diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/oldtype/IntermediateNodeWritable.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/oldtype/IntermediateNodeWritable.java
new file mode 100644
index 0000000..82eb51c
--- /dev/null
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/oldtype/IntermediateNodeWritable.java
@@ -0,0 +1,152 @@
+package edu.uci.ics.genomix.oldtype;
+
+import java.io.DataInput;
+import java.io.DataOutput;
+import java.io.IOException;
+import java.io.Serializable;
+
+import org.apache.hadoop.io.WritableComparable;
+
+import edu.uci.ics.genomix.type.KmerListWritable;
+import edu.uci.ics.genomix.type.PositionWritable;
+
+public class IntermediateNodeWritable implements WritableComparable<IntermediateNodeWritable>, Serializable{
+
+    private static final long serialVersionUID = 1L;
+    public static final IntermediateNodeWritable EMPTY_NODE = new IntermediateNodeWritable();
+    
+    private KmerListWritable forwardForwardList;
+    private KmerListWritable forwardReverseList;
+    private KmerListWritable reverseForwardList;
+    private KmerListWritable reverseReverseList;
+    private PositionWritable nodeId;
+    
+    public IntermediateNodeWritable(){
+        forwardForwardList = new KmerListWritable();
+        forwardReverseList = new KmerListWritable();
+        reverseForwardList = new KmerListWritable();
+        reverseReverseList = new KmerListWritable();
+        nodeId = new PositionWritable();
+    }
+    
+    public IntermediateNodeWritable(KmerListWritable FFList, KmerListWritable FRList,
+            KmerListWritable RFList, KmerListWritable RRList, PositionWritable uniqueKey) {
+        this();
+        set(FFList, FRList, RFList, RRList, uniqueKey);
+    }
+    
+    public void set(IntermediateNodeWritable node){
+        set(node.forwardForwardList, node.forwardReverseList, node.reverseForwardList, 
+                node.reverseReverseList, node.nodeId);
+    }
+    
+    public void set(KmerListWritable FFList, KmerListWritable FRList,
+            KmerListWritable RFList, KmerListWritable RRList, PositionWritable uniqueKey) {
+        this.forwardForwardList.set(FFList);
+        this.forwardReverseList.set(FRList);
+        this.reverseForwardList.set(RFList);
+        this.reverseReverseList.set(RRList);
+        this.nodeId.set(uniqueKey);
+    }
+
+    public void reset(int kmerSize) {
+        forwardForwardList.reset();
+        forwardReverseList.reset();
+        reverseForwardList.reset();
+        reverseReverseList.reset();
+        nodeId.reset();
+    }
+    
+    public KmerListWritable getFFList() {
+        return forwardForwardList;
+    }
+
+    public void setFFList(KmerListWritable forwardForwardList) {
+        this.forwardForwardList.set(forwardForwardList);
+    }
+
+    public KmerListWritable getFRList() {
+        return forwardReverseList;
+    }
+
+    public void setFRList(KmerListWritable forwardReverseList) {
+        this.forwardReverseList.set(forwardReverseList);
+    }
+
+    public KmerListWritable getRFList() {
+        return reverseForwardList;
+    }
+
+    public void setRFList(KmerListWritable reverseForwardList) {
+        this.reverseForwardList.set(reverseForwardList);
+    }
+
+    public KmerListWritable getRRList() {
+        return reverseReverseList;
+    }
+
+    public void setRRList(KmerListWritable reverseReverseList) {
+        this.reverseReverseList.set(reverseReverseList);
+    }
+
+	public PositionWritable getNodeId() {
+        return nodeId;
+    }
+
+    public void setNodeId(PositionWritable nodeId) {
+        this.nodeId.set(nodeId);
+    }
+
+    @Override
+    public void readFields(DataInput in) throws IOException {
+        this.forwardForwardList.readFields(in);
+        this.forwardReverseList.readFields(in);
+        this.reverseForwardList.readFields(in);
+        this.reverseReverseList.readFields(in);
+        this.nodeId.readFields(in);
+    }
+
+    @Override
+    public void write(DataOutput out) throws IOException {
+        this.forwardForwardList.write(out);
+        this.forwardReverseList.write(out);
+        this.reverseForwardList.write(out);
+        this.reverseReverseList.write(out);
+        this.nodeId.write(out);
+    }
+
+    @Override
+    public int compareTo(IntermediateNodeWritable other) {
+        // TODO Auto-generated method stub
+        return this.nodeId.compareTo(other.nodeId);
+    }
+    
+    @Override
+    public int hashCode() {
+        return this.nodeId.hashCode();
+    }
+    
+    @Override
+    public boolean equals(Object o) {
+        if (o instanceof IntermediateNodeWritable) {
+            IntermediateNodeWritable nw = (IntermediateNodeWritable) o;
+            return (this.forwardForwardList.equals(nw.forwardForwardList)
+                    && this.forwardReverseList.equals(nw.forwardReverseList)
+                    && this.reverseForwardList.equals(nw.reverseForwardList)
+                    && this.reverseReverseList.equals(nw.reverseReverseList) && (this.nodeId.equals(nw.nodeId)));
+        }
+        return false;
+    }
+    
+    @Override
+    public String toString() {
+        StringBuilder sbuilder = new StringBuilder();
+        sbuilder.append('(');
+        sbuilder.append(nodeId.toString()).append('\t');
+        sbuilder.append(forwardForwardList.toString()).append('\t');
+        sbuilder.append(forwardReverseList.toString()).append('\t');
+        sbuilder.append(reverseForwardList.toString()).append('\t');
+        sbuilder.append(reverseReverseList.toString()).append('\t').append(')');
+        return sbuilder.toString();
+    }
+}
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 e265fa9..161d31f 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
@@ -10,16 +10,21 @@
 
