diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/driver/Driver.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/driver/Driver.java
index 6d6e1e6..c903645 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/driver/Driver.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/driver/Driver.java
@@ -1,3 +1,18 @@
+/*
+ * Copyright 2009-2013 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
 package edu.uci.ics.genomix.hyracks.newgraph.driver;
 
 import java.net.URL;
@@ -6,11 +21,12 @@
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
+import org.apache.hadoop.fs.Path;
+import org.apache.hadoop.util.GenericOptionsParser;
 
-import edu.uci.ics.genomix.hyracks.driver.Driver.Plan;
-import edu.uci.ics.genomix.hyracks.job.GenomixJobConf;
-import edu.uci.ics.genomix.hyracks.job.JobGen;
-import edu.uci.ics.genomix.hyracks.newgraph.job.JobGenCheckReader;
+import edu.uci.ics.genomix.hyracks.newgraph.job.GenomixJobConf;
+import edu.uci.ics.genomix.hyracks.newgraph.job.JobGen;
+import edu.uci.ics.genomix.hyracks.newgraph.job.JobGenBrujinGraph;
 
 import edu.uci.ics.hyracks.api.client.HyracksConnection;
 import edu.uci.ics.hyracks.api.client.IHyracksClientConnection;
@@ -23,19 +39,20 @@
 
 public class Driver {
     public static enum Plan {
-        CHECK_KMERREADER,
+        BUILD_DEBRUJIN_GRAPH,
     }
-    
+
     private static final String IS_PROFILING = "genomix.driver.profiling";
     private static final String CPARTITION_PER_MACHINE = "genomix.driver.duplicate.num";
     private static final Log LOG = LogFactory.getLog(Driver.class);
     private JobGen jobGen;
     private boolean profiling;
+
     private int numPartitionPerMachine;
 
     private IHyracksClientConnection hcc;
     private Scheduler scheduler;
-    
+
     public Driver(String ipAddress, int port, int numPartitionPerMachine) throws HyracksException {
         try {
             hcc = new HyracksConnection(ipAddress, port);
@@ -45,9 +62,9 @@
         }
         this.numPartitionPerMachine = numPartitionPerMachine;
     }
-    
+
     public void runJob(GenomixJobConf job) throws HyracksException {
-        runJob(job, Plan.CHECK_KMERREADER, false);
+        runJob(job, Plan.BUILD_DEBRUJIN_GRAPH, false);
     }
 
     public void runJob(GenomixJobConf job, Plan planChoice, boolean profiling) throws HyracksException {
@@ -69,9 +86,9 @@
             Map<String, NodeControllerInfo> ncMap = hcc.getNodeControllerInfos();
             LOG.info("ncmap:" + ncMap.size() + " " + ncMap.keySet().toString());
             switch (planChoice) {
-                case CHECK_KMERREADER:
+                case BUILD_DEBRUJIN_GRAPH:
                 default:
-                    jobGen = new JobGenCheckReader(job, scheduler, ncMap, numPartitionPerMachine);
+                    jobGen = new JobGenBrujinGraph(job, scheduler, ncMap, numPartitionPerMachine);
                     break;
             }
 
@@ -85,7 +102,7 @@
             throw new HyracksException(e);
         }
     }
-    
+
     private void run(JobGen jobGen) throws Exception {
         try {
             JobSpecification createJob = jobGen.generateJob();
@@ -95,11 +112,38 @@
             throw e;
         }
     }
-    
+
     private void execute(JobSpecification job) throws Exception {
         job.setUseConnectorPolicyForScheduling(false);
         JobId jobId = hcc
                 .startJob(job, profiling ? EnumSet.of(JobFlag.PROFILE_RUNTIME) : EnumSet.noneOf(JobFlag.class));
         hcc.waitForCompletion(jobId);
     }
+
+    public static void main(String[] args) throws Exception {
+        GenomixJobConf jobConf = new GenomixJobConf();
+        String[] otherArgs = new GenericOptionsParser(jobConf, args).getRemainingArgs();
+        if (otherArgs.length < 4) {
+            System.err.println("Need <serverIP> <port> <input> <output>");
+            System.exit(-1);
+        }
+        String ipAddress = otherArgs[0];
+        int port = Integer.parseInt(otherArgs[1]);
+        int numOfDuplicate = jobConf.getInt(CPARTITION_PER_MACHINE, 2);
+        boolean bProfiling = jobConf.getBoolean(IS_PROFILING, true);
+        // FileInputFormat.setInputPaths(job, otherArgs[2]);
+        {
+            @SuppressWarnings("deprecation")
+            Path path = new Path(jobConf.getWorkingDirectory(), otherArgs[2]);
+            jobConf.set("mapred.input.dir", path.toString());
+
+            @SuppressWarnings("deprecation")
+            Path outputDir = new Path(jobConf.getWorkingDirectory(), otherArgs[3]);
+            jobConf.set("mapred.output.dir", outputDir.toString());
+        }
+        // FileInputFormat.addInputPath(jobConf, new Path(otherArgs[2]));
+        // FileOutputFormat.setOutputPath(job, new Path(otherArgs[3]));
+        Driver driver = new Driver(ipAddress, port, numOfDuplicate);
+        driver.runJob(jobConf, Plan.BUILD_DEBRUJIN_GRAPH, bProfiling);
+    }
 }
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/job/JobGenBrujinGraph.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/job/JobGenBrujinGraph.java
index f35d0ef..369f874 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/job/JobGenBrujinGraph.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/job/JobGenBrujinGraph.java
@@ -194,28 +194,6 @@
         return kmerCrossAggregator;
     }
 
