><name>mapred.job.tracker.persist.jobstatus.dir</name><value>/jobtracker/jobsInfo</value></property>
-<property><name>ipc.client.kill.max</name><value>10</value></property>
-<property><name>mapred.tasktracker.instrumentation</name><value>org.apache.hadoop.mapred.TaskTrackerMetricsInst</value></property>
-<property><name>mapred.reduce.tasks.speculative.execution</name><value>true</value></property>
-<property><name>io.sort.record.percent</name><value>0.05</value></property>
-<property><name>hadoop.security.authorization</name><value>false</value></property>
-<property><name>mapred.max.tracker.failures</name><value>4</value></property>
-<property><name>mapred.jobtracker.taskScheduler</name><value>org.apache.hadoop.mapred.JobQueueTaskScheduler</value></property>
-<property><name>mapred.tasktracker.dns.interface</name><value>default</value></property>
-<property><name>mapred.map.tasks</name><value>2</value></property>
-<property><name>mapred.job.tracker.persist.jobstatus.hours</name><value>0</value></property>
-<property><name>fs.s3.sleepTimeSeconds</name><value>10</value></property>
-<property><name>fs.default.name</name><value>file:///</value></property>
-<property><name>mapred.output.key.class</name><value>edu.uci.ics.genomix.type.KmerBytesWritable</value></property>
-<property><name>tasktracker.http.threads</name><value>40</value></property>
-<property><name>mapred.tasktracker.taskmemorymanager.monitoring-interval</name><value>5000</value></property>
-<property><name>hadoop.rpc.socket.factory.class.default</name><value>org.apache.hadoop.net.StandardSocketFactory</value></property>
-<property><name>mapred.reduce.tasks</name><value>1</value></property>
-<property><name>topology.node.switch.mapping.impl</name><value>org.apache.hadoop.net.ScriptBasedMapping</value></property>
-<property><name>pregelix.vertexClass</name><value>edu.uci.ics.genomix.pregelix.operator.pathmerge.P4ForPathMergeVertex</value></property>
-<property><name>mapred.skip.reduce.max.skip.groups</name><value>0</value></property>
-<property><name>io.file.buffer.size</name><value>4096</value></property>
-<property><name>mapred.jobtracker.maxtasks.per.job</name><value>-1</value></property>
-<property><name>mapred.tasktracker.indexcache.mb</name><value>10</value></property>
-<property><name>mapred.tasktracker.map.tasks.maximum</name><value>2</value></property>
-<property><name>fs.har.impl.disable.cache</name><value>true</value></property>
-<property><name>mapred.task.profile.maps</name><value>0-2</value></property>
-<property><name>hadoop.native.lib</name><value>true</value></property>
-<property><name>fs.s3.block.size</name><value>67108864</value></property>
-<property><name>mapred.job.reuse.jvm.num.tasks</name><value>1</value></property>
-<property><name>mapred.job.tracker.http.address</name><value>0.0.0.0:50030</value></property>
-<property><name>mapred.tasktracker.reduce.tasks.maximum</name><value>2</value></property>
-<property><name>io.compression.codecs</name><value>org.apache.hadoop.io.compress.DefaultCodec,org.apache.hadoop.io.compress.GzipCodec,org.apache.hadoop.io.compress.BZip2Codec</value></property>
-<property><name>mapred.job.shuffle.input.buffer.percent</name><value>0.70</value></property>
-<property><name>io.seqfile.compress.blocksize</name><value>1000000</value></property>
-<property><name>mapred.queue.names</name><value>default</value></property>
-<property><name>fs.har.impl</name><value>org.apache.hadoop.fs.HarFileSystem</value></property>
-<property><name>io.mapfile.bloom.error.rate</name><value>0.005</value></property>
-<property><name>mapred.job.tracker</name><value>local</value></property>
-<property><name>io.skip.checksum.errors</name><value>false</value></property>
-<property><name>mapred.reduce.max.attempts</name><value>4</value></property>
-<property><name>fs.s3.maxRetries</name><value>4</value></property>
-<property><name>ipc.server.listen.queue.size</name><value>128</value></property>
-<property><name>fs.trash.interval</name><value>0</value></property>
-<property><name>mapred.local.dir.minspacestart</name><value>0</value></property>
-<property><name>fs.s3.impl</name><value>org.apache.hadoop.fs.s3.S3FileSystem</value></property>
-<property><name>io.seqfile.sorter.recordlimit</name><value>1000000</value></property>
-<property><name>io.mapfile.bloom.size</name><value>1048576</value></property>
-<property><name>io.sort.mb</name><value>100</value></property>