 public class NodeWritable implements WritableComparable<NodeWritable>, Serializable{
 
+    public static class KMER{
+        public static final byte EXIST = 0;
+        public static final byte NON_EXIST = 1;
+    }
+    
     private static final long serialVersionUID = 1L;
     public static final NodeWritable EMPTY_NODE = new NodeWritable(0);
     
-    private PositionListWritable nodeId;
+    private PositionListWritable nodeIdList;
     private KmerListWritable forwardForwardList;
     private KmerListWritable forwardReverseList;
     private KmerListWritable reverseForwardList;
     private KmerListWritable reverseReverseList;
     private KmerBytesWritable kmer;
-    
+    private byte kmerMark;
     
     // merge/update directions
     public static class DirectionFlag {
@@ -35,42 +40,54 @@
     }
     
     public NodeWritable(int kmerSize) {
-        nodeId = new PositionListWritable();
+        nodeIdList = new PositionListWritable();
         forwardForwardList = new KmerListWritable();
         forwardReverseList = new KmerListWritable();
         reverseForwardList = new KmerListWritable();
         reverseReverseList = new KmerListWritable();
         kmer = new KmerBytesWritable(kmerSize);
+        kmerMark = KMER.NON_EXIST;
     }
     
-    public NodeWritable(PositionListWritable nodeId, KmerListWritable FFList, KmerListWritable FRList,
+    public NodeWritable(PositionListWritable nodeIdList, KmerListWritable FFList, KmerListWritable FRList,
             KmerListWritable RFList, KmerListWritable RRList, KmerBytesWritable kmer) {
         this(kmer.getKmerLength());
-        set(nodeId, FFList, FRList, RFList, RRList, kmer);
+        set(nodeIdList, FFList, FRList, RFList, RRList, kmer);
     }
     
     public void set(NodeWritable node){
-        set(node.nodeId, node.forwardForwardList, node.forwardReverseList, node.reverseForwardList, 
+        set(node.nodeIdList, node.forwardForwardList, node.forwardReverseList, node.reverseForwardList, 
                 node.reverseReverseList, node.kmer);
     }
     
-    public void set(PositionListWritable nodeId, KmerListWritable FFList, KmerListWritable FRList,
+    public void set(PositionListWritable nodeIdList, KmerListWritable FFList, KmerListWritable FRList,
             KmerListWritable RFList, KmerListWritable RRList, KmerBytesWritable kmer) {
-        this.nodeId.set(nodeId);
+        this.nodeIdList.set(nodeIdList);
         this.forwardForwardList.set(FFList);
         this.forwardReverseList.set(FRList);
         this.reverseForwardList.set(RFList);
         this.reverseReverseList.set(RRList);
         this.kmer.set(kmer);
+        kmerMark = KMER.EXIST;
     }
 
     public void reset(int kmerSize) {
-        nodeId.reset();
+        nodeIdList.reset();
         forwardForwardList.reset();
         forwardReverseList.reset();
         reverseForwardList.reset();
         reverseReverseList.reset();
         kmer.reset(kmerSize);
+        kmerMark = KMER.NON_EXIST;
+    }
+    
+    
+    public PositionListWritable getNodeIdList() {
+        return nodeIdList;
+    }
+
+    public void setNodeIdList(PositionListWritable nodeIdList) {
+        this.nodeIdList.set(nodeIdList);
     }
 
