diff --git a/genomix/genomix-pregelix/data/PathTestSet/2/part-0 b/genomix/genomix-pregelix/data/PathTestSet/2/part-0
new file mode 100755
index 0000000..f7f0186
--- /dev/null
+++ b/genomix/genomix-pregelix/data/PathTestSet/2/part-0
Binary files differ
diff --git a/genomix/genomix-pregelix/data/PathTestSet/2/part-1 b/genomix/genomix-pregelix/data/PathTestSet/2/part-1
new file mode 100755
index 0000000..7b40564
--- /dev/null
+++ b/genomix/genomix-pregelix/data/PathTestSet/2/part-1
Binary files differ
diff --git a/genomix/genomix-pregelix/data/PathTestSet/3/part-0 b/genomix/genomix-pregelix/data/PathTestSet/3/part-0
new file mode 100755
index 0000000..055931c
--- /dev/null
+++ b/genomix/genomix-pregelix/data/PathTestSet/3/part-0
Binary files differ
diff --git a/genomix/genomix-pregelix/data/PathTestSet/3/part-1 b/genomix/genomix-pregelix/data/PathTestSet/3/part-1
new file mode 100755
index 0000000..4487006
--- /dev/null
+++ b/genomix/genomix-pregelix/data/PathTestSet/3/part-1
Binary files differ
diff --git a/genomix/genomix-pregelix/data/PathTestSet/4/part-0 b/genomix/genomix-pregelix/data/PathTestSet/4/part-0
new file mode 100755
index 0000000..d3baf9f
--- /dev/null
+++ b/genomix/genomix-pregelix/data/PathTestSet/4/part-0
Binary files differ
diff --git a/genomix/genomix-pregelix/data/PathTestSet/4/part-1 b/genomix/genomix-pregelix/data/PathTestSet/4/part-1
new file mode 100755
index 0000000..877d4f3
--- /dev/null
+++ b/genomix/genomix-pregelix/data/PathTestSet/4/part-1
Binary files differ
diff --git a/genomix/genomix-pregelix/data/PathTestSet/5/part-0 b/genomix/genomix-pregelix/data/PathTestSet/5/part-0
new file mode 100755
index 0000000..9a38afb
--- /dev/null
+++ b/genomix/genomix-pregelix/data/PathTestSet/5/part-0
Binary files differ
diff --git a/genomix/genomix-pregelix/data/PathTestSet/5/part-1 b/genomix/genomix-pregelix/data/PathTestSet/5/part-1
new file mode 100755
index 0000000..36a623e
--- /dev/null
+++ b/genomix/genomix-pregelix/data/PathTestSet/5/part-1
Binary files differ
diff --git a/genomix/genomix-pregelix/data/PathTestSet/6/part-0 b/genomix/genomix-pregelix/data/PathTestSet/6/part-0
new file mode 100755
index 0000000..fee737e
--- /dev/null
+++ b/genomix/genomix-pregelix/data/PathTestSet/6/part-0
Binary files differ
diff --git a/genomix/genomix-pregelix/data/PathTestSet/6/part-1 b/genomix/genomix-pregelix/data/PathTestSet/6/part-1
new file mode 100755
index 0000000..07f3452
--- /dev/null
+++ b/genomix/genomix-pregelix/data/PathTestSet/6/part-1
Binary files differ
diff --git a/genomix/genomix-pregelix/data/PathTestSet/7/part-0 b/genomix/genomix-pregelix/data/PathTestSet/7/part-0
new file mode 100755
index 0000000..3d4cc9b
--- /dev/null
+++ b/genomix/genomix-pregelix/data/PathTestSet/7/part-0
Binary files differ
diff --git a/genomix/genomix-pregelix/data/PathTestSet/7/part-1 b/genomix/genomix-pregelix/data/PathTestSet/7/part-1
new file mode 100755
index 0000000..b7fb670
--- /dev/null
+++ b/genomix/genomix-pregelix/data/PathTestSet/7/part-1
Binary files differ
diff --git a/genomix/genomix-pregelix/data/PathTestSet/8/part-0 b/genomix/genomix-pregelix/data/PathTestSet/8/part-0
new file mode 100755
index 0000000..778fbe8
--- /dev/null
+++ b/genomix/genomix-pregelix/data/PathTestSet/8/part-0
Binary files differ
diff --git a/genomix/genomix-pregelix/data/PathTestSet/8/part-1 b/genomix/genomix-pregelix/data/PathTestSet/8/part-1
new file mode 100755
index 0000000..a045391
--- /dev/null
+++ b/genomix/genomix-pregelix/data/PathTestSet/8/part-1
Binary files differ
diff --git a/genomix/genomix-pregelix/data/PathTestSet/9/part-0 b/genomix/genomix-pregelix/data/PathTestSet/9/part-0
