diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/client/Client.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/client/Client.java
index f849b21..e49063b 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/client/Client.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/client/Client.java
@@ -11,6 +11,7 @@
 
 import edu.uci.ics.genomix.pregelix.operator.LogAlgorithmForPathMergeVertex;
 import edu.uci.ics.genomix.pregelix.operator.NaiveAlgorithmForPathMergeVertex;
+import edu.uci.ics.genomix.pregelix.operator.P3ForPathMergeVertex;
 import edu.uci.ics.pregelix.api.job.PregelixJob;
 import edu.uci.ics.pregelix.core.base.IDriver.Plan;
 import edu.uci.ics.pregelix.core.driver.Driver;
@@ -41,6 +42,12 @@
 
         @Option(name = "-runtime-profiling", usage = "whether to do runtime profifling", required = false)
         public String profiling = "false";
+        
+        @Option(name = "-pseudo-rate", usage = "the rate of pseduHead", required = false)
+        public float pseudoRate = -1;
+        
+        @Option(name = "-max-patitionround", usage = "max rounds in partition phase", required = false)
+        public int maxRound = -1;
     }
 
     public static void run(String[] args, PregelixJob job) throws Exception {
@@ -64,7 +71,12 @@
         if (options.numIteration > 0) {
             job.getConfiguration().setInt(NaiveAlgorithmForPathMergeVertex.ITERATIONS, options.numIteration);
             job.getConfiguration().setInt(LogAlgorithmForPathMergeVertex.ITERATIONS, options.numIteration);
+            job.getConfiguration().setInt(P3ForPathMergeVertex.ITERATIONS, options.numIteration);
         }
+        if (options.pseudoRate > 0 && options.pseudoRate <= 1)
+            job.getConfiguration().setFloat(P3ForPathMergeVertex.PSEUDORATE, options.pseudoRate);
+        if (options.maxRound > 0)
+            job.getConfiguration().setInt(P3ForPathMergeVertex.MAXROUND, options.maxRound);
         return options;
     }
 }
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/P3ForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/P3ForPathMergeVertex.java
index 96886de..e189800 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/P3ForPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/P3ForPathMergeVertex.java
@@ -54,11 +54,12 @@
         Vertex<KmerBytesWritable, ValueStateWritable, NullWritable, NaiveAlgorithmMessageWritable> {
     public static final String KMER_SIZE = "P3ForPathMergeVertex.kmerSize";
     public static final String ITERATIONS = "P3ForPathMergeVertex.iteration";
+    public static final String PSEUDORATE = "P3ForPathMergeVertex.pseudoRate";
+    public static final String MAXROUND = "P3ForPathMergeVertex.maxRound";
     public static int kmerSize = -1;
     private int maxIteration = -1;
-    public static final double pseudoRatio = 0.2;
-    public static int maxPseudoHeads = 1;
-    public static int maxRound = 2;
+    public static float pseudoRate = -1;
+    public static int maxRound = -1;
 
     private NaiveAlgorithmMessageWritable incomingMsg = new NaiveAlgorithmMessageWritable();
     private NaiveAlgorithmMessageWritable outgoingMsg = new NaiveAlgorithmMessageWritable();
@@ -75,6 +76,10 @@
             kmerSize = getContext().getConfiguration().getInt(KMER_SIZE, 5);
         if (maxIteration < 0)
             maxIteration = getContext().getConfiguration().getInt(ITERATIONS, 1000000);
+        if(pseudoRate < 0)
+            pseudoRate = getContext().getConfiguration().getFloat(PSEUDORATE, 0.2f);
+        if (maxRound < 0)
+            maxRound = getContext().getConfiguration().getInt(MAXROUND, 4);
         outgoingMsg.reset();
     }
 
@@ -149,17 +154,17 @@
                 }
             } while (msgIterator.hasNext());
         } else {
-            /*double random = Math.random();
-            if (random < pseudoRatio)
+            float random = (float) Math.random();
+            if (random < pseudoRate)
                 markPseudoHead();
             else{
-                getVertexValue().setState(State.NON);
+                getVertexValue().setState(State.NON_VERTEX);
                 voteToHalt();
-            }*/
-            if (getVertexId().toString().equals("CCTCA")) //AGTAC
+            }
+            /*if (getVertexId().toString().equals("CCTCA") || getVertexId().toString().equals("CTCAG")) //AGTAC CCTCA CTCAG CGCCC ACGCC
                 markPseudoHead();
             else
-                voteToHalt();
+                voteToHalt();*/
         }
     }
 