-
-    public AbstractOperatorDescriptor generateKmerWritorOperator(JobSpecification jobSpec,
-            AbstractOperatorDescriptor kmerCrossAggregator) throws HyracksException {
-        // Output Kmer
-        ITupleWriterFactory kmerWriter = null;
-        switch (outputFormat) {
-            case TEXT:
-                kmerWriter = new KMerTextWriterFactory(kmerSize);
-                break;
-            case BINARY:
-            default:
-                kmerWriter = new KMerSequenceWriterFactory(hadoopJobConfFactory.getConf());
-                break;
-        }
-        logDebug("WriteOperator");
-        HDFSWriteOperatorDescriptor writeKmerOperator = new HDFSWriteOperatorDescriptor(jobSpec,
-                hadoopJobConfFactory.getConf(), kmerWriter);
-        connectOperators(jobSpec, kmerCrossAggregator, ncNodeNames, writeKmerOperator, ncNodeNames,
-                new OneToOneConnectorDescriptor(jobSpec));
-        return writeKmerOperator;
-    }
-
     public AbstractOperatorDescriptor generateNodeWriterOpertator(JobSpecification jobSpec,
             AbstractOperatorDescriptor mapEachReadToNode) throws HyracksException {
         ITupleWriterFactory nodeWriter = null;
diff --git a/genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/hyracks/newgraph/test/JobRun.java b/genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/hyracks/newgraph/test/JobRun.java
index dfae011..6cc4475 100644
--- a/genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/hyracks/newgraph/test/JobRun.java
+++ b/genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/hyracks/newgraph/test/JobRun.java
@@ -24,11 +24,11 @@
 import org.junit.Before;
 import org.junit.Test;
 
-import edu.uci.ics.genomix.hyracks.job.GenomixJobConf;
+import edu.uci.ics.genomix.hyracks.newgraph.job.GenomixJobConf;
 import edu.uci.ics.genomix.hyracks.newgraph.driver.Driver;
 import edu.uci.ics.genomix.hyracks.newgraph.driver.Driver.Plan;
 import edu.uci.ics.genomix.hyracks.test.TestUtils;
-import edu.uci.ics.genomix.oldtype.NodeWritable;
+//import edu.uci.ics.genomix.oldtype.NodeWritable;
 
 @SuppressWarnings("deprecation")
 public class JobRun {
@@ -43,11 +43,6 @@
 
     private static final String EXPECTED_DIR = "src/test/resources/expected/";
     private static final String EXPECTED_READER_RESULT = EXPECTED_DIR + "result_after_initial_read";
-//    private static final String EXPECTED_OUPUT_KMER = EXPECTED_DIR + "result_after_kmerAggregate";
-//    private static final String EXPECTED_KMER_TO_READID = EXPECTED_DIR + "result_after_kmer2readId";
-//    private static final String EXPECTED_GROUPBYREADID = EXPECTED_DIR + "result_after_readIDAggreage";
-//    private static final String EXPECTED_OUPUT_NODE = EXPECTED_DIR + "result_after_generateNode";
-//    private static final String EXPECTED_UNMERGED = EXPECTED_DIR + "result_unmerged";
 
     private static final String DUMPED_RESULT = ACTUAL_RESULT_DIR + HDFS_OUTPUT_PATH + "/merged.txt";
     private static final String CONVERT_RESULT = DUMPED_RESULT + ".txt";
@@ -62,14 +57,14 @@
     
     @Test
     public void TestAll() throws Exception {
-        TestReader();
+        TestGroupby();
     }
     
-    public void TestReader() throws Exception {
-        cleanUpReEntry();
+    public void TestGroupby() throws Exception {
         conf.set(GenomixJobConf.OUTPUT_FORMAT, GenomixJobConf.OUTPUT_FORMAT_TEXT);
-        driver.runJob(new GenomixJobConf(conf), Plan.CHECK_KMERREADER, true);
-        Assert.assertEquals(true, checkResults(EXPECTED_READER_RESULT, null));
+        cleanUpReEntry();
+        conf.set(GenomixJobConf.GROUPBY_TYPE, GenomixJobConf.GROUPBY_TYPE_PRECLUSTER);
+        driver.runJob(new GenomixJobConf(conf), Plan.BUILD_DEBRUJIN_GRAPH, true);
     }
     
     @Before
@@ -129,7 +124,7 @@
         }
     }
     
-    private boolean checkResults(String expectedPath, int[] poslistField) throws Exception {
+/*    private boolean checkResults(String expectedPath, int[] poslistField) throws Exception {
         File dumped = null;
         String format = conf.get(GenomixJobConf.OUTPUT_FORMAT);
         if (GenomixJobConf.OUTPUT_FORMAT_TEXT.equalsIgnoreCase(format)) {
@@ -177,7 +172,7 @@
             TestUtils.compareWithSortedResult(new File(expectedPath), dumped);
         }
         return true;
-    }
+    }*/
     
     @After
     public void tearDown() throws Exception {