diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/NodeWritable.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/NodeWritable.java
index e8b241c..2c4ac0d 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/NodeWritable.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/NodeWritable.java
@@ -39,8 +39,9 @@
     }
     
     public static class MergeDirFlag extends DirectionFlag{
-        public static final byte SHOULD_MERGEWITHNEXT = 0b000 << 0;
-        public static final byte SHOULD_MERGEWITHPREV = 0b001 << 0;
+        public static final byte SHOULD_MERGEWITHNEXT = 0b0 << 2;
+        public static final byte SHOULD_MERGEWITHPREV = 0b1 << 2;
+        public static final byte SHOULD_MERGE_MASK = 0b1 << 2;
     }
 
     private PositionWritable nodeID;
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/PositionListWritable.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/PositionListWritable.java
index c793609..8620445 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/PositionListWritable.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/PositionListWritable.java
@@ -163,10 +163,12 @@
     }
 
     public void append(PositionWritable pos) {
-        setSize((1 + valueCount) * PositionWritable.LENGTH);
-        System.arraycopy(pos.getByteArray(), pos.getStartOffset(), storage, offset + valueCount
-                * PositionWritable.LENGTH, pos.getLength());
-        valueCount += 1;
+        if(pos != null){
+            setSize((1 + valueCount) * PositionWritable.LENGTH);
+            System.arraycopy(pos.getByteArray(), pos.getStartOffset(), storage, offset + valueCount
+                    * PositionWritable.LENGTH, pos.getLength());
+            valueCount += 1;
+        }
     }
 
     public void append(int readID, byte posInRead) {
diff --git a/genomix/genomix-pregelix/data/graphbuild.test/read.txt b/genomix/genomix-pregelix/data/graphbuild.test/read.txt
index bd5f3c4..37f02de 100755
--- a/genomix/genomix-pregelix/data/graphbuild.test/read.txt
+++ b/genomix/genomix-pregelix/data/graphbuild.test/read.txt
@@ -1 +1 @@
-1	AATAGAAC
+1	AATAGAA
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/DataCleanOutputFormat.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/DataCleanOutputFormat.java
index 4c38255..c4365ff 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/DataCleanOutputFormat.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/DataCleanOutputFormat.java
@@ -8,7 +8,6 @@
 
 import edu.uci.ics.genomix.pregelix.api.io.binary.BinaryDataCleanVertexOutputFormat;
 import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
-import edu.uci.ics.genomix.pregelix.type.State;
 import edu.uci.ics.genomix.type.PositionWritable;
 import edu.uci.ics.pregelix.api.graph.Vertex;
 import edu.uci.ics.pregelix.api.io.VertexWriter;
@@ -36,8 +35,7 @@
         @Override
         public void writeVertex(Vertex<PositionWritable, VertexValueWritable, NullWritable, ?> vertex)
                 throws IOException, InterruptedException {
-            if(vertex.getVertexValue().getState() != State.END_VERTEX)
-                getRecordWriter().write(vertex.getVertexId(), vertex.getVertexValue());
+            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 df49879..314dff6 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
@@ -19,7 +19,7 @@
      * file stores the point to the file that stores the chains of connected DNA
      */
     private PositionWritable sourceVertexId;
-    private KmerBytesWritable chainVertexId;
+    private KmerBytesWritable kmer;
     private AdjacencyListWritable neighberNode; //incoming or outgoing
     private byte flag;
 
@@ -27,7 +27,7 @@
 
     public MessageWritable() {
         sourceVertexId = new PositionWritable();
-        chainVertexId = new KmerBytesWritable(0);
+        kmer = new KmerBytesWritable(0);
         neighberNode = new AdjacencyListWritable();
         flag = Message.NON;
         checkMessage = (byte) 0;
@@ -39,9 +39,9 @@
             checkMessage |= CheckMessage.SOURCE;
             this.sourceVertexId.set(msg.getSourceVertexId());
         }
-        if (chainVertexId != null) {
+        if (kmer != null) {
             checkMessage |= CheckMessage.CHAIN;
-            this.chainVertexId.set(msg.getChainVertexId());
+            this.kmer.set(msg.getKmer());
         }
         if (neighberNode != null) {
             checkMessage |= CheckMessage.NEIGHBER;
@@ -59,7 +59,7 @@
         }
         if (chainVertexId != null) {
             checkMessage |= CheckMessage.CHAIN;
-            this.chainVertexId.set(chainVertexId);
+            this.kmer.set(chainVertexId);
         }
         if (neighberNode != null) {
             checkMessage |= CheckMessage.NEIGHBER;
@@ -70,7 +70,7 @@
 