-<property><name>mapred.local.dir</name><value>${hadoop.tmp.dir}/mapred/local</value></property>
-<property><name>io.sort.factor</name><value>10</value></property>
-<property><name>BasicPathMergeVertex.kmerSize</name><value>3</value></property>
-<property><name>mapred.task.profile</name><value>false</value></property>
-<property><name>job.end.retry.interval</name><value>30000</value></property>
-<property><name>mapred.tasktracker.procfsbasedprocesstree.sleeptime-before-sigkill</name><value>5000</value></property>
-<property><name>mapred.jobtracker.completeuserjobs.maximum</name><value>100</value></property>
-<property><name>mapred.task.profile.reduces</name><value>0-2</value></property>
-<property><name>webinterface.private.actions</name><value>false</value></property>
-<property><name>hadoop.tmp.dir</name><value>/tmp/hadoop-${user.name}</value></property>
-<property><name>mapred.output.compression.codec</name><value>org.apache.hadoop.io.compress.DefaultCodec</value></property>
-<property><name>mapred.skip.attempts.to.start.skipping</name><value>2</value></property>
-<property><name>mapred.temp.dir</name><value>${hadoop.tmp.dir}/mapred/temp</value></property>
-<property><name>mapred.merge.recordsBeforeProgress</name><value>10000</value></property>
-<property><name>mapred.map.output.compression.codec</name><value>org.apache.hadoop.io.compress.DefaultCodec</value></property>
-<property><name>mapred.compress.map.output</name><value>false</value></property>
-<property><name>io.sort.spill.percent</name><value>0.80</value></property>
-<property><name>fs.checkpoint.edits.dir</name><value>${fs.checkpoint.dir}</value></property>
-<property><name>mapred.userlog.retain.hours</name><value>24</value></property>
-<property><name>mapred.system.dir</name><value>${hadoop.tmp.dir}/mapred/system</value></property>
-<property><name>mapred.line.input.format.linespermap</name><value>1</value></property>
-<property><name>job.end.retry.attempts</name><value>0</value></property>
-<property><name>ipc.client.idlethreshold</name><value>4000</value></property>
-<property><name>pregelix.vertexOutputFormatClass</name><value>edu.uci.ics.genomix.pregelix.format.GraphCleanOutputFormat</value></property>
-<property><name>mapred.reduce.copy.backoff</name><value>300</value></property>
-<property><name>mapred.map.tasks.speculative.execution</name><value>true</value></property>
-<property><name>mapred.inmem.merge.threshold</name><value>1000</value></property>
-<property><name>hadoop.logfile.size</name><value>10000000</value></property>
-<property><name>pregelix.vertexInputFormatClass</name><value>edu.uci.ics.genomix.pregelix.format.InitialGraphCleanInputFormat</value></property>
-<property><name>mapred.job.queue.name</name><value>default</value></property>
-<property><name>mapred.job.tracker.persist.jobstatus.active</name><value>false</value></property>
-<property><name>pregelix.incStateLength</name><value>true</value></property>
-<property><name>mapred.reduce.slowstart.completed.maps</name><value>0.05</value></property>
-<property><name>topology.script.number.args</name><value>100</value></property>
-<property><name>mapred.skip.map.max.skip.records</name><value>0</value></property>
-<property><name>fs.ftp.impl</name><value>org.apache.hadoop.fs.ftp.FTPFileSystem</value></property>
-<property><name>mapred.task.cache.levels</name><value>2</value></property>
-<property><name>mapred.job.tracker.handler.count</name><value>10</value></property>
-<property><name>io.serializations</name><value>org.apache.hadoop.io.serializer.WritableSerialization</value></property>
-<property><name>ipc.client.connect.max.retries</name><value>10</value></property>
-<property><name>mapred.min.split.size</name><value>0</value></property>
-<property><name>mapred.map.max.attempts</name><value>4</value></property>
-<property><name>jobclient.output.filter</name><value>FAILED</value></property>
-<property><name>ipc.client.tcpnodelay</name><value>false</value></property>
-<property><name>mapred.acls.enabled</name><value>false</value></property>
-</configuration>
\ No newline at end of file
diff --git a/genomix/genomix-pregelix/src/test/resources/only_pathmerge.txt b/genomix/genomix-pregelix/src/test/resources/only_pathmerge.txt
index 3d007d2..5a15ca0 100644
--- a/genomix/genomix-pregelix/src/test/resources/only_pathmerge.txt
+++ b/genomix/genomix-pregelix/src/test/resources/only_pathmerge.txt
@@ -1 +1 @@
-P4ForMergeGraph.xml
+LogAlgorithmForMergeGraph.xml