diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/GraphCleanInputFormat.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/GraphCleanInputFormat.java
index e36e344..5c28134 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/GraphCleanInputFormat.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/GraphCleanInputFormat.java
@@ -66,6 +66,7 @@
              * set the vertex value
              */
             vertexValue.set(getRecordReader().getCurrentValue());
+            vertexValue.setKmerlength(getRecordReader().getCurrentValue().getKmerlength());
             vertex.setVertexValue(vertexValue);
         }
 
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bridgeremove/BridgeAddVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bridgeremove/BridgeAddVertex.java
index f56fbf9..11f6af1 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bridgeremove/BridgeAddVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bridgeremove/BridgeAddVertex.java
@@ -58,7 +58,7 @@
     public void initVertex() {
         if (kmerSize == -1)
             kmerSize = getContext().getConfiguration().getInt(KMER_SIZE, 5);
-        if(length == -1)
+        if (length == -1)
             length = getContext().getConfiguration().getInt(LENGTH, kmerSize + 5);
     }
 
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicGraphCleanVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicGraphCleanVertex.java
index 912cfa5..8112b58 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicGraphCleanVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicGraphCleanVertex.java
@@ -26,7 +26,7 @@
     
     protected MessageWritable incomingMsg = null; 
     protected MessageWritable outgoingMsg = null; 
-    protected KmerBytesWritable destVertexId = new KmerBytesWritable();
+    protected KmerBytesWritable destVertexId = null;
     protected Iterator<KmerBytesWritable> kmerIterator;
     protected KmerBytesWritable tmpKmer = new KmerBytesWritable(kmerSize);
     byte headFlag;
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/MapReduceVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/MapReduceVertex.java
index a12c583..c7fc7bc 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/MapReduceVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/MapReduceVertex.java
@@ -53,6 +53,8 @@
             String random = generaterRandomString(kmerSize + 1);
             fakeVertex.setByRead(random.getBytes(), 0); 
         }
+        if(destVertexId == null)
+            destVertexId = new KmerBytesWritable(kmerSize);
     }
     
     /**
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P2ForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P2ForPathMergeVertex.java
index b7ab62b..835b42d 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P2ForPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P2ForPathMergeVertex.java
@@ -78,6 +78,8 @@
             fakeVertex.setByRead(random.getBytes(), 0); 
         }
         isFakeVertex = ((byte)getVertexValue().getState() & State.FAKEFLAG_MASK) > 0 ? true : false;
+        if(destVertexId == null)
+            destVertexId = new KmerBytesWritable(kmerSize);
     }
 
     /**
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 8f97c5a..59270fa 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
@@ -80,6 +80,8 @@
             outgoingMsg = new MessageWritable(kmerSize);
         else
             outgoingMsg.reset(kmerSize);
+        if(destVertexId == null)
+            destVertexId = new KmerBytesWritable(kmerSize);
         randSeed = getSuperstep();
         randGenerator = new Random(randSeed);
         if (probBeingRandomHead < 0)
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
deleted file mode 100644
index 8a2a301..0000000
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P5ForPathMergeVertex.java
+++ /dev/null
@@ -1,501 +0,0 @@
-package edu.uci.ics.genomix.pregelix.operator.pathmerge;
-
-import java.io.IOException;
-import java.util.Iterator;
-import java.util.Random;
-
-import org.apache.hadoop.io.NullWritable;
-
-
-import edu.uci.ics.pregelix.api.graph.Vertex;
-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.NaiveAlgorithmForPathMergeInputFormat;
-import edu.uci.ics.genomix.pregelix.format.NaiveAlgorithmForPathMergeOutputFormat;
-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.Message;
-import edu.uci.ics.genomix.pregelix.type.MessageFlag;
-import edu.uci.ics.genomix.pregelix.util.VertexUtil;
-
-/*
- * vertexId: BytesWritable
- * vertexValue: ByteWritable
- * edgeValue: NullWritable
- * message: MessageWritable
- * 
- * DNA:
- * A: 00
- * C: 01
- * G: 10
- * T: 11
- * 
- * succeed node
- *  A 00000001 1
- *  G 00000010 2
- *  C 00000100 4
- *  T 00001000 8
- * precursor node
- *  A 00010000 16
- *  G 00100000 32
- *  C 01000000 64
- *  T 10000000 128
- *  
- * For example, ONE LINE in input file: 00,01,10    0001,0010,
- * That means that vertexId is ACG, its succeed node is A and its precursor node is C.