     public void reset() {
         checkMessage = 0;
-        chainVertexId.reset(1);
+        kmer.reset(1);
         neighberNode.reset();
         flag = Message.NON;
     }
@@ -86,14 +86,14 @@
         }
     }
     
-    public KmerBytesWritable getChainVertexId() {
-        return chainVertexId;
+    public KmerBytesWritable getKmer() {
+        return kmer;
     }
 
     public void setChainVertexId(KmerBytesWritable chainVertexId) {
         if (chainVertexId != null) {
             checkMessage |= CheckMessage.CHAIN;
-            this.chainVertexId.set(chainVertexId);
+            this.kmer.set(chainVertexId);
         }
     }
     
@@ -109,7 +109,7 @@
     }
     
     public int getLengthOfChain() {
-        return chainVertexId.getKmerLength();
+        return kmer.getKmerLength();
     }
 
     public byte getFlag() {
@@ -126,7 +126,7 @@
         if ((checkMessage & CheckMessage.SOURCE) != 0)
             sourceVertexId.write(out);
         if ((checkMessage & CheckMessage.CHAIN) != 0)
-            chainVertexId.write(out);
+            kmer.write(out);
         if ((checkMessage & CheckMessage.NEIGHBER) != 0)
             neighberNode.write(out);
         out.write(flag);
@@ -139,7 +139,7 @@
         if ((checkMessage & CheckMessage.SOURCE) != 0)
             sourceVertexId.readFields(in);
         if ((checkMessage & CheckMessage.CHAIN) != 0)
-            chainVertexId.readFields(in);
+            kmer.readFields(in);
         if ((checkMessage & CheckMessage.NEIGHBER) != 0)
             neighberNode.readFields(in);
         flag = in.readByte();
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 104fe84..2defa0c 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
@@ -4,7 +4,7 @@
 
 import org.apache.hadoop.io.WritableComparable;
 
-import edu.uci.ics.genomix.hadoop.pmcommon.NodeWithFlagWritable.MessageFlag;
+import edu.uci.ics.genomix.pregelix.type.MessageFlag;
 import edu.uci.ics.genomix.pregelix.type.State;
 import edu.uci.ics.genomix.type.KmerBytesWritable;
 import edu.uci.ics.genomix.type.PositionListWritable;
@@ -174,6 +174,10 @@
      */
     public void processUpdates(byte neighborToDeleteDir, PositionWritable nodeToDelete,
             byte neighborToMergeDir, PositionWritable nodeToAdd){
+//        TODO
+//        this.getListFromDir(neighborToDeleteDir).remove(nodeToDelete);
+//        this.getListFromDir(neighborToMergeDir).append(nodeToDelete);
+        
         switch (neighborToDeleteDir & MessageFlag.DIR_MASK) {
             case MessageFlag.DIR_FF:
                 this.getFFList().remove(nodeToDelete);
@@ -224,6 +228,9 @@
                 this.getRRList().remove(nodeToDelete);
                 break;
         }
+        // TODO: remove switch below and replace with general direction merge
+//        this.getKmer().mergeWithDirKmer(neighborToMergeDir);
+        
         switch (neighborToMergeDir & MessageFlag.DIR_MASK) {
             case MessageFlag.DIR_FF:
                 this.getKmer().mergeWithFFKmer(kmerSize, kmer);
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/log/LogAlgorithmLogFormatter.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/log/LogAlgorithmLogFormatter.java
index 0e4ff95..c29e1b3 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/log/LogAlgorithmLogFormatter.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/log/LogAlgorithmLogFormatter.java
@@ -78,7 +78,7 @@
             builder.append("Message is: " + Message.MESSAGE_CONTENT.getContentFromCode(msg.getFlag()) + "\r\n");
 