     public KmerBytesWritable getKmer() {
@@ -78,7 +95,8 @@
     }
 
     public void setKmer(KmerBytesWritable kmer) {
-        this.kmer = kmer;
+        kmerMark = KMER.EXIST;
+        this.kmer.set(kmer);
     }
     
     public int getCount() {
@@ -102,19 +120,19 @@
     }
     
 	public void setFFList(KmerListWritable forwardForwardList) {
-		this.forwardForwardList = forwardForwardList;
+		this.forwardForwardList.set(forwardForwardList);
 	}
 
 	public void setFRList(KmerListWritable forwardReverseList) {
-		this.forwardReverseList = forwardReverseList;
+		this.forwardReverseList.set(forwardReverseList);
 	}
 
 	public void setRFList(KmerListWritable reverseForwardList) {
-		this.reverseForwardList = reverseForwardList;
+		this.reverseForwardList.set(reverseForwardList);
 	}
 
 	public void setRRList(KmerListWritable reverseReverseList) {
-		this.reverseReverseList = reverseReverseList;
+		this.reverseReverseList.set(reverseReverseList);
 	}
 
 	public KmerListWritable getListFromDir(byte dir) {
@@ -133,22 +151,26 @@
     }
     @Override
     public void write(DataOutput out) throws IOException {
-        this.nodeId.write(out);
+        out.writeByte(kmerMark);
+        this.nodeIdList.write(out);
         this.forwardForwardList.write(out);
         this.forwardReverseList.write(out);
         this.reverseForwardList.write(out);
         this.reverseReverseList.write(out);
-        this.kmer.write(out);
+        if(kmerMark == KMER.EXIST) 
+            this.kmer.write(out);
     }
 
     @Override
     public void readFields(DataInput in) throws IOException {
-        this.nodeId.readFields(in);
+        kmerMark = in.readByte();
+        this.nodeIdList.readFields(in);
         this.forwardForwardList.readFields(in);
         this.forwardReverseList.readFields(in);
         this.reverseForwardList.readFields(in);
         this.reverseReverseList.readFields(in);
-        this.kmer.readFields(in);
+        if(kmerMark == KMER.EXIST)
+            this.kmer.readFields(in);
     }
 
     @Override
@@ -165,7 +187,7 @@
     public boolean equals(Object o) {
         if (o instanceof NodeWritable) {
             NodeWritable nw = (NodeWritable) o;
-            return (this.nodeId.equals(nw.nodeId)
+            return (this.nodeIdList.equals(nw.nodeIdList)
                     && this.forwardForwardList.equals(nw.forwardForwardList)
                     && this.forwardReverseList.equals(nw.forwardReverseList)
                     && this.reverseForwardList.equals(nw.reverseForwardList)
@@ -178,7 +200,7 @@
     public String toString() {
         StringBuilder sbuilder = new StringBuilder();
         sbuilder.append('(');
-        sbuilder.append(nodeId.toString()).append('\t');
+        sbuilder.append(nodeIdList.toString()).append('\t');
         sbuilder.append(forwardForwardList.toString()).append('\t');
         sbuilder.append(forwardReverseList.toString()).append('\t');
         sbuilder.append(reverseForwardList.toString()).append('\t');
diff --git a/genomix/genomix-hadoop/data/webmap/test.txt b/genomix/genomix-hadoop/data/webmap/test.txt
new file mode 100644
index 0000000..17770fa
--- /dev/null
+++ b/genomix/genomix-hadoop/data/webmap/test.txt
@@ -0,0 +1 @@
+1	AATAGAAG
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixMapper.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixMapper.java
index 8c9cfc8..50223e2 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixMapper.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixMapper.java
@@ -15,6 +15,7 @@
 import edu.uci.ics.genomix.type.KmerBytesWritable;
 import edu.uci.ics.genomix.type.KmerListWritable;
 import edu.uci.ics.genomix.type.NodeWritable;
+import edu.uci.ics.genomix.type.PositionListWritable;
 import edu.uci.ics.genomix.type.PositionWritable;
 