new file mode 100755
index 0000000..b2d3f50
--- /dev/null
+++ b/genomix/genomix-pregelix/data/PathTestSet/9/part-0
Binary files differ
diff --git a/genomix/genomix-pregelix/data/PathTestSet/9/part-1 b/genomix/genomix-pregelix/data/PathTestSet/9/part-1
new file mode 100755
index 0000000..dacf119
--- /dev/null
+++ b/genomix/genomix-pregelix/data/PathTestSet/9/part-1
Binary files differ
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/LogAlgorithmForPathMergeOutputFormat.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/LogAlgorithmForPathMergeOutputFormat.java
index 39e1e41..f0b2915 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/LogAlgorithmForPathMergeOutputFormat.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/LogAlgorithmForPathMergeOutputFormat.java
@@ -37,8 +37,8 @@
             @Override
             public void writeVertex(Vertex<KmerBytesWritable, ValueStateWritable, NullWritable, ?> vertex) throws IOException,
                     InterruptedException {
-            	if(vertex.getVertexValue().getState() != State.FINAL_DELETE
-            			&& vertex.getVertexValue().getState() != State.END_VERTEX){
+            	if(vertex.getVertexValue().getState() != State.END_VERTEX
+            			&& vertex.getVertexValue().getState() != State.MID_VERTEX){
             		getRecordWriter().write(vertex.getVertexId(),vertex.getVertexValue());
             	}
                     
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/TwoStepLogAlgorithmForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/TwoStepLogAlgorithmForPathMergeVertex.java
index c5788ff..2353529 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/TwoStepLogAlgorithmForPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/TwoStepLogAlgorithmForPathMergeVertex.java
@@ -168,7 +168,7 @@
 			if(getVertexValue().getState() == State.START_VERTEX){
 				sendStartMsgToNextNode();
 			}
-			else if(getVertexValue().getState() != State.END_VERTEX && getVertexValue().getState() != State.FINAL_DELETE){
+			else if(getVertexValue().getState() != State.END_VERTEX){ //FINAL_DELETE
 				sendEndMsgToNextNode();
 			}
 		}
@@ -191,9 +191,9 @@
 	 */
 	public void setMessageType(int message){
 		//kill Message because it has been merged by the head
-		if(getVertexValue().getState() == State.END_VERTEX || getVertexValue().getState() == State.FINAL_DELETE){
+		if(getVertexValue().getState() == State.END_VERTEX){ //FINAL_DELETE
 			msg.setMessage(Message.END);
-			getVertexValue().setState(State.FINAL_DELETE);
+			getVertexValue().setState(State.END_VERTEX); //FINAL_DELETE
 			setVertexValue(getVertexValue());
 		}
 		else
@@ -294,7 +294,7 @@
 				else
 					voteToHalt();
 			}
-			if(getVertexValue().getState() == State.END_VERTEX || getVertexValue().getState() == State.FINAL_DELETE){
+			if(getVertexValue().getState() == State.END_VERTEX){ //FINAL_DELETE
 				voteToHalt();
 			}
 			if(getVertexValue().getState() == State.FINAL_VERTEX){
@@ -313,7 +313,7 @@
 		}
 		else{
 			if(getVertexValue().getState() != State.START_VERTEX 
-					&& getVertexValue().getState() != State.END_VERTEX && getVertexValue().getState() != State.FINAL_DELETE){
+					&& getVertexValue().getState() != State.END_VERTEX){ //FINAL_DELETE
 				deleteVertex(getVertexId());//killSelf because it doesn't receive any message
 			}
 		}
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 78cc005..68e29ee 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
@@ -27,7 +27,7 @@
         job.setDynamicVertexValueSize(true);