             if (msg.getLengthOfChain() != -1) {
-                chain = msg.getChainVertexId().toString();
+                chain = msg.getKmer().toString();
                 builder.append("Chain Message: " + chain + "\r\n");
                 builder.append("Chain Length: " + msg.getLengthOfChain() + "\r\n");
             }
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 8e234e9..9238f9d 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
@@ -27,6 +27,7 @@
     protected MessageWritable outgoingMsg = new MessageWritable();
     protected PositionWritable destVertexId = new PositionWritable();
     protected Iterator<PositionWritable> posIterator;
+    byte headFlag;
     protected byte outFlag;
     
     /**
@@ -42,6 +43,13 @@
     }
     
     /**
+     * reset headFlag
+     */
+    public void resetHeadFlag(){
+        headFlag = (byte)(getVertexValue().getState() & MessageFlag.IS_HEAD);
+    }
+    
+    /**
      * get destination vertex
      */
     public PositionWritable getNextDestVertexId(VertexValueWritable value) {
@@ -205,7 +213,7 @@
         if(getVertexValue().getRFList().getLength() > 0)
             outFlag |= MessageFlag.DIR_RF;
         else
-            outFlag |= MessageFlag.DIR_RF;
+            outFlag |= MessageFlag.DIR_RR;
     }
     
     /**
@@ -248,8 +256,10 @@
             newState |= MessageFlag.IS_OLDHEAD;
             getVertexValue().setState(newState);
             outFlag |= MessageFlag.IS_HEAD;
+            voteToHalt();
         } else if((getVertexValue().getState() & MessageFlag.IS_OLDHEAD) > 0){
             outFlag |= MessageFlag.IS_OLDHEAD;
+            voteToHalt();
         }
         byte meToNeighborDir = (byte) (incomingMsg.getFlag() & MessageFlag.DIR_MASK);
         byte neighborToMeDir = mirrorDirection(meToNeighborDir);
@@ -286,7 +296,7 @@
     public void broadcastMergeMsg(){
         if((getVertexValue().getState() & MessageFlag.IS_HEAD) > 0)
             outFlag |= MessageFlag.IS_HEAD;
-        switch(getVertexValue().getState() & 0b0001){
+        switch(getVertexValue().getState() & MessageFlag.SHOULD_MERGE_MASK) {
             case MessageFlag.SHOULD_MERGEWITHNEXT:
                 setSuccessorAdjMsg();
                 if(ifFlipWithPredecessor())
@@ -314,7 +324,7 @@
      * This vertex tries to merge with next vertex and send update msg to neighber
      * @throws IOException 
      */
-    public void sendUpMsgFromPredecessor(){
+    public void sendUpMsgToPredecessor(){
         byte state = getVertexValue().getState();
         state |= MessageFlag.SHOULD_MERGEWITHNEXT;
         getVertexValue().setState(state);
@@ -329,7 +339,7 @@
      * This vertex tries to merge with next vertex and send update msg to neighber
      * @throws IOException 
      */
-    public void sendUpMsgFromSuccessor(){
+    public void sendUpMsgToSuccessor(){
         byte state = getVertexValue().getState();
         state |= MessageFlag.SHOULD_MERGEWITHPREV;
         getVertexValue().setState(state);
@@ -398,7 +408,7 @@
     }
     
     /**
-     * merge and updateAdjList
+     * merge and updateAdjList merge with one neighbor
      */
     public void processMerge(){
         byte meToNeighborDir = (byte) (incomingMsg.getFlag() & MessageFlag.DIR_MASK);
@@ -413,7 +423,7 @@
         
         getVertexValue().processMerges(neighborToMeDir, incomingMsg.getSourceVertexId(), 
                 neighborToMergeDir, VertexUtil.getNodeIdFromAdjacencyList(incomingMsg.getNeighberNode()),
-                kmerSize, incomingMsg.getChainVertexId());
+                kmerSize, incomingMsg.getKmer());
     }
     