- * The succeed node and precursor node will be stored in vertexValue and we don't use edgeValue.
- * The details about message are in edu.uci.ics.pregelix.example.io.MessageWritable. 
- */
-/**
- * Naive Algorithm for path merge graph
- */
-public class P5ForPathMergeVertex extends
-        Vertex<PositionWritable, VertexValueWritable, NullWritable, MessageWritable> {
-    public static final String KMER_SIZE = "P5ForPathMergeVertex.kmerSize";
-    public static final String ITERATIONS = "P5ForPathMergeVertex.iteration";
-    public static final String RANDSEED = "P5ForPathMergeVertex.randSeed";
-    public static final String PROBBEINGRANDOMHEAD = "P4ForPathMergeVertex.probBeingRandomHead";
-    public static int kmerSize = -1;
-    private int maxIteration = -1;
-
-    private static long randSeed = -1;
-    private float probBeingRandomHead = -1;
-    private Random randGenerator;
-    
-    private PositionWritable curID = new PositionWritable();
-    private PositionWritable nextID = new PositionWritable();
-    private PositionWritable prevID = new PositionWritable();
-    private boolean hasNext;
-    private boolean hasPrev;
-    private boolean curHead;
-    private boolean nextHead;
-    private boolean prevHead;
-    private byte headFlag;
-    private byte tailFlag;
-    private byte outFlag;
-    
-    private MessageWritable incomingMsg = new MessageWritable();
-    private MessageWritable outgoingMsg = new MessageWritable();
-    private PositionWritable destVertexId = new PositionWritable();
-    private Iterator<PositionWritable> posIterator;
-    
-    /**
-     * initiate kmerSize, maxIteration
-     */
-    public void initVertex() {
-        if (kmerSize == -1)
-            kmerSize = getContext().getConfiguration().getInt(KMER_SIZE, 5);
-        if (maxIteration < 0)
-            maxIteration = getContext().getConfiguration().getInt(ITERATIONS, 1000000);
-        if (randSeed < 0)
-            randSeed = getContext().getConfiguration().getLong("randomSeed", 0);
-        randGenerator = new Random(randSeed);
-        if (probBeingRandomHead < 0)
-            probBeingRandomHead = getContext().getConfiguration().getFloat("probBeingRandomHead", 0.5f);
-        hasNext = false;
-        hasPrev = false;
-        curHead = false;
-        nextHead = false;
-        prevHead = false;
-        outgoingMsg.reset();
-    }
-
-    protected boolean isNodeRandomHead(PositionWritable nodeID) {
-        // "deterministically random", based on node id
-        randGenerator.setSeed(randSeed ^ nodeID.hashCode());
-        return randGenerator.nextFloat() < probBeingRandomHead;
-    }
-
-    /**
-     * set nextID to the element that's next (in the node's FF or FR list), returning true when there is a next neighbor
-     */
-    protected boolean setNextInfo(VertexValueWritable value) {
-        if (value.getFFList().getCountOfPosition() > 0) {
-            nextID.set(value.getFFList().getPosition(0));
-            nextHead = isNodeRandomHead(nextID);
-            return true;
-        }
-        if (value.getFRList().getCountOfPosition() > 0) {
-            nextID.set(value.getFRList().getPosition(0));
-            nextHead = isNodeRandomHead(nextID);
-            return true;
-        }
-        return false;
-    }
-
-    /**
-     * set prevID to the element that's previous (in the node's RR or RF list), returning true when there is a previous neighbor
-     */
-    protected boolean setPrevInfo(VertexValueWritable value) {
-        if (value.getRRList().getCountOfPosition() > 0) {
-            prevID.set(value.getRRList().getPosition(0));
-            prevHead = isNodeRandomHead(prevID);
-            return true;
-        }
-        if (value.getRFList().getCountOfPosition() > 0) {