         job.setOutputKeyClass(KmerBytesWritable.class);
         job.setOutputValueClass(ValueStateWritable.class);
-        job.getConfiguration().setInt(NaiveAlgorithmForPathMergeVertex.KMER_SIZE, 7);
+        job.getConfiguration().setInt(NaiveAlgorithmForPathMergeVertex.KMER_SIZE, 5);
         job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
     }
     
@@ -43,7 +43,7 @@
         job.setDynamicVertexValueSize(true);
         job.setOutputKeyClass(KmerBytesWritable.class);
         job.setOutputValueClass(ValueStateWritable.class);
-        job.getConfiguration().setInt(TwoStepLogAlgorithmForPathMergeVertex.KMER_SIZE, 7);
+        job.getConfiguration().setInt(TwoStepLogAlgorithmForPathMergeVertex.KMER_SIZE, 5);
         job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
     }
     
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/GraphBuildTestCase.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/GraphBuildTestCase.java
new file mode 100644
index 0000000..a625a79
--- /dev/null
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/GraphBuildTestCase.java
@@ -0,0 +1,122 @@
+package edu.uci.ics.genomix.pregelix.pathmerge;
+
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+
+import junit.framework.Assert;
+import junit.framework.TestCase;
+
+import org.apache.hadoop.conf.Configuration;
+import org.apache.hadoop.fs.FileSystem;
+import org.apache.hadoop.fs.FileUtil;
+import org.apache.hadoop.fs.Path;
+import org.apache.hadoop.io.SequenceFile;
+import org.apache.hadoop.mapred.JobConf;
+import org.apache.hadoop.util.ReflectionUtils;
+import org.junit.Test;
+
+import edu.uci.ics.genomix.driver.Driver;
+import edu.uci.ics.genomix.driver.Driver.Plan;
+import edu.uci.ics.genomix.job.GenomixJob;
+import edu.uci.ics.genomix.type.KmerBytesWritable;
+import edu.uci.ics.genomix.type.KmerCountValue;
+
+public class GraphBuildTestCase extends TestCase {
+	private final JobConf conf;
+	private Driver driver;
+	private int numberOfNC = 2;
+	private int numPartitionPerMachine = 1;
+	
+	private static final String ACTUAL_RESULT_DIR = "graphbuildresult";
+	private static final String HDFS_OUTPUT_PATH = "/result";
+	private static final String DUMPED_RESULT = ACTUAL_RESULT_DIR
+			+ HDFS_OUTPUT_PATH + "/result.txt";
+	private static final String CONVERT_RESULT = ACTUAL_RESULT_DIR
+			+ HDFS_OUTPUT_PATH + "/result.txt.txt";
+	
+	public GraphBuildTestCase(JobConf conf, Driver driver){
+		this.conf = conf;
+		this.driver = driver;
+	}
+	
+	private void cleanUpReEntry() throws IOException {
+		FileSystem lfs = FileSystem.getLocal(new Configuration());
+		if (lfs.exists(new Path(DUMPED_RESULT))) {
+			lfs.delete(new Path(DUMPED_RESULT), true);
+		}
+		FileSystem dfs = FileSystem.get(conf);
+		if (dfs.exists(new Path(HDFS_OUTPUT_PATH))) {
+			dfs.delete(new Path(HDFS_OUTPUT_PATH), true);
+		}
+	}
+
+	@Test
+	public void Test() throws Exception {
+		cleanUpReEntry();
+		TestPreClusterGroupby();
+	}
+
+	public void TestPreClusterGroupby() throws Exception {
+		conf.set(GenomixJob.GROUPBY_TYPE, "precluster");
+		//conf.set(GenomixJob.OUTPUT_FORMAT, "text");
+		System.err.println("Testing PreClusterGroupBy");
+		driver.runJob(new GenomixJob(conf), Plan.BUILD_DEBRUJIN_GRAPH, true);
+		Assert.assertEquals(true, checkResults());
+	}
+
+
+	private boolean checkResults() throws Exception {
+		File dumped = null;
+		String format = conf.get(GenomixJob.OUTPUT_FORMAT);
+		if ("text".equalsIgnoreCase(format)) {
+			FileUtil.copyMerge(FileSystem.get(conf),
+					new Path(HDFS_OUTPUT_PATH), FileSystem
+							.getLocal(new Configuration()), new Path(
