diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/velvetgraphbuilding/DeepGraphBuildingMapper.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/velvetgraphbuilding/DeepGraphBuildingMapper.java
index e02b4f3..1b677c1 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/velvetgraphbuilding/DeepGraphBuildingMapper.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/velvetgraphbuilding/DeepGraphBuildingMapper.java
@@ -76,9 +76,7 @@
                 }
             }
             outputListAndKmer.set(tempPosList, kmer);
-//            if(positionEntry.getReadID() == 1){
                 output.collect(positionEntry, outputListAndKmer);
-//            }
         }
     }
 }
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/velvetgraphbuilding/DeepGraphBuildingReducer.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/velvetgraphbuilding/DeepGraphBuildingReducer.java
index ec394fe..470b7fa 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/velvetgraphbuilding/DeepGraphBuildingReducer.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/velvetgraphbuilding/DeepGraphBuildingReducer.java
@@ -8,7 +8,6 @@
 import org.apache.hadoop.mapred.OutputCollector;
 import org.apache.hadoop.mapred.Reducer;
 import org.apache.hadoop.mapred.Reporter;
-import org.apache.hadoop.mapred.lib.MultipleOutputs;
 import edu.uci.ics.genomix.type.NodeWritable;
 import edu.uci.ics.genomix.type.PositionListWritable;
 import edu.uci.ics.genomix.type.PositionWritable;
@@ -44,14 +43,6 @@
     public void reduce(PositionWritable key, Iterator<PositionListAndKmerWritable> values,
             OutputCollector<NodeWritable, NullWritable> output, Reporter reporter) throws IOException {
         int readID = key.getReadID();
-        if(readID == 1) {
-            int x = 4;
-            int y =x ;
-            System.out.println((int)key.getPosInRead());
-        }
-/*        while(values.hasNext()) {
-            System.out.println(values.next().getKmer().toString());
-        }*/
         byte posInRead = (byte) 1;
         resetNode(curNode, readID, posInRead);
         assembleFirstTwoNodesInRead(curNodePosiListAndKmer, nextNodePosiListAndKmer, nextNodeNegaListAndKmer,
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/velvetgraphbuilding/GraphBuildingDriver.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/velvetgraphbuilding/GraphBuildingDriver.java
index 1c68114..eaf2a6f 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/velvetgraphbuilding/GraphBuildingDriver.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/velvetgraphbuilding/GraphBuildingDriver.java
@@ -38,29 +38,29 @@
 
         @Option(name = "-kmer-size", usage = "the size of kmer", required = true)
         public int sizeKmer;
-        
+
         @Option(name = "-read-length", usage = "the length of read", required = true)
         public int readLength;
 
         @Option(name = "-onlytest1stjob", usage = "test", required = true)
-        public boolean onlyTest1stJob;
+        public String onlyTest1stJob;
 
         @Option(name = "-seq-output", usage = "sequence ouput format", required = true)
-        public boolean seqOutput;
+        public String seqOutput;
     }
 
-    public void run(String inputPath, String outputPath, int numReducers, int sizeKmer, int readLength, boolean onlyTest1stJob,
-            boolean seqOutput, String defaultConfPath) throws IOException {
+    public void run(String inputPath, String outputPath, int numReducers, int sizeKmer, int readLength,
+            boolean onlyTest1stJob, boolean seqOutput, String defaultConfPath) throws IOException {
         if (onlyTest1stJob == true) {
             runfirstjob(inputPath, numReducers, sizeKmer, readLength, seqOutput, defaultConfPath);
         } else {
-            runfirstjob(inputPath, 2, sizeKmer, readLength, true, defaultConfPath);
+            runfirstjob(inputPath, numReducers, sizeKmer, readLength, true, defaultConfPath);
             runsecondjob(inputPath, outputPath, numReducers, sizeKmer, readLength, seqOutput, defaultConfPath);
         }
     }
 