-            prevID.set(value.getRFList().getPosition(0));
-            prevHead = isNodeRandomHead(prevID);
-            return true;
-        }
-        return false;
-    }
-    
-    /**
-     * get destination vertex
-     */
-    public PositionWritable getNextDestVertexId(VertexValueWritable value) {
-        if(value.getFFList().getCountOfPosition() > 0) // #FFList() > 0
-            posIterator = value.getFFList().iterator();
-        else // #FRList() > 0
-            posIterator = value.getFRList().iterator();
-        return posIterator.next();
-    }
-
-    public PositionWritable getPreDestVertexId(VertexValueWritable value) {
-        if(value.getRFList().getCountOfPosition() > 0) // #RFList() > 0
-            posIterator = value.getRFList().iterator();
-        else // #RRList() > 0
-            posIterator = value.getRRList().iterator();
-        return posIterator.next();
-    }
-
-    /**
-     * head send message to all next nodes
-     */
-    public void sendMsgToAllNextNodes(VertexValueWritable value) {
-        posIterator = value.getFFList().iterator(); // FFList
-        while(posIterator.hasNext()){
-            destVertexId.set(posIterator.next());
-            sendMsg(destVertexId, outgoingMsg);
-        }
-        posIterator = value.getFRList().iterator(); // FRList
-        while(posIterator.hasNext()){
-            destVertexId.set(posIterator.next());
-            sendMsg(destVertexId, outgoingMsg);
-        }
-    }
-
-    /**
-     * head send message to all previous nodes
-     */
-    public void sendMsgToAllPreviousNodes(VertexValueWritable value) {
-        posIterator = value.getRFList().iterator(); // RFList
-        while(posIterator.hasNext()){
-            destVertexId.set(posIterator.next());
-            sendMsg(destVertexId, outgoingMsg);
-        }
-        posIterator = value.getRRList().iterator(); // RRList
-        while(posIterator.hasNext()){
-            destVertexId.set(posIterator.next());
-            sendMsg(destVertexId, outgoingMsg);
-        }
-    }
-
-    /**
-     * start sending message
-     */
-    public void startSendMsg() {
-        if (VertexUtil.isHeadVertexWithIndegree(getVertexValue())) {
-            outgoingMsg.setFlag(Message.START);
-            sendMsgToAllNextNodes(getVertexValue());
-            voteToHalt();
-        }
-        if (VertexUtil.isRearVertexWithOutdegree(getVertexValue())) {
-            outgoingMsg.setFlag(Message.END);
-            sendMsgToAllPreviousNodes(getVertexValue());
-            voteToHalt();
-        }
-        if (VertexUtil.isHeadWithoutIndegree(getVertexValue())){
-            outgoingMsg.setFlag(Message.START);
-            sendMsg(getVertexId(), outgoingMsg); //send to itself
-            voteToHalt();
-        }
-        if (VertexUtil.isRearWithoutOutdegree(getVertexValue())){
-            outgoingMsg.setFlag(Message.END);
-            sendMsg(getVertexId(), outgoingMsg); //send to itself
-            voteToHalt();
-        }
-    }
-
-    /**
-     * initiate head, rear and path node
-     */
-    public void initState(Iterator<MessageWritable> msgIterator) {
-        while (msgIterator.hasNext()) {
-            if (!VertexUtil.isPathVertex(getVertexValue())
-                    && !VertexUtil.isHeadWithoutIndegree(getVertexValue())
-                    && !VertexUtil.isRearWithoutOutdegree(getVertexValue())) {
-                msgIterator.next();
-                voteToHalt();
-            } else {
-                incomingMsg = msgIterator.next();
-                setState();
-            }
-        }
-    }
-
-    /**
-     * set vertex state
-     */
-    public void setState() {
-        if (incomingMsg.getFlag() == Message.START) {