+							DUMPED_RESULT), false, conf, null);
+			dumped = new File(DUMPED_RESULT);
+		} else {
+
+			FileSystem.getLocal(new Configuration()).mkdirs(
+					new Path(ACTUAL_RESULT_DIR + HDFS_OUTPUT_PATH));
+			File filePathTo = new File(CONVERT_RESULT);
+			BufferedWriter bw = new BufferedWriter(new FileWriter(filePathTo));
+			for (int i = 0; i < numPartitionPerMachine * numberOfNC; i++) {
+				String partname = "/part-" + i;
+				FileUtil.copy(FileSystem.get(conf), new Path(HDFS_OUTPUT_PATH
+						+ partname), FileSystem.getLocal(new Configuration()),
+						new Path(ACTUAL_RESULT_DIR + HDFS_OUTPUT_PATH
+								+ partname), false, conf);
+
+				Path path = new Path(HDFS_OUTPUT_PATH + partname);
+				FileSystem dfs = FileSystem.get(conf);
+				if (dfs.getFileStatus(path).getLen() == 0) {
+					continue;
+				}
+				SequenceFile.Reader reader = new SequenceFile.Reader(dfs, path,
+						conf);
+				KmerBytesWritable key = new KmerBytesWritable(conf.getInt(
+						GenomixJob.KMER_LENGTH, GenomixJob.DEFAULT_KMER));
+				KmerCountValue value = (KmerCountValue) ReflectionUtils
+						.newInstance(reader.getValueClass(), conf);
+
+				while (reader.next(key, value)) {
+					if (key == null || value == null) {
+						break;
+					}
+					bw.write(key.toString() + "\t" + value.toString());
+					System.out
+							.println(key.toString() + "\t" + value.toString());
+					bw.newLine();
+				}
+				reader.close();
+			}
+			bw.close();
+			dumped = new File(CONVERT_RESULT);
+		}
+
+		// TestUtils.compareWithSortedResult(new File(expectedPath), dumped);
+		return true;
+	}
+}
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/GraphBuildTestSuite.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/GraphBuildTestSuite.java
new file mode 100644
index 0000000..d361c40
--- /dev/null
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/GraphBuildTestSuite.java
@@ -0,0 +1,131 @@
+package edu.uci.ics.genomix.pregelix.pathmerge;
+
+import java.io.BufferedWriter;
+import java.io.DataOutputStream;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.FileWriter;
+import java.io.IOException;
+
+import org.apache.commons.io.FileUtils;
+import org.apache.hadoop.conf.Configuration;
+import org.apache.hadoop.fs.FileSystem;
+import org.apache.hadoop.fs.FileUtil;
+import org.apache.hadoop.fs.Path;
+import org.apache.hadoop.hdfs.MiniDFSCluster;
+import org.apache.hadoop.io.SequenceFile;
+import org.apache.hadoop.mapred.FileInputFormat;
+import org.apache.hadoop.mapred.FileOutputFormat;
+import org.apache.hadoop.mapred.JobConf;
+import org.apache.hadoop.util.ReflectionUtils;
+
+import edu.uci.ics.genomix.driver.Driver;
+import edu.uci.ics.genomix.driver.Driver.Plan;
+import edu.uci.ics.genomix.job.GenomixJob;
+import edu.uci.ics.genomix.type.KmerBytesWritable;
+import edu.uci.ics.genomix.type.KmerCountValue;
+import junit.framework.Assert;
+import junit.framework.Test;
+import junit.framework.TestResult;
+import junit.framework.TestSuite;
+
+public class GraphBuildTestSuite extends TestSuite {
+	private static final String ACTUAL_RESULT_DIR = "graphbuildresult";
+	private static final String PATH_TO_HADOOP_CONF = "src/test/resources/hadoop/conf";
+
+	private static final String DATA_PATH = "graph/7/TreePath";
+	private static final String HDFS_INPUT_PATH = "/test";
+	private static final String HDFS_OUTPUT_PATH = "/result";
+
+	private static final String HADOOP_CONF_PATH = ACTUAL_RESULT_DIR
+			+ File.separator + "conf.xml";
+	private MiniDFSCluster dfsCluster;
+
+	private static JobConf conf = new JobConf();
+	private int numberOfNC = 2;