@@ -170,7 +175,8 @@
         getVertexValue().setState(State.PSEUDOHEAD);
         outgoingMsg.setMessage(Message.FROMPSEUDOHEAD);
         destVertexId
-                .set(getPreDestVertexId(getVertexId(), GeneCode.getGeneCodeFromBitMap(getVertexValue().getAdjMap())));
+                .set(getPreDestVertexId(getVertexId(), 
+                        GeneCode.getGeneCodeFromBitMap((byte) ((getVertexValue().getAdjMap() >> 4) & 0x0F))));
         sendMsg(destVertexId, outgoingMsg);
     }
 
@@ -238,9 +244,7 @@
                             .set(getDestVertexIdFromChain(getVertexValue().getMergeChain(), incomingMsg.getAdjMap()));
                     sendMsg(destVertexId, outgoingMsg);
                 } else {
-                    getVertexValue().setMergeChain(
-                            kmerFactory.mergeKmerWithNextCode(getVertexValue().getMergeChain(),
-                                    incomingMsg.getLastGeneCode()));
+                    mergeChainVertex();
                     byte adjMap = VertexUtil.updateRightNeighber(getVertexValue().getAdjMap(), incomingMsg.getAdjMap());
                     getVertexValue().setAdjMap(adjMap);
                     getVertexValue().setState(State.FINAL_VERTEX);
@@ -276,10 +280,7 @@
                 outgoingMsg.setSourceVertexId(getVertexId());
                 destVertexId.set(getDestVertexIdFromChain(getVertexValue().getMergeChain(), getVertexValue().getAdjMap()));
                 sendMsg(destVertexId, outgoingMsg);
-            }
-            else{
-                outgoingMsg.setMessage(Message.FROMSELF);
-                sendMsg(getVertexId(), outgoingMsg);
+                voteToHalt();
             }
         } else {
             while (msgIterator.hasNext()) {
@@ -289,19 +290,23 @@
                     mergeChainVertex();
                     byte adjMap = VertexUtil.updateRightNeighber(getVertexValue().getAdjMap(), incomingMsg.getAdjMap());
                     getVertexValue().setAdjMap(adjMap);
-                    if (incomingMsg.getMessage() != Message.STOP && incomingMsg.getMessage() != Message.FROMREAR) {
+                    if (incomingMsg.getMessage() != Message.STOP 
+                            && incomingMsg.getMessage() != Message.FROMPSEUDOREAR) {
                         outgoingMsg.setSourceVertexId(getVertexId());
                         destVertexId.set(getDestVertexIdFromChain(getVertexValue().getMergeChain(),
                                 incomingMsg.getAdjMap()));
                         sendMsg(destVertexId, outgoingMsg);
+                        voteToHalt();
                     } else {
                         //check head or pseudoHead
                         if (getVertexValue().getState() == State.START_VERTEX
-                                && incomingMsg.getMessage() == Message.FROMREAR) {
+                                && incomingMsg.getMessage() == Message.STOP) {
                             getVertexValue().setState(State.FINAL_VERTEX);
                             //String source = getVertexValue().getMergeChain().toString();
                             //System.out.println();
-                        }
+                        } else if(getVertexValue().getState() == State.PSEUDOHEAD
+                                && incomingMsg.getMessage() == Message.STOP)
+                            getVertexValue().setState(State.END_VERTEX);
                     }
                 }
             }
@@ -312,46 +317,42 @@
      * path node sends message back to head node in partition phase
      */
     public void responseMsgToHeadVertexPartitionPhase() {
-        if(incomingMsg.getMessage() == Message.FROMSELF){
-            outgoingMsg.setMessage(Message.FROMSELF);
-            sendMsg(getVertexId(), outgoingMsg);
-        } else{
-            if (getVertexValue().getState() == State.PSEUDOHEAD)
-                outgoingMsg.setMessage(Message.FROMPSEUDOHEAD);
-            else {
-                deleteVertex(getVertexId());
-                outgoingMsg.setAdjMap(getVertexValue().getAdjMap());
-                if(getVertexValue().getLengthOfMergeChain() == 0)
-                    outgoingMsg.setLastGeneCode(getVertexId().getGeneCodeAtPosition(kmerSize - 1));
-                else
-                    outgoingMsg.setChainVertexId(getVertexValue().getMergeChain());
-                if (getVertexValue().getState() == State.PSEUDOREAR)
-                    outgoingMsg.setMessage(Message.FROMPSEUDOREAR);
-                else if (getVertexValue().getState() == State.END_VERTEX)
-                    outgoingMsg.setMessage(Message.STOP);
-            }
-            sendMsg(incomingMsg.getSourceVertexId(), outgoingMsg);
-        }   
+        if (getVertexValue().getState() == State.PSEUDOHEAD)
+            outgoingMsg.setMessage(Message.FROMPSEUDOHEAD);
+        else {
+            deleteVertex(getVertexId());
+            outgoingMsg.setAdjMap(getVertexValue().getAdjMap());
+            if(getVertexValue().getLengthOfMergeChain() == 0)
+                outgoingMsg.setLastGeneCode(getVertexId().getGeneCodeAtPosition(kmerSize - 1));
+            else
+                outgoingMsg.setChainVertexId(getVertexValue().getMergeChain());
+            if (getVertexValue().getState() == State.PSEUDOREAR)
+                outgoingMsg.setMessage(Message.FROMPSEUDOREAR);
+            else if (getVertexValue().getState() == State.END_VERTEX)
+                outgoingMsg.setMessage(Message.STOP);
+        }
+        sendMsg(incomingMsg.getSourceVertexId(), outgoingMsg);
+        voteToHalt();
     }
     