-            getVertexValue().setState(MessageFlag.IS_HEAD); //State.START_VERTEX
-        } else if (incomingMsg.getFlag() == Message.END && getVertexValue().getState() != State.IS_HEAD) {
-            getVertexValue().setState(MessageFlag.IS_HEAD);
-            getVertexValue().setKmer(getVertexValue().getKmer());
-            //voteToHalt();
-        } //else
-            //voteToHalt();
-    }
-    
-    /**
-     * check if A need to be flipped with successor
-     */
-    public boolean ifFilpWithSuccessor(){
-        if(getVertexValue().getFRList().getLength() > 0)
-            return true;
-        else
-            return false;
-    }
-    
-    /**
-     * check if A need to be filpped with predecessor
-     */
-    public boolean ifFlipWithPredecessor(){
-        if(getVertexValue().getRFList().getLength() > 0)
-            return true;
-        else
-            return false;
-    }
-    
-    /**
-     * set adjMessage to successor(from predecessor)
-     */
-    public void setSuccessorAdjMsg(){
-        if(getVertexValue().getFFList().getLength() > 0)
-            outFlag |= MessageFlag.DIR_FF;
-        else
-            outFlag |= MessageFlag.DIR_FR;
-    }
-    
-    /**
-     * set adjMessage to predecessor(from successor)
-     */
-    public void setPredecessorAdjMsg(){
-        if(getVertexValue().getRFList().getLength() > 0)
-            outFlag |= MessageFlag.DIR_RF;
-        else
-            outFlag |= MessageFlag.DIR_RF;
-    }
-    
-    /**
-     * send update message to neighber
-     * @throws IOException 
-     */
-    public void broadcastUpdateMsg(){
-       /* switch(getVertexValue().getState() & 0b0001){
-            case MessageFlag.SHOULD_MERGEWITHPREV:
-                setSuccessorAdjMsg();
-                if(ifFlipWithPredecessor())
-                    outFlag |= MessageFlag.FLIP;
-                outgoingMsg.setFlag(outFlag);
-                outgoingMsg.setNeighberNode(getVertexValue().getIncomingList());
-                outgoingMsg.setSourceVertexId(getVertexId());
-                sendMsg(getNextDestVertexId(getVertexValue()), outgoingMsg);
-                break;
-            case MessageFlag.SHOULD_MERGEWITHNEXT:
-                setPredecessorAdjMsg();
-                if(ifFilpWithSuccessor())
-                    outFlag |= MessageFlag.FLIP;
-                outgoingMsg.setFlag(outFlag);
-                outgoingMsg.setNeighberNode(getVertexValue().getOutgoingList());
-                outgoingMsg.setSourceVertexId(getVertexId());
-                sendMsg(getPreDestVertexId(getVertexValue()), outgoingMsg);
-                break; 
-        }*/
-    }
-    
-    /**
-     * This vertex tries to merge with next vertex and send update msg to neighber
-     * @throws IOException 
-     */
-    public void sendUpMsgFromPredecessor(){
-        byte state = getVertexValue().getState();
-        state |= MessageFlag.SHOULD_MERGEWITHNEXT;
-        getVertexValue().setState(state);
-        if(getVertexValue().getFFList().getLength() > 0)
-            getVertexValue().setMergeDest(getVertexValue().getFFList().getPosition(0));
-        else
-            getVertexValue().setMergeDest(getVertexValue().getFRList().getPosition(0));
-        broadcastUpdateMsg();
-    }
-    
-    /**
-     * This vertex tries to merge with next vertex and send update msg to neighber
-     * @throws IOException 
-     */
-    public void sendUpMsgFromSuccessor(){
-        byte state = getVertexValue().getState();
-        state |= MessageFlag.SHOULD_MERGEWITHPREV;
-        getVertexValue().setState(state);
-        if(getVertexValue().getRFList().getLength() > 0)
-            getVertexValue().setMergeDest(getVertexValue().getRFList().getPosition(0));
-        else