-    public void runfirstjob(String inputPath, int numReducers, int sizeKmer, int readLength, boolean seqOutput, String defaultConfPath)
-            throws IOException {
+    public void runfirstjob(String inputPath, int numReducers, int sizeKmer, int readLength, boolean seqOutput,
+            String defaultConfPath) throws IOException {
         JobConf conf = new JobConf(GraphBuildingDriver.class);
         conf.setInt("sizeKmer", sizeKmer);
         if (defaultConfPath != null) {
@@ -85,16 +85,18 @@
 
         FileInputFormat.setInputPaths(conf, new Path(inputPath));
         FileOutputFormat.setOutputPath(conf, new Path(inputPath + "-step1"));
-        if(numReducers == 0)
-        conf.setNumReduceTasks(numReducers + 2);
+        if (numReducers == 0)
+            conf.setNumReduceTasks(numReducers + 2);
+        else
+            conf.setNumReduceTasks(numReducers);
 
         FileSystem dfs = FileSystem.get(conf);
         dfs.delete(new Path(inputPath + "-step1"), true);
         JobClient.runJob(conf);
     }
 
-    public void runsecondjob(String inputPath, String outputPath, int numReducers, int sizeKmer, int readLength, boolean seqOutput,
-            String defaultConfPath) throws IOException {
+    public void runsecondjob(String inputPath, String outputPath, int numReducers, int sizeKmer, int readLength,
+            boolean seqOutput, String defaultConfPath) throws IOException {
         JobConf conf = new JobConf(GraphBuildingDriver.class);
         if (defaultConfPath != null) {
             conf.addResource(new Path(defaultConfPath));
@@ -102,7 +104,7 @@
         conf.setJobName("deep build");
         conf.setInt("sizeKmer", sizeKmer);
         conf.setInt("readLength", readLength);
-        
+
         conf.setMapperClass(DeepGraphBuildingMapper.class);
         conf.setReducerClass(DeepGraphBuildingReducer.class);
 
@@ -113,13 +115,13 @@
 
         conf.setOutputKeyComparatorClass(PositionWritable.Comparator.class);
         conf.setOutputValueGroupingComparator(PositionWritable.FirstComparator.class);
-        
+
         conf.setInputFormat(SequenceFileInputFormat.class);
         if (seqOutput == true)
             conf.setOutputFormat(SequenceFileOutputFormat.class);
         else
             conf.setOutputFormat(TextOutputFormat.class);
-        
+
         if (numReducers != 0) {
             conf.setOutputKeyClass(NodeWritable.class);
             conf.setOutputValueClass(NullWritable.class);
@@ -141,7 +143,17 @@
         CmdLineParser parser = new CmdLineParser(options);
         parser.parseArgument(args);
         GraphBuildingDriver driver = new GraphBuildingDriver();
+        boolean onlyTest1stJob = true;
+        boolean seqOutput = true;
+        if (options.onlyTest1stJob.equals("true"))
+            onlyTest1stJob = true;
+        else
+            onlyTest1stJob = false;
+        if (options.seqOutput.equals("true"))
+            seqOutput = true;
+        else
+            seqOutput = false;
         driver.run(options.inputPath, options.outputPath, options.numReducers, options.sizeKmer, options.readLength,
-                options.onlyTest1stJob, options.seqOutput, null);
+                onlyTest1stJob, seqOutput, null);
     }
 }
\ No newline at end of file
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/velvetgraphbuilding/GraphInvertedIndexBuildingMapper.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/velvetgraphbuilding/GraphInvertedIndexBuildingMapper.java
index a44dcd2..4eb7e28 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/velvetgraphbuilding/GraphInvertedIndexBuildingMapper.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/velvetgraphbuilding/GraphInvertedIndexBuildingMapper.java
@@ -1,6 +1,9 @@
 package edu.uci.ics.genomix.hadoop.velvetgraphbuilding;
 