     /**
@@ -432,7 +442,7 @@
         
         getVertexValue().processMerges(neighborToMeDir, msg.getSourceVertexId(), 
                 neighborToMergeDir, VertexUtil.getNodeIdFromAdjacencyList(msg.getNeighberNode()),
-                kmerSize, msg.getChainVertexId());
+                kmerSize, msg.getKmer());
     }
     
     @Override
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 4f1cefb..429282b 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
@@ -11,10 +11,6 @@
 import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
 import edu.uci.ics.genomix.pregelix.type.MessageFlag;
 import edu.uci.ics.genomix.pregelix.type.MessageFromHead;
-import edu.uci.ics.genomix.pregelix.type.State;
-import edu.uci.ics.genomix.pregelix.util.VertexUtil;
-import edu.uci.ics.genomix.type.KmerBytesWritable;
-import edu.uci.ics.genomix.type.KmerBytesWritableFactory;
 import edu.uci.ics.genomix.type.PositionWritable;
 /*
  * vertexId: BytesWritable
@@ -47,12 +43,11 @@
 public class LogAlgorithmForPathMergeVertex extends
     BasicPathMergeVertex {
 
-    private KmerBytesWritableFactory kmerFactory = new KmerBytesWritableFactory(1);
-    private KmerBytesWritable lastKmer = new KmerBytesWritable(1);
     private ArrayList<MessageWritable> receivedMsgList = new ArrayList<MessageWritable>();
+    protected MessageWritable outgoingMsg2 = new MessageWritable();
+    protected PositionWritable destVertexId2 = new PositionWritable();
     
-    byte headFlag;
-    byte oldHeadFlag;
+    byte finalFlag;
     /**
      * initiate kmerSize, maxIteration
      */
@@ -61,7 +56,7 @@
             kmerSize = getContext().getConfiguration().getInt(KMER_SIZE, 5);
         if (maxIteration < 0)
             maxIteration = getContext().getConfiguration().getInt(ITERATIONS, 1000000);
-        headFlag = (byte)0;
+        headFlag = (byte)(getVertexValue().getState() & MessageFlag.IS_HEAD);
         outgoingMsg.reset();
     }
 
@@ -76,10 +71,10 @@
         sendMsg(destVertexId, outgoingMsg);
         
         ////send wantToMerge to prev
-        destVertexId.set(getPreDestVertexId(getVertexValue()));
-        outgoingMsg.setFlag(outFlag);
-        outgoingMsg.setSourceVertexId(getVertexId());
-        sendMsg(destVertexId, outgoingMsg);
+        destVertexId2.set(getPreDestVertexId(getVertexValue()));
+        outgoingMsg2.setFlag(outFlag);
+        outgoingMsg2.setSourceVertexId(getVertexId());
+        sendMsg(destVertexId2, outgoingMsg2);
     }
     
     /**
@@ -89,9 +84,9 @@
         int countHead = 0;
         int countOldHead = 0;
         for(int i = 0; i < receivedMsgList.size(); i++){
-            if((byte)(receivedMsgList.get(i).getFlag() | MessageFlag.IS_HEAD) > 0)
+            if((byte)(receivedMsgList.get(i).getFlag() & MessageFlag.IS_HEAD) > 0)
                 countHead++;
-            if((byte)(receivedMsgList.get(i).getFlag() | MessageFlag.IS_OLDHEAD) > 0)
+            if((byte)(receivedMsgList.get(i).getFlag() & MessageFlag.IS_OLDHEAD) > 0)
                 countOldHead++;
         }
         if(countHead == 0 && countOldHead == 0)
@@ -100,8 +95,10 @@
             return MessageFromHead.BothMsgsFromHead;
         else if(countOldHead == 2)
             return MessageFromHead.BothMsgsFromOldHead;
-        else if(countHead == 1)
-            return MessageFromHead.OneMsgFromHead;
+        else if(countHead == 1 && headFlag == 0)
+            return MessageFromHead.OneMsgFromHeadToNonHead;
+        else if(countHead == 1 && headFlag > 0)
+            return MessageFromHead.OneMsgFromHeadToHead;
         else if(countOldHead == 1)
             return MessageFromHead.OneMsgFromNonHead;
         