 @SuppressWarnings("deprecation")
@@ -33,10 +34,11 @@
     private KmerBytesWritable curReverseKmer;
     private KmerBytesWritable nextForwardKmer;
     private KmerBytesWritable nextReverseKmer;
-    private NodeWritable outputNode;
     private PositionWritable nodeId;
+    private PositionListWritable nodeIdList;
     private KmerListWritable edgeListForPreKmer;
     private KmerListWritable edgeListForNextKmer;
+    private NodeWritable outputNode;
     
     private KmerDir preKmerDir;
     private KmerDir curKmerDir;
@@ -53,10 +55,11 @@
         curReverseKmer = new KmerBytesWritable(KMER_SIZE);
         nextForwardKmer = new KmerBytesWritable(KMER_SIZE);
         nextReverseKmer = new KmerBytesWritable(KMER_SIZE);
-        outputNode = new NodeWritable();
         nodeId = new PositionWritable();
+        nodeIdList = new PositionListWritable();
         edgeListForPreKmer = new KmerListWritable();
         edgeListForNextKmer = new KmerListWritable();
+        outputNode = new NodeWritable();
         preKmerDir = KmerDir.FORWARD;
         curKmerDir = KmerDir.FORWARD;
         nextKmerDir = KmerDir.FORWARD;
@@ -83,13 +86,13 @@
             }
             
             /** first kmer **/
+            outputNode.reset(0);
             curForwardKmer.setByRead(array, 0);
             curReverseKmer.setByReadReverse(array, 0);
             curKmerDir = curForwardKmer.compareTo(curReverseKmer) <= 0 ? KmerDir.FORWARD : KmerDir.REVERSE;
             setNextKmer(array[KMER_SIZE]);
             //set value.nodeId
-            nodeId.set(mateId, readID, 1);
-            outputNode.setNodeId(nodeId);
+            setNodeId(mateId, readID, 1);
             //set value.edgeList
             setEdgeListForNextKmer();
             //output mapper result
@@ -97,12 +100,12 @@
             
             /** middle kmer **/
             for (int i = KMER_SIZE + 1; i < array.length; i++) {
+                outputNode.reset(0);
             	setPreKmerByOldCurKmer();
             	setCurKmerByOldNextKmer();
             	setNextKmer(array[i]);
         	    //set value.nodeId
-                nodeId.set(mateId, readID, i - KMER_SIZE + 1);
-                outputNode.setNodeId(nodeId);
+            	setNodeId(mateId, readID, i - KMER_SIZE + 1);
                 //set value.edgeList
                 setEdgeListForPreKmer();
                 setEdgeListForNextKmer();
@@ -111,11 +114,11 @@
             }
             
             /** last kmer **/
+            outputNode.reset(0);
         	setPreKmerByOldCurKmer();
         	setCurKmerByOldNextKmer();
         	//set value.nodeId
-            nodeId.set(mateId, readID, array.length - KMER_SIZE + 1);
-            outputNode.setNodeId(nodeId);
+        	setNodeId(mateId, readID, array.length - KMER_SIZE + 1);
             //set value.edgeList
             setEdgeListForPreKmer();
             //output mapper result
@@ -123,6 +126,13 @@
         }
     }
     
+    public void setNodeId(byte mateId, long readID, int posId){
+        nodeId.set(mateId, readID, posId);
+        nodeIdList.reset();
+        nodeIdList.append(nodeId);
+        outputNode.setNodeIdList(nodeIdList);
+    }
+    
     public void setEdgeListForPreKmer(){
     	switch(curKmerDir){
     		case FORWARD:
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixReducer.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixReducer.java
index d53e3bf..625984d 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixReducer.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixReducer.java
@@ -24,12 +24,19 @@
 		outputNode.reset(GenomixMapper.KMER_SIZE);
 		
 		//copy first item to outputNode
-		if(values.hasNext())
-		    outputNode.set(values.next());
+		if(values.hasNext()){
+		    NodeWritable tmpNode = values.next();
+		    outputNode.set(tmpNode);
+		}
 		while (values.hasNext()) {
 		    NodeWritable tmpNode = values.next();
+		    outputNode.getNodeIdList().appendList(tmpNode.getNodeIdList());
 		    outputNode.getFFList().appendList(tmpNode.getFFList());
+		    outputNode.getFRList().appendList(tmpNode.getFRList());
+		    outputNode.getRFList().appendList(tmpNode.getRFList());
+		    outputNode.getRRList().appendList(tmpNode.getRRList());
 		}
+		output.collect(key,outputNode);
 	}
 
 }
diff --git a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GraphBuildingTest.java b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GraphBuildingTest.java
index b756839..8aef9a8 100644
--- a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GraphBuildingTest.java
+++ b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GraphBuildingTest.java
@@ -43,7 +43,7 @@
     
     public void TestMapKmerToNode() throws Exception {
         GenomixDriver driver = new GenomixDriver();
-        driver.run(HDFS_PATH, RESULT_PATH, 0, SIZE_KMER, READ_LENGTH, false, HADOOP_CONF_PATH);
+        driver.run(HDFS_PATH, RESULT_PATH, 2, SIZE_KMER, READ_LENGTH, false, HADOOP_CONF_PATH);
         dumpResult();
     }