-            getVertexValue().setMergeDest(getVertexValue().getRRList().getPosition(0));
-        broadcastUpdateMsg();
-    }
-    
-    /**
-     * Returns the edge dir for B->A when the A->B edge is type @dir
-     */
-    public byte mirrorDirection(byte dir) {
-        switch (dir) {
-            case MessageFlag.DIR_FF:
-                return MessageFlag.DIR_RR;
-            case MessageFlag.DIR_FR:
-                return MessageFlag.DIR_FR;
-            case MessageFlag.DIR_RF:
-                return MessageFlag.DIR_RF;
-            case MessageFlag.DIR_RR:
-                return MessageFlag.DIR_FF;
-            default:
-                throw new RuntimeException("Unrecognized direction in flipDirection: " + dir);
-        }
-    }
-    
-    /**
-     * check if need filp
-     */
-    public byte flipDirection(byte neighborDir, boolean flip){
-        if(flip){
-            switch (neighborDir) {
-                case MessageFlag.DIR_FF:
-                    return MessageFlag.DIR_FR;
-                case MessageFlag.DIR_FR:
-                    return MessageFlag.DIR_FF;
-                case MessageFlag.DIR_RF:
-                    return MessageFlag.DIR_RR;
-                case MessageFlag.DIR_RR:
-                    return MessageFlag.DIR_RF;
-                default:
-                    throw new RuntimeException("Unrecognized direction for neighborDir: " + neighborDir);
-            }
-        } else 
-            return neighborDir;
-    }
-    
-    /**
-     * updateAdjList
-     */
-    public void processUpdate(){
-        /*byte meToNeighborDir = (byte) (incomingMsg.getFlag() & MessageFlag.DIR_MASK);
-        byte neighborToMeDir = mirrorDirection(meToNeighborDir);
-        
-        boolean flip;
-        if((outFlag & MessageFlag.FLIP) > 0)
-            flip = true;
-        else
-            flip = false;
-        byte neighborToMergeDir = flipDirection(neighborToMeDir, flip);
-        
-        getVertexValue().processUpdates(neighborToMeDir, incomingMsg.getSourceVertexId(), 
-                neighborToMergeDir, VertexUtil.getNodeIdFromAdjacencyList(incomingMsg.getNeighberNode()));*/
-    }
-    
-    /**
-     * merge and updateAdjList
-     */
-    public void processMerge(){
-        /*byte meToNeighborDir = (byte) (incomingMsg.getFlag() & MessageFlag.DIR_MASK);
-        byte neighborToMeDir = mirrorDirection(meToNeighborDir);
-        
-        boolean flip;
-        if((outFlag & MessageFlag.FLIP) > 0)
-            flip = true;
-        else
-            flip = false;
-        byte neighborToMergeDir = flipDirection(neighborToMeDir, flip);
-        
-        getVertexValue().processMerges(neighborToMeDir, incomingMsg.getSourceVertexId(), 
-                neighborToMergeDir, VertexUtil.getNodeIdFromAdjacencyList(incomingMsg.getNeighberNode()),
-                kmerSize, incomingMsg.getKmer());*/
-    }
-    
-    @Override
-    public void compute(Iterator<MessageWritable> msgIterator) {
-        initVertex();
-        if (getSuperstep() == 1)
-            startSendMsg();
-        else if (getSuperstep() == 2)
-            initState(msgIterator);
-        else if (getSuperstep() % 4 == 3){
-            // Node may be marked as head b/c it's a real head or a real tail
-            headFlag = (byte) (State.IS_HEAD & getVertexValue().getState());
-            tailFlag = (byte) (State.IS_HEAD & getVertexValue().getState()); //is_tail
-            outFlag = (byte) (headFlag | tailFlag);
-            
-            // only PATH vertices are present. Find the ID's for my neighbors
-            curID.set(getVertexId());
-            
-            curHead = isNodeRandomHead(curID);
-            
-            // the headFlag and tailFlag's indicate if the node is at the beginning or end of a simple path. 