@@ -125,29 +122,36 @@
                         processMerge(receivedMsgList.get(i));
                     break;
                 case MessageFromHead.BothMsgsFromHead:
+                case MessageFromHead.BothMsgsFromOldHead:
                     for(int i = 0; i < 2; i++)
                         processMerge(receivedMsgList.get(i));
                     getVertexValue().setState(MessageFlag.IS_FINAL);
                     break;
-                case MessageFromHead.BothMsgsFromOldHead:
-                    deleteVertex(getVertexId());
-                    break;
-                case MessageFromHead.OneMsgFromHead:
+                case MessageFromHead.OneMsgFromHeadToNonHead:
                     for(int i = 0; i < 2; i++)
                         processMerge(receivedMsgList.get(i));
                     getVertexValue().setState(MessageFlag.IS_HEAD);
                     break;
+                case MessageFromHead.OneMsgFromHeadToHead: //stop condition
+                    for(int i = 0; i < 2; i++){
+                        if(headFlag > 0){
+                            processMerge(receivedMsgList.get(i));
+                            break;
+                        }
+                    }
+                    getVertexValue().setState(MessageFlag.IS_FINAL);
+                    //voteToHalt();
+                    break;
                 case MessageFromHead.OneMsgFromNonHead:
                     //halt
-                    voteToHalt();
+                    //voteToHalt();
                     break;
             }
-        } else 
-            voteToHalt();
+        }
         //send out wantToMerge msg
-        headFlag = (byte)(getVertexValue().getState() | MessageFlag.IS_HEAD);
-        oldHeadFlag = (byte)(getVertexValue().getState() | MessageFlag.IS_OLDHEAD);
-        outFlag = (byte)(headFlag | oldHeadFlag);
+        resetHeadFlag();
+        finalFlag = (byte)(getVertexValue().getState() & MessageFlag.IS_FINAL);
+        outFlag = (byte)(headFlag | finalFlag);
         if(outFlag == 0)
             sendOutMsg();
     }
@@ -156,25 +160,10 @@
      * path response message to head
      */
     public void responseMsgToHeadVertex(Iterator<MessageWritable> msgIterator) {
-        sendMergeMsg();
-    }
-
-    /**
-     * merge chainVertex and store in vertexVal.chainVertexId
-     */
-    public boolean mergeChainVertex() {
-        //merge chain
-        lastKmer.set(kmerFactory.getLastKmerFromChain(incomingMsg.getLengthOfChain() - kmerSize + 1,
-                incomingMsg.getChainVertexId()));
-        KmerBytesWritable chainVertexId = kmerFactory.mergeTwoKmer(getVertexValue().getKmer(), lastKmer);
-        getVertexValue().setKmer(chainVertexId);
-        getVertexValue().setOutgoingList(incomingMsg.getNeighberNode());
-        if (VertexUtil.isCycle(kmerFactory.getFirstKmerFromChain(kmerSize, getVertexValue().getKmer()),
-                chainVertexId, kmerSize)) {
-            getVertexValue().setState(State.CYCLE);
-            return false;
-        } 
-        return true;
+        while (msgIterator.hasNext()) {
+            incomingMsg = msgIterator.next();
+            sendMergeMsg();
+        }
     }
 