+	private int numPartitionPerMachine = 1;
+
+	private static Driver driver;
+
+	public void setUp() throws Exception {
+		cleanupStores();
+		edu.uci.ics.hyracks.hdfs.utils.HyracksUtils.init();
+		FileUtils.forceMkdir(new File(ACTUAL_RESULT_DIR));
+		FileUtils.cleanDirectory(new File(ACTUAL_RESULT_DIR));
+		startHDFS();
+
+		FileInputFormat.setInputPaths(conf, HDFS_INPUT_PATH);
+		FileOutputFormat.setOutputPath(conf, new Path(HDFS_OUTPUT_PATH));
+
+		conf.setInt(GenomixJob.KMER_LENGTH, 7);
+		driver = new Driver(
+				edu.uci.ics.hyracks.hdfs.utils.HyracksUtils.CC_HOST,
+				edu.uci.ics.hyracks.hdfs.utils.HyracksUtils.TEST_HYRACKS_CC_CLIENT_PORT,
+				numPartitionPerMachine);
+	}
+
+	private void cleanupStores() throws IOException {
+		FileUtils.forceMkdir(new File("teststore"));
+		FileUtils.forceMkdir(new File("build"));
+		FileUtils.cleanDirectory(new File("teststore"));
+		FileUtils.cleanDirectory(new File("build"));
+	}
+
+	private void startHDFS() throws IOException {
+		conf.addResource(new Path(PATH_TO_HADOOP_CONF + "/core-site.xml"));
+		conf.addResource(new Path(PATH_TO_HADOOP_CONF + "/mapred-site.xml"));
+		conf.addResource(new Path(PATH_TO_HADOOP_CONF + "/hdfs-site.xml"));
+
+		FileSystem lfs = FileSystem.getLocal(new Configuration());
+		lfs.delete(new Path("build"), true);
+		System.setProperty("hadoop.log.dir", "logs");
+		dfsCluster = new MiniDFSCluster(conf, numberOfNC, true, null);
+		FileSystem dfs = FileSystem.get(conf);
+		Path src = new Path(DATA_PATH);
+		Path dest = new Path(HDFS_INPUT_PATH);
+		dfs.mkdirs(dest);
+		dfs.copyFromLocalFile(src, dest);
+
+		DataOutputStream confOutput = new DataOutputStream(
+				new FileOutputStream(new File(HADOOP_CONF_PATH)));
+		conf.writeXml(confOutput);
+		confOutput.flush();
+		confOutput.close();
+	}
+	
+	public static Test suite() throws Exception {
+		GraphBuildTestSuite testSuite = new GraphBuildTestSuite();
+		testSuite.setUp();
+		testSuite.addTest(new GraphBuildTestCase(conf, driver));
+		return testSuite;
+	}
+	
+	/**
+	 * Runs the tests and collects their result in a TestResult.
+	 */
+	@Override
+	public void run(TestResult result) {
+		try {
+			int testCount = countTestCases();
+			for (int i = 0; i < testCount; i++) {
+				// cleanupStores();
+				Test each = this.testAt(i);
+				if (result.shouldStop())
+					break;
+				runTest(each, result);
+			}
+			tearDown();
+		} catch (Exception e) {
+			throw new IllegalStateException(e);
+		}
+	}
+	
+	public void tearDown() throws Exception {
+		edu.uci.ics.hyracks.hdfs.utils.HyracksUtils.deinit();
+		cleanupHDFS();
+	}
+
+	private void cleanupHDFS() throws Exception {
+		dfsCluster.shutdown();
+	}
+}
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/MergePathTest.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/MergePathTest.java
index 5e99cc9..d813709 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/MergePathTest.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/MergePathTest.java
@@ -20,9 +20,9 @@
 public class MergePathTest {
 	public static final String PATH_TO_TESTSTORE = "testcase/pathmerge/"; 
 	//"genomix_result/pathmerge/new_naive";
-	public static final String NAIVE_DATA_INPUT = "genomix_result/pathmerge/new_naive";//"actual/NaiveAlgorithmForMergeGraph/BinaryOutput/test";
+	public static final String NAIVE_DATA_INPUT = "genomix_result/pathmerge/naive_newest";//"actual/NaiveAlgorithmForMergeGraph/BinaryOutput/test";
 	//"genomix_result/pathmerge/new_log";
-	public static final String LOG_DATA_INPUT = "genomix_result/pathmerge/new_log";//"actual/TwoStepLogAlgorithmForMergeGraph/BinaryOutput/test";