-            // We prevent merging towards non-path nodes
-            hasNext = setNextInfo(getVertexValue()) && tailFlag == 0;
-            hasPrev = setPrevInfo(getVertexValue()) && headFlag == 0;
-            if ((outFlag & MessageFlag.IS_HEAD) > 0 && (outFlag & MessageFlag.IS_HEAD) > 0) {
-                getVertexValue().setState(outFlag);
-                voteToHalt();
-            }
-            if (hasNext || hasPrev) {
-                if (curHead) {
-                    if (hasNext && !nextHead) {
-                        // compress this head to the forward tail
-                        sendUpMsgFromPredecessor();
-                    } else if (hasPrev && !prevHead) {
-                        // compress this head to the reverse tail
-                        sendUpMsgFromSuccessor();
-                    }
-                } else {
-                    // I'm a tail
-                    if (hasNext && hasPrev) {
-                        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();
-                        }
-                    } else if (!hasPrev) {
-                        // no previous node
-                        if (!nextHead && curID.compareTo(nextID) < 0) {
-                            // merge towards tail in forward dir
-                            sendUpMsgFromPredecessor();
-                        }
-                    } else if (!hasNext) {
-                        // no next node
-                        if (!prevHead && curID.compareTo(prevID) < 0) {
-                            // merge towards tail in reverse dir
-                            sendUpMsgFromSuccessor();
-                        }
-                    }
-                }
-            }
-        }
-      
-    }
-
-    public static void main(String[] args) throws Exception {
-        PregelixJob job = new PregelixJob(P5ForPathMergeVertex.class.getSimpleName());
-        job.setVertexClass(P5ForPathMergeVertex.class);
-        /**
-         * BinaryInput and BinaryOutput
-         */
-        job.setVertexInputFormatClass(NaiveAlgorithmForPathMergeInputFormat.class);
-        job.setVertexOutputFormatClass(NaiveAlgorithmForPathMergeOutputFormat.class);
-        job.setDynamicVertexValueSize(true);
-        job.setOutputKeyClass(PositionWritable.class);
-        job.setOutputValueClass(VertexValueWritable.class);
-        Client.run(args, job);
-    }
-}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/splitrepeat/SplitRepeatVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/splitrepeat/SplitRepeatVertex.java
index 3d87c60..4533f55 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/splitrepeat/SplitRepeatVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/splitrepeat/SplitRepeatVertex.java
@@ -97,6 +97,8 @@
             outgoingEdgeList = new KmerListWritable(kmerSize);
         if(createdVertexId == null)
             createdVertexId = new KmerBytesWritable(kmerSize);//kmerSize + 1
+        if(destVertexId == null)
+            destVertexId = new KmerBytesWritable(kmerSize);
     }
     
     /**
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/TipRemoveVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/TipRemoveVertex.java
index bee2008..ddf2964 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/TipRemoveVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/TipRemoveVertex.java
@@ -11,6 +11,7 @@
 import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
 import edu.uci.ics.genomix.pregelix.operator.pathmerge.BasicGraphCleanVertex;
 import edu.uci.ics.genomix.pregelix.util.VertexUtil;
+import edu.uci.ics.genomix.type.KmerBytesWritable;
 
 /*
  * vertexId: BytesWritable
@@ -56,7 +57,14 @@
             kmerSize = getContext().getConfiguration().getInt(KMER_SIZE, 5);
         if(length == -1)
             length = getContext().getConfiguration().getInt(LENGTH, kmerSize); //kmerSize + 5
-        outgoingMsg.reset();
+        if(incomingMsg == null)