 import java.io.IOException;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
 import org.apache.hadoop.io.LongWritable;
 import org.apache.hadoop.io.Text;
 import org.apache.hadoop.mapred.JobConf;
@@ -37,33 +40,34 @@
         }
         int readID = 0;
         readID = Integer.parseInt(rawLine[0]);
-        if(readID == 6) {
-            int  x = 4;
-            int y = x;
-        }
         String geneLine = rawLine[1];
-        byte[] array = geneLine.getBytes();
-        if (KMER_SIZE >= array.length) {
-            throw new IOException("short read");
-        }
-        outputKmer.setByRead(array, 0);
-        outputVertexID.set(readID, (byte) 1);
-        output.collect(outputKmer, outputVertexID);
-        /** middle kmer */
-        for (int i = KMER_SIZE; i < array.length; i++) {
-            outputKmer.shiftKmerWithNextChar(array[i]);
-            outputVertexID.set(readID, (byte) (i - KMER_SIZE + 2));
+        Pattern genePattern = Pattern.compile("[AGCT]+");
+        Matcher geneMatcher = genePattern.matcher(geneLine);
+        boolean isValid = geneMatcher.matches();
+        if (isValid == true) {
+            byte[] array = geneLine.getBytes();
+            if (KMER_SIZE >= array.length) {
+                throw new IOException("short read");
+            }
+            outputKmer.setByRead(array, 0);
+            outputVertexID.set(readID, (byte) 1);
             output.collect(outputKmer, outputVertexID);
-        }
-        /** reverse first kmer */
-        outputKmer.setByReadReverse(array, 0);
-        outputVertexID.set(readID, (byte) -1);
-        output.collect(outputKmer, outputVertexID);
-        /** reverse middle kmer */
-        for (int i = KMER_SIZE; i < array.length; i++) {
-            outputKmer.shiftKmerWithPreCode(GeneCode.getPairedCodeFromSymbol(array[i]));
-            outputVertexID.set(readID, (byte)(KMER_SIZE - i - 2));
+            /** middle kmer */
+            for (int i = KMER_SIZE; i < array.length; i++) {
+                outputKmer.shiftKmerWithNextChar(array[i]);
+                outputVertexID.set(readID, (byte) (i - KMER_SIZE + 2));
+                output.collect(outputKmer, outputVertexID);
+            }
+            /** reverse first kmer */
+            outputKmer.setByReadReverse(array, 0);
+            outputVertexID.set(readID, (byte) -1);
             output.collect(outputKmer, outputVertexID);
+            /** reverse middle kmer */
+            for (int i = KMER_SIZE; i < array.length; i++) {
+                outputKmer.shiftKmerWithPreCode(GeneCode.getPairedCodeFromSymbol(array[i]));
+                outputVertexID.set(readID, (byte) (KMER_SIZE - i - 2));
+                output.collect(outputKmer, outputVertexID);
+            }
         }
     }
 }
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/velvetgraphbuilding/GraphInvertedIndexBuildingReducer.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/velvetgraphbuilding/GraphInvertedIndexBuildingReducer.java
index beba5ad..d2b6476 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/velvetgraphbuilding/GraphInvertedIndexBuildingReducer.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/velvetgraphbuilding/GraphInvertedIndexBuildingReducer.java
@@ -19,10 +19,6 @@
     public void reduce(KmerBytesWritable key, Iterator<PositionWritable> values,
             OutputCollector<KmerBytesWritable, PositionListWritable> output, Reporter reporter) throws IOException {
         outputlist.reset();
-        if(key.toString().equals("CTTCT")) {
-            int x = 4;
-            int y = x;
-        }
         while (values.hasNext()) {
             outputlist.append(values.next());
         }
diff --git a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/velvetgraphbuilding/NewGraphBuildingTest.java b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/velvetgraphbuilding/NewGraphBuildingTest.java
index 3e9a098..f6236d2 100644
--- a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/velvetgraphbuilding/NewGraphBuildingTest.java
+++ b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/velvetgraphbuilding/NewGraphBuildingTest.java
@@ -15,7 +15,6 @@
 import org.apache.hadoop.io.SequenceFile;
 import org.apache.hadoop.mapred.JobConf;
 import org.apache.hadoop.mapred.MiniMRCluster;
-import org.apache.hadoop.util.ReflectionUtils;
 import org.junit.Test;
 