     @Override
@@ -186,10 +175,10 @@
             initState(msgIterator);
         else if (getSuperstep() % 2 == 1 && getSuperstep() <= maxIteration) {
             sendMsgToPathVertex(msgIterator);
-            //voteToHalt();
+            if(headFlag == 0)
+                voteToHalt();
         } else if (getSuperstep() % 2 == 0 && getSuperstep() <= maxIteration) {
             responseMsgToHeadVertex(msgIterator);
-            voteToHalt();
         } else
             voteToHalt();
     }
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/NaiveAlgorithmForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/NaiveAlgorithmForPathMergeVertex.java
index e8fb61a..0b636ee 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/NaiveAlgorithmForPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/NaiveAlgorithmForPathMergeVertex.java
@@ -185,7 +185,7 @@
     public void mergeChainVertex() {
         //merge chain
         lastKmer.set(kmerFactory.getLastKmerFromChain(incomingMsg.getLengthOfChain() - kmerSize + 1,
-                incomingMsg.getChainVertexId()));
+                incomingMsg.getKmer()));
         getVertexValue().setKmer(kmerFactory.mergeTwoKmer(getVertexValue().getKmer(), lastKmer));
         getVertexValue().setOutgoingList(incomingMsg.getNeighberNode());
     }
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P3ForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P3ForPathMergeVertex.java
index 3e1b87e..69e1fb6 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P3ForPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P3ForPathMergeVertex.java
@@ -231,7 +231,7 @@
      */
     public void mergeChainVertex(){
         lastKmer.set(kmerFactory.getLastKmerFromChain(incomingMsg.getLengthOfChain() - kmerSize + 1,
-                incomingMsg.getChainVertexId()));
+                incomingMsg.getKmer()));
         getVertexValue().setKmer(
                 kmerFactory.mergeTwoKmer(getVertexValue().getKmer(), 
                         lastKmer));
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 2457c1c..f250afc 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
@@ -159,10 +159,10 @@
                 if (curHead) {
                     if (hasNext && !nextHead) {
                         // compress this head to the forward tail
-                        sendUpMsgFromPredecessor();
+                        sendUpMsgToPredecessor(); //TODO up -> update  From -> to
                     } else if (hasPrev && !prevHead) {
                         // compress this head to the reverse tail
-                        sendUpMsgFromSuccessor();
+                        sendUpMsgToSuccessor();
                     }
                 } else {
                     // I'm a tail
@@ -170,19 +170,19 @@
                         if ((!nextHead && !prevHead) && (curID.compareTo(nextID) < 0 && curID.compareTo(prevID) < 0)) {
                             // tails on both sides, and I'm the "local minimum"
                             // compress me towards the tail in forward dir
-                            sendUpMsgFromPredecessor();
+                            sendUpMsgToPredecessor();
                         }
                     } else if (!hasPrev) {
                         // no previous node
                         if (!nextHead && curID.compareTo(nextID) < 0) {
                             // merge towards tail in forward dir
-                            sendUpMsgFromPredecessor();
+                            sendUpMsgToPredecessor();
                         }
                     } else if (!hasNext) {
                         // no next node
                         if (!prevHead && curID.compareTo(prevID) < 0) {
                             // merge towards tail in reverse dir
-                            sendUpMsgFromSuccessor();
+                            sendUpMsgToSuccessor();
                         }
                     }
                 }
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P5ForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P5ForPathMergeVertex.java
index 18e7d23..27eb40a 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P5ForPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P5ForPathMergeVertex.java
@@ -420,7 +420,7 @@
         
         getVertexValue().processMerges(neighborToMeDir, incomingMsg.getSourceVertexId(), 
                 neighborToMergeDir, VertexUtil.getNodeIdFromAdjacencyList(incomingMsg.getNeighberNode()),
-                kmerSize, incomingMsg.getChainVertexId());
+                kmerSize, incomingMsg.getKmer());
     }
     
     @Override
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/type/MessageFromHead.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/type/MessageFromHead.java
index e7a0ff1..f343c2e 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/type/MessageFromHead.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/type/MessageFromHead.java
@@ -2,10 +2,12 @@
 
 public class MessageFromHead {
     public static final byte BothMsgsFromHead = 1 << 0;
-    public static final byte BothMsgsFromNonHead = 2 << 0;
-    public static final byte BothMsgsFromOldHead = 3 << 0;
-    public static final byte OneMsgFromHead = 4 << 1;
-    public static final byte OneMsgFromNonHead = 5 << 1;
+    public static final byte BothMsgsFromNonHead = 1 << 1;
+    public static final byte BothMsgsFromOldHead = 1 << 2;
+    public static final byte OneMsgFromHead = 1 << 3;
+    public static final byte OneMsgFromNonHead = 1 << 4;
+    public static final byte OneMsgFromHeadToNonHead = 1 << 5;
+    public static final byte OneMsgFromHeadToHead = 1 << 6;
     