+            incomingMsg = new MessageWritable(kmerSize);
+        if(outgoingMsg == null)
+            outgoingMsg = new MessageWritable(kmerSize);
+        else
+            outgoingMsg.reset(kmerSize);
+        if(destVertexId == null)
+            destVertexId = new KmerBytesWritable(kmerSize);
     }
 
     @Override
@@ -81,7 +89,7 @@
             }
         }
         else if(getSuperstep() == 2){
-        	if(msgIterator.hasNext()){
+        	while(msgIterator.hasNext()){
         		incomingMsg = msgIterator.next();
         		responseToDeadVertex();
         	}
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 c49332e..8c39af3 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
@@ -144,24 +144,24 @@
         generateTipAddGraphJob("TipAddGraph", outputBase
                 + "TipAddGraph.xml");
     }
-//    
-//    private static void generateTipRemoveGraphJob(String jobName, String outputPath) throws IOException {
-//        PregelixJob job = new PregelixJob(jobName);
-//        job.setVertexClass(TipRemoveVertex.class);
-//        job.setVertexInputFormatClass(NaiveAlgorithmForPathMergeInputFormat.class);
-//        job.setVertexOutputFormatClass(GraphCleanOutputFormat.class);
-//        job.setDynamicVertexValueSize(true);
-//        job.setOutputKeyClass(PositionWritable.class);
-//        job.setOutputValueClass(VertexValueWritable.class);
-//        job.getConfiguration().setInt(TipRemoveVertex.KMER_SIZE, 5);
-//        job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
-//    }
-//
-//    private static void genTipRemoveGraph() throws IOException {
-//        generateTipRemoveGraphJob("TipRemoveGraph", outputBase
-//                + "TipRemoveGraph.xml");
-//    }
-//    
+    
+    private static void generateTipRemoveGraphJob(String jobName, String outputPath) throws IOException {
+        PregelixJob job = new PregelixJob(jobName);
+        job.setVertexClass(TipRemoveVertex.class);
+        job.setVertexInputFormatClass(GraphCleanInputFormat.class);
+        job.setVertexOutputFormatClass(GraphCleanOutputFormat.class);
+        job.setDynamicVertexValueSize(true);
+        job.setOutputKeyClass(KmerBytesWritable.class);
+        job.setOutputValueClass(VertexValueWritable.class);
+        job.getConfiguration().setInt(TipRemoveVertex.KMER_SIZE, 3);
+        job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
+    }
+
+    private static void genTipRemoveGraph() throws IOException {
+        generateTipRemoveGraphJob("TipRemoveGraph", outputBase
+                + "TipRemoveGraph.xml");
+    }
+    
     private static void generateBridgeAddGraphJob(String jobName, String outputPath) throws IOException {
         PregelixJob job = new PregelixJob(jobName);
         job.setVertexClass(BridgeAddVertex.class);
@@ -245,6 +245,7 @@
         genSplitRepeatGraph();
         genTipAddGraph();
         genBridgeAddGraph();
+        genTipRemoveGraph();
     }
 
 }
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/TipRemoveSmallTestSuite.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/TipRemoveSmallTestSuite.java
index def24e4..e8ca43f 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/TipRemoveSmallTestSuite.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/TipRemoveSmallTestSuite.java
@@ -43,10 +43,9 @@
 public class TipRemoveSmallTestSuite extends TestSuite {
     private static final Logger LOGGER = Logger.getLogger(TipRemoveSmallTestSuite.class.getName());
     //P4ForMergeGraph/bin/read
-    public static final String PreFix = "data/input"; //"graphbuildresult";
+    public static final String PreFix = "data/actual/tipadd/TipAddGraph/bin";
     public static final String[] TestDir = { PreFix + File.separator
-    + "graphs/tipremove/fr_with_tip"};
-    //+ "bridgeadd/BridgeAddGraph/bin/tworeads"};
+    + "5"};
     private static final String ACTUAL_RESULT_DIR = "data/actual/tipremove";
     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";