+	public static final String LOG_DATA_INPUT = "genomix_result/pathmerge/log_newest";//"actual/TwoStepLogAlgorithmForMergeGraph/BinaryOutput/test";
 	public static final String TEXT_OUTPUT = PATH_TO_TESTSTORE + "textfile";
 	public static final String CHAIN_OUTPUT = PATH_TO_TESTSTORE + "chain";
 	
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/PathMergeSmallTestCase.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/PathMergeSmallTestCase.java
index 52fd4c7..67b6f21 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/PathMergeSmallTestCase.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/PathMergeSmallTestCase.java
@@ -77,7 +77,7 @@
 	private void compareResults() throws Exception {
 		dfs.copyToLocalFile(FileOutputFormat.getOutputPath(job), new Path(
 				resultFileDir));
-		GenerateTextFile.generateFromPathmergeResult(7, resultFileDir, textFileDir);
+		GenerateTextFile.generateFromPathmergeResult(5, resultFileDir, textFileDir);
 		// TestUtils.compareWithResultDir(new File(expectedFileDir), new
 		// File(resultFileDir));
 	}
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/PathMergeSmallTestSuite.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/PathMergeSmallTestSuite.java
index 901706e..c1ddfef 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/PathMergeSmallTestSuite.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/PathMergeSmallTestSuite.java
@@ -44,14 +44,14 @@
 	private static final Logger LOGGER = Logger
 			.getLogger(PathMergeSmallTestSuite.class.getName());
 
-	public static final String PreFix = "data/7";
+	public static final String PreFix = "data/PathTestSet";
 	public static final String[] TestDir = { PreFix + File.separator
-		+ "BridgePath", PreFix + File.separator
+		/*+ "BridgePath", PreFix + File.separator
 		+ "CyclePath", PreFix + File.separator
 		+ "SimplePath", PreFix + File.separator
 		+ "SinglePath", PreFix + File.separator
-		+ "TreePath"};
-		/*+ "2", PreFix + File.separator
+		+ "TreePath"};*/
+		+ "2", PreFix + File.separator
 		+ "3", PreFix + File.separator
 		+ "4", PreFix + File.separator
 		+ "5", PreFix + File.separator
@@ -59,7 +59,7 @@
 		+ "7", PreFix + File.separator
 		+ "8", PreFix + File.separator
 		+ "9", PreFix + File.separator
-		+ "10"}; , PreFix + File.separator
+		+ "10", PreFix + File.separator
 		+ "TwoKmer", PreFix + File.separator
 		+ "ThreeKmer", PreFix + File.separator
 		+ "SinglePath", PreFix + File.separator
@@ -69,7 +69,7 @@
 		+ "CyclePath", PreFix + File.separator
 		+ "RingPath", PreFix + File.separator
 		+ "LongPath", PreFix + File.separator
-		+ "TreePath"};*/
+		+ "TreePath"};
 	private static final String ACTUAL_RESULT_DIR = "actual";
 	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";
@@ -97,13 +97,6 @@
 		startHDFS();
 	}
 
-	private void cleanupStores() throws IOException {
-		FileUtils.forceMkdir(new File("teststore"));
-		FileUtils.forceMkdir(new File("build"));
-		FileUtils.cleanDirectory(new File("teststore"));
-		FileUtils.cleanDirectory(new File("build"));
-	}
-
 	private void startHDFS() throws IOException {
 		conf.addResource(new Path(PATH_TO_HADOOP_CONF + "/core-site.xml"));
 		conf.addResource(new Path(PATH_TO_HADOOP_CONF + "/mapred-site.xml"));
@@ -130,6 +123,13 @@
 		confOutput.flush();
 		confOutput.close();
 	}
+	
+	private void cleanupStores() throws IOException {
+		FileUtils.forceMkdir(new File("teststore"));
+		FileUtils.forceMkdir(new File("build"));
+		FileUtils.cleanDirectory(new File("teststore"));
+		FileUtils.cleanDirectory(new File("build"));
+	}
 
 	/**
 	 * cleanup hdfs cluster