 @SuppressWarnings("deprecation")
@@ -32,8 +31,6 @@
     private static final int COUNT_REDUCER = 2;
     private static final int SIZE_KMER = 5;
     private static final int READ_LENGTH = 8;
-    private static final String GRAPHVIZ = "Graphviz";
-    private static final String EXPECTED_OUPUT_KMER = EXPECTED_PATH + "result_after_kmerAggregate";
     
     private MiniDFSCluster dfsCluster;
     private MiniMRCluster mrCluster;
@@ -45,57 +42,15 @@
         FileUtils.forceMkdir(new File(ACTUAL_RESULT_DIR));
         FileUtils.cleanDirectory(new File(ACTUAL_RESULT_DIR));
         startHadoop();
-//        TestGroupbyKmer();
-//        TestMapKmerToRead();
-        TestGroupByReadID();
-/*        SequenceFile.Reader reader = null;
-        Path path = new Path(RESULT_PATH + "/part-00000");
-        reader = new SequenceFile.Reader(dfs, path, conf); 
-        KmerBytesWritable key = new KmerBytesWritable(SIZE_KMER);
-        KmerCountValue value = (KmerCountValue) ReflectionUtils.newInstance(reader.getValueClass(), conf);
-        File filePathTo = new File(TEST_SOURCE_DIR);
-        FileUtils.forceMkdir(filePathTo);
-        FileUtils.cleanDirectory(filePathTo);
-        BufferedWriter bw = new BufferedWriter(new FileWriter(new File(TEST_SOURCE_DIR + "/comparesource.txt")));
-        File GraphViz = new File(GRAPHVIZ);
-        FileUtils.forceMkdir(GraphViz);
-        FileUtils.cleanDirectory(GraphViz);
-        BufferedWriter bw2 = new BufferedWriter(new FileWriter(new File(GRAPHVIZ + "/GenomixSource.txt")));
-        
-        while (reader.next(key, value)) {
-            byte succeed = (byte) 0x0F;
-            byte adjBitMap = value.getAdjBitMap();
-            succeed = (byte) (succeed & adjBitMap);
-            byte shiftedCode = 0;
-            for(int i = 0 ; i < 4; i ++){
-                byte temp = 0x01;
-                temp  = (byte)(temp << i);
-                temp = (byte) (succeed & temp);
-                if(temp != 0 ){
-                    bw2.write(key.toString());
-                    bw2.newLine();                    
-                    byte succeedCode = GeneCode.getGeneCodeFromBitMap(temp);
-                    shiftedCode = key.shiftKmerWithNextCode(succeedCode);
-                    bw2.write(key.toString());
-                    bw2.newLine();
-                    key.shiftKmerWithPreCode(shiftedCode);
-                }
-            }
-            bw.write(key.toString() + "\t" + value.toString());
-            bw.newLine();            
-        }
-       bw2.close();
-       bw.close();*/
-
+        TestGroupbyKmer();
+        TestMapKmerToRead();
         cleanupHadoop();
-
     }
 
     public void TestGroupbyKmer() throws Exception {
         GraphBuildingDriver tldriver = new GraphBuildingDriver();
         tldriver.run(HDFS_PATH, RESULT_PATH, COUNT_REDUCER, SIZE_KMER, READ_LENGTH, true, false, HADOOP_CONF_PATH);
         dumpGroupByKmerResult();
-//        TestUtils.compareWithResult(new File(ACTUAL_RESULT_DIR + HDFS_PATH + "-step1" + "/part-00000"), new File(EXPECTED_OUPUT_KMER));
     }
 
     public void TestMapKmerToRead() throws Exception {