     /**
      * final process the result of partition phase
      */
     public void finalProcessPartitionPhase(Iterator<NaiveAlgorithmMessageWritable> msgIterator){
-        if(incomingMsg.getMessage() != Message.FROMSELF){
-            while (msgIterator.hasNext()) {
-                incomingMsg = msgIterator.next();
-                mergeChainVertex();
-                byte adjMap = VertexUtil.updateRightNeighber(getVertexValue().getAdjMap(), incomingMsg.getAdjMap());
-                getVertexValue().setAdjMap(adjMap);
-                //check head or pseudoHead
-                if (getVertexValue().getState() == State.START_VERTEX
-                        && incomingMsg.getMessage() == Message.FROMREAR) {
-                    getVertexValue().setState(State.FINAL_VERTEX);
-                    //String source = getVertexValue().getMergeChain().toString();
-                    //System.out.println();
-                }
-            }
+        while (msgIterator.hasNext()) {
+            incomingMsg = msgIterator.next();
+            mergeChainVertex();
+            byte adjMap = VertexUtil.updateRightNeighber(getVertexValue().getAdjMap(), incomingMsg.getAdjMap());
+            getVertexValue().setAdjMap(adjMap);
+            //check head or pseudoHead
+            if (getVertexValue().getState() == State.START_VERTEX
+                    && incomingMsg.getMessage() == Message.STOP) {
+                getVertexValue().setState(State.FINAL_VERTEX);
+                //String source = getVertexValue().getMergeChain().toString();
+                //System.out.println();
+            } else if(getVertexValue().getState() == State.PSEUDOHEAD
+                    && incomingMsg.getMessage() == Message.STOP)
+                getVertexValue().setState(State.END_VERTEX);
         }
     }
     /**
@@ -379,13 +380,11 @@
             }
         } else if (getSuperstep() % 2 == 0 && getSuperstep() <= 3 + 2 * maxRound && getSuperstep() <= maxIteration) {
             sendMsgToPathVertexPartitionPhase(msgIterator);
-            voteToHalt();
         } else if (getSuperstep() % 2 == 1 && getSuperstep() <= 3 + 2 * maxRound && getSuperstep() <= maxIteration) {
             while (msgIterator.hasNext()) {
                 incomingMsg = msgIterator.next();
                 responseMsgToHeadVertexPartitionPhase();
             }
-            voteToHalt();
         } else if(getSuperstep() == 3 + 2 * maxRound + 1 && getSuperstep() <= maxIteration){
             finalProcessPartitionPhase(msgIterator);
         } else if (getSuperstep() % 2 == 1 && getSuperstep() <= maxIteration) {
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/type/Message.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/type/Message.java
index 21d732e..fa5f73b 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/type/Message.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/type/Message.java
@@ -8,8 +8,7 @@
     public static final byte STOP = 3;
     public static final byte FROMPSEUDOHEAD = 4;
     public static final byte FROMPSEUDOREAR = 5;
-    public static final byte FROMREAR = 6;
-    public static final byte FROMSELF = 7;
+    public static final byte FROMSELF = 6;
 
     public final static class MESSAGE_CONTENT {
 
@@ -34,9 +33,6 @@
                 case FROMPSEUDOREAR:
                     r = "FROMPSEUDOREAR";
                     break;
-                case FROMREAR:
-                    r = "FROMREAR";
-                    break;
                 case FROMSELF:
                     r = "FROMSELF";
                     break;
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 306e083..c8aaa84 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
@@ -50,7 +50,7 @@
             + "SimplePath", PreFix + File.separator
             + "SinglePath", PreFix + File.separator
             + "TreePath"};*/
-            /*+ "2", PreFix + File.separator + "3", PreFix + File.separator + "4", PreFix + File.separator + "5",
+           /* + "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", PreFix + File.separator + "TwoKmer", PreFix + File.separator + "ThreeKmer",
             PreFix + File.separator + "SinglePath", PreFix + File.separator + "SimplePath",