     public static final byte NO_INFO = 0 << 0;
 }
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/util/VertexUtil.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/util/VertexUtil.java
index 7e56c65..e9197db 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/util/VertexUtil.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/util/VertexUtil.java
@@ -117,7 +117,9 @@
     public static PositionWritable getNodeIdFromAdjacencyList(AdjacencyListWritable adj){
         if(adj.getForwardList().getCountOfPosition() > 0)
             return adj.getForwardList().getPosition(0);
-        else 
+        else if(adj.getReverseList().getCountOfPosition() > 0)
             return adj.getReverseList().getPosition(0);
+        else
+            return null;
     }
 }
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 f52957e..a63da20 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
@@ -183,8 +183,8 @@
     
     public static void main(String[] args) throws IOException {
         //genNaiveAlgorithmForMergeGraph();
-        //genLogAlgorithmForMergeGraph();
-        genP3ForMergeGraph();
+        genLogAlgorithmForMergeGraph();
+        //genP3ForMergeGraph();
         //genTipAddGraph();
         //genTipRemoveGraph();
         //genBridgeAddGraph();
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 f86ef23..cd81a97 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
@@ -45,7 +45,7 @@
 
     public static final String PreFix = "data/input"; //"graphbuildresult";
     public static final String[] TestDir = { PreFix + File.separator
-    + "read"};/*, PreFix + File.separator
+    + "pathmerge"};/*, PreFix + File.separator
             /*+ "CyclePath"};, PreFix + File.separator
             + "SimplePath", PreFix + File.separator
             + "SinglePath", PreFix + File.separator
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/graphbuilding/JobRunStepByStepTest.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/graphbuilding/JobRunStepByStepTest.java
index c5aa0eb..355bc7a 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/graphbuilding/JobRunStepByStepTest.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/graphbuilding/JobRunStepByStepTest.java
@@ -46,11 +46,11 @@
 @SuppressWarnings("deprecation")
 public class JobRunStepByStepTest {
     private static final int KmerSize = 3;
-    private static final int ReadLength = 8;
+    private static final int ReadLength = 7;
     private static final String ACTUAL_RESULT_DIR = "actual";
     private static final String PATH_TO_HADOOP_CONF = "src/test/resources/hadoop/conf";
 
-    private static final String DATA_INPUT_PATH = "data/graphbuild.test/tworeads.txt";
+    private static final String DATA_INPUT_PATH = "data/graphbuild.test/read.txt";
     private static final String HDFS_INPUT_PATH = "/webmap";
     private static final String HDFS_OUTPUT_PATH = "/webmap_result";
 
@@ -71,8 +71,8 @@
 
     @Test
     public void TestAll() throws Exception {
-        TestEndToEnd();
-        //TestUnMergedNode();
+        //TestEndToEnd();
+        TestUnMergedNode();
     }
 
     public void TestEndToEnd() throws Exception {
diff --git a/genomix/genomix-pregelix/src/test/resources/jobs/P3ForMergeGraph.xml b/genomix/genomix-pregelix/src/test/resources/jobs/P3ForMergeGraph.xml
deleted file mode 100644
index 6cfeda1..0000000
--- a/genomix/genomix-pregelix/src/test/resources/jobs/P3ForMergeGraph.xml
+++ /dev/null
@@ -1,144 +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>P3ForPathMergeVertex.kmerSize</name><value>3</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>P3ForPathMergeVertex.pseudoRate</name><value>0.3</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.ValueStateWritable</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>P3ForMergeGraph</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.PositionWritable</value></property>
-<property><name>P3ForPathMergeVertex.maxRound</name><value>2</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.P3ForPathMergeVertex</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>${hadoop.tmp.dir}/mapred/local</value></property>
-<property><name>io.sort.factor</name><value>10</value></property>
-<property><name>mapred.task.profile</name><value>false</value></property>
-<property><name>job.end.retry.interval</name><value>30000</value></property>
-<property><name>mapred.tasktracker.procfsbasedprocesstree.sleeptime-before-sigkill</name><value>5000</value></property>
-<property><name>mapred.jobtracker.completeuserjobs.maximum</name><value>100</value></property>
-<property><name>mapred.task.profile.reduces</name><value>0-2</value></property>
-<property><name>webinterface.private.actions</name><value>false</value></property>
-<property><name>hadoop.tmp.dir</name><value>/tmp/hadoop-${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.DataCleanOutputFormat</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.NaiveAlgorithmForPathMergeInputFormat</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