diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleMergeVertex.java
index 9b8a03d..83686fb 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleMergeVertex.java
@@ -34,7 +34,14 @@
             kmerSize = getContext().getConfiguration().getInt(KMER_SIZE, 5);
         if (maxIteration < 0)
             maxIteration = getContext().getConfiguration().getInt(ITERATIONS, 1000000);
-        outgoingMsg.reset();
+        if(incomingMsg == null)
+            incomingMsg = new MessageWritable();
+        if(outgoingMsg == null)
+            outgoingMsg = new MessageWritable();
+        else
+            outgoingMsg.reset(kmerSize);
+        if(destVertexId == null)
+            destVertexId = new VKmerBytesWritable();
     }
     
     public void sendBubbleAndMajorVertexMsgToMinorVertex(){
@@ -64,7 +71,24 @@
         }
     }
     
-    @SuppressWarnings("unchecked")
+    @SuppressWarnings({ "unchecked" })
+    public void aggregateBubbleNodesByMajorNode(Iterator<MessageWritable> msgIterator){
+        while (msgIterator.hasNext()) {
+            incomingMsg = msgIterator.next();
+            if(!receivedMsgMap.containsKey(incomingMsg.getStartVertexId())){
+                receivedMsgList.clear();
+                receivedMsgList.add(incomingMsg);
+                receivedMsgMap.put(incomingMsg.getStartVertexId(), (ArrayList<MessageWritable>)receivedMsgList.clone());
+            }
+            else{
+                receivedMsgList.clear();
+                receivedMsgList.addAll(receivedMsgMap.get(incomingMsg.getStartVertexId()));
+                receivedMsgList.add(incomingMsg);
+                receivedMsgMap.put(incomingMsg.getStartVertexId(), (ArrayList<MessageWritable>)receivedMsgList.clone());
+            }
+        }
+    }
+    
     @Override
     public void compute(Iterator<MessageWritable> msgIterator) {
         initVertex();
@@ -82,20 +106,9 @@
                 }
             }
         } else if (getSuperstep() == 3){
-            while (msgIterator.hasNext()) {
-                incomingMsg = msgIterator.next();
-                if(!receivedMsgMap.containsKey(incomingMsg.getStartVertexId())){
-                    receivedMsgList.clear();
-                    receivedMsgList.add(incomingMsg);
-                    receivedMsgMap.put(incomingMsg.getStartVertexId(), (ArrayList<MessageWritable>)receivedMsgList.clone());
-                }
-                else{
-                    receivedMsgList.clear();
-                    receivedMsgList.addAll(receivedMsgMap.get(incomingMsg.getStartVertexId()));
-                    receivedMsgList.add(incomingMsg);
-                    receivedMsgMap.put(incomingMsg.getStartVertexId(), (ArrayList<MessageWritable>)receivedMsgList.clone());
-                }
-            }
+            /** aggregate bubble nodes and grouped by major vertex **/ 
+            aggregateBubbleNodesByMajorNode(msgIterator);
+            
             for(VKmerBytesWritable prevId : receivedMsgMap.keySet()){
                 if(receivedMsgList.size() > 1){ // filter bubble
                     /** for each startVertex, sort the node by decreasing order of coverage **/
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 2ef9958..fb51e52 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
@@ -12,6 +12,7 @@
 import edu.uci.ics.genomix.pregelix.operator.bridgeremove.BridgeAddVertex;
 import edu.uci.ics.genomix.pregelix.operator.bridgeremove.BridgeRemoveVertex;
 import edu.uci.ics.genomix.pregelix.operator.bubblemerge.BubbleAddVertex;
+import edu.uci.ics.genomix.pregelix.operator.bubblemerge.BubbleMergeVertex;
 import edu.uci.ics.genomix.pregelix.operator.pathmerge.P2ForPathMergeVertex;
 import edu.uci.ics.genomix.pregelix.operator.pathmerge.MapReduceVertex;
 import edu.uci.ics.genomix.pregelix.operator.pathmerge.P3ForPathMergeVertex;
@@ -210,42 +211,32 @@
         generateBubbleAddGraphJob("BubbleAddGraph", outputBase
                 + "BubbleAddGraph.xml");
     }
-//    
-//    private static void generateBubbleMergeGraphJob(String jobName, String outputPath) throws IOException {
-//        PregelixJob job = new PregelixJob(jobName);
-//        job.setVertexClass(BubbleMergeVertex.class);
-//        job.setVertexInputFormatClass(NaiveAlgorithmForPathMergeInputFormat.class);
-//        job.setVertexOutputFormatClass(GraphCleanOutputFormat.class);
-//        job.setDynamicVertexValueSize(true);
-//        job.setOutputKeyClass(PositionWritable.class);
-//        job.setOutputValueClass(VertexValueWritable.class);
-//        job.getConfiguration().setInt(BubbleMergeVertex.KMER_SIZE, 5);
-//        job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
-//    }
-//
-//    private static void genBubbleMergeGraph() throws IOException {
-//        generateBubbleMergeGraphJob("BubbleMergeGraph", outputBase
-//                + "BubbleMergeGraph.xml");
-//    }
+    
+    private static void generateBubbleMergeGraphJob(String jobName, String outputPath) throws IOException {
+        PregelixJob job = new PregelixJob(jobName);
+        job.setVertexClass(BubbleMergeVertex.class);
+        job.setVertexInputFormatClass(GraphCleanInputFormat.class);
+        job.setVertexOutputFormatClass(GraphCleanOutputFormat.class);
+        job.setDynamicVertexValueSize(true);
+        job.setOutputKeyClass(VKmerBytesWritable.class);
+        job.setOutputValueClass(VertexValueWritable.class);
+        job.getConfiguration().setInt(BubbleMergeVertex.KMER_SIZE, 3);
+        job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
+    }
+
+    private static void genBubbleMergeGraph() throws IOException {
+        generateBubbleMergeGraphJob("BubbleMergeGraph", outputBase
+                + "BubbleMergeGraph.xml");
+    }
     
     public static void main(String[] args) throws IOException {
-        //genNaiveAlgorithmForMergeGraph();
-//        genLogAlgorithmForMergeGraph();
-        //genP3ForMergeGraph();
-        //genTipAddGraph();
-//        genTipRemoveGraph();
-//        genBridgeAddGraph();
-//        genBridgeRemoveGraph();
-//        genBubbleAddGraph();
-//        genBubbleMergeGraph();
-//        genP4ForMergeGraph();
-//        genMapReduceGraph();
         genSplitRepeatGraph();
         genTipAddGraph();
         genBridgeAddGraph();
         genTipRemoveGraph();
         genBridgeRemoveGraph();
         genBubbleAddGraph();
+        genBubbleMergeGraph();
     }
 
 }
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BubbleMergeSmallTestSuite.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BubbleMergeSmallTestSuite.java
index 57647ab..21020ce 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BubbleMergeSmallTestSuite.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BubbleMergeSmallTestSuite.java
@@ -43,9 +43,9 @@
 public class BubbleMergeSmallTestSuite extends TestSuite {
     private static final Logger LOGGER = Logger.getLogger(BubbleMergeSmallTestSuite.class.getName());
 
-    public static final String PreFix = "data/input"; //"graphbuildresult";
+    public static final String PreFix = "data/actual/bubbleadd/BubbleAddGraph/bin"; 
     public static final String[] TestDir = { PreFix + File.separator
-    + "graphs/bubblemerge/fr_bubble"};
+    + "5"};
     private static final String ACTUAL_RESULT_DIR = "data/actual/bubblemerge";
     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";