diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerBytesWritable.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerBytesWritable.java
index 96e1cc4..da6dd0d 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerBytesWritable.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerBytesWritable.java
@@ -467,7 +467,8 @@
                 posnInByte = 0;
             }
         }
-        bytes[offset] = cacheByte;
+        if(cacheByte != 0)
+            bytes[offset] = cacheByte;
         clearLeadBit();
     }
 
diff --git a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerBytesWritableTest.java b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerBytesWritableTest.java
index b4361ac..bda73e5 100644
--- a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerBytesWritableTest.java
+++ b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerBytesWritableTest.java
@@ -236,7 +236,7 @@
         k1.setByRead(test1.getBytes(), 0);
         k2.setByRead(test2.getBytes(), 0);
         k1.mergeWithRFKmer(3, k2);
-        Assert.assertEquals("CTAT", k1);
+        Assert.assertEquals("TCTA", k1.toString());
     }
     
     
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 7185616..49bca8e 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
@@ -6,12 +6,13 @@
 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.LogAlgorithmForPathMergeInputFormat;
-import edu.uci.ics.genomix.pregelix.format.LogAlgorithmForPathMergeOutputFormat;
+import edu.uci.ics.genomix.pregelix.format.GraphCleanOutputFormat;
+import edu.uci.ics.genomix.pregelix.format.InitialGraphCleanInputFormat;
 import edu.uci.ics.genomix.pregelix.io.MessageWritable;
 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.type.KmerBytesWritable;
 /*
  * vertexId: BytesWritable
  * vertexValue: VertexValueWritable
@@ -44,7 +45,7 @@
     BasicPathMergeVertex {
 
     private ArrayList<MessageWritable> receivedMsgList = new ArrayList<MessageWritable>();
-    PositionWritable tempPostition = new PositionWritable();
+    KmerBytesWritable tempPostition = new KmerBytesWritable();
 
     /**
      * initiate kmerSize, maxIteration
@@ -207,8 +208,8 @@
         /**
          * BinaryInput and BinaryOutput~/
          */
-        job.setVertexInputFormatClass(LogAlgorithmForPathMergeInputFormat.class);
-        job.setVertexOutputFormatClass(LogAlgorithmForPathMergeOutputFormat.class);
+        job.setVertexInputFormatClass(InitialGraphCleanInputFormat.class);
+        job.setVertexOutputFormatClass(GraphCleanOutputFormat.class);
         job.setOutputKeyClass(PositionWritable.class);
         job.setOutputValueClass(VertexValueWritable.class);
         job.setDynamicVertexValueSize(true);
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 5aedeb7..115f090 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
@@ -45,14 +45,14 @@
 
     public static final String PreFix = "data/PathMergeTestSet"; //"graphbuildresult";
     public static final String[] TestDir = { PreFix + File.separator
-//    + "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
-    + "4"};
+    + "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"};
     private static final String ACTUAL_RESULT_DIR = "data/actual/pathmerge";
     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";