diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/NaiveAlgorithmForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/NaiveAlgorithmForPathMergeVertex.java
index 4a55889..d75ea48 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/NaiveAlgorithmForPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/NaiveAlgorithmForPathMergeVertex.java
@@ -143,11 +143,13 @@
 				sendMsg(destVertexId,msg);
 			}
 		}else{// is Rear
-			getVertexValue().set(GraphVertexOperation.updateRightNeighberByVertexId(getVertexValue().getAdjMap(), msg.getSourceVertexId(), kmerSize),
-					State.FINAL_VERTEX, msg.getChainVertexId());
-			setVertexValue(getVertexValue());
-			//String source = msg.getChainVertexId().toString();
-			//System.out.print("");
+			if(msg.getLengthOfChain() > kmerSize){
+				byte tmp = GraphVertexOperation.updateRightNeighberByVertexId(getVertexValue().getAdjMap(), msg.getSourceVertexId(), kmerSize);
+				getVertexValue().set(tmp, State.FINAL_VERTEX, msg.getChainVertexId());
+				setVertexValue(getVertexValue());
+				//String source = msg.getChainVertexId().toString();
+				//System.out.print("");
+			}
 		}
 	}
 	
@@ -169,8 +171,12 @@
 		//head node sends message to path node
 		else if(getSuperstep()%2 == 1 && getSuperstep() <= maxIteration){
 			while (msgIterator.hasNext()){
-				msg = msgIterator.next();
-				sendMsgToPathVertex();
+				if(getSuperstep() == 3 && GraphVertexOperation.isRearVertex(getVertexValue().getAdjMap()))
+					voteToHalt();
+				else{
+					msg = msgIterator.next();
+					sendMsgToPathVertex();
+				}
 			}
 		}
 		//path node sends message back to head node
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/testcase/GenerateTestInput.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/testcase/GenerateTestInput.java
index 6d81b74..fc26f66 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/testcase/GenerateTestInput.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/testcase/GenerateTestInput.java
@@ -56,9 +56,9 @@
 		OutputStreamWriter writer;
 		try {
 			writer = new OutputStreamWriter(new FileOutputStream("graph/55/SinglePath_55"));
-			writer.write(simplePath(55,60,1));
+			writer.write(simplePath(55,500,1));
 			writer.close();
-			writer = new OutputStreamWriter(new FileOutputStream("graph/55/SimplePath_55"));
+			/*writer = new OutputStreamWriter(new FileOutputStream("graph/55/SimplePath_55"));
 			writer.write(simplePath(55,60,3));
 			writer.close();
 			writer = new OutputStreamWriter(new FileOutputStream("graph/55/TreePath"));
@@ -69,7 +69,7 @@
 			writer.close();
 			writer = new OutputStreamWriter(new FileOutputStream("graph/55/BridgePath"));
 			writer.write(bridgePath(55,2));
-			writer.close();
+			writer.close();*/
 		} catch (IOException e) {
 			e.printStackTrace();
 		}
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/RunJobTestSuite.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/RunJobTestSuite.java
index fd0749a..45d8185 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/RunJobTestSuite.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/RunJobTestSuite.java
@@ -40,7 +40,7 @@
 	private static final String PATH_TO_ONLY = "src/test/resources/only.txt";
 	private static final String FILE_EXTENSION_OF_RESULTS = "result";
 
-	private static final String DATA_PATH = "data/sequencefile/LongPath";
+	private static final String DATA_PATH = "data/sequencefile/TreePath";
 	private static final String HDFS_PATH = "/webmap/";
 
 	private static final String HYRACKS_APP_NAME = "pregelix";
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/ResultGen/ReportGenerator.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/ResultGen/ReportGenerator.java
index 4bb37f7..3281a3b 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/ResultGen/ReportGenerator.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/ResultGen/ReportGenerator.java
@@ -44,5 +44,7 @@
 		generateReportFromLoginfo("naive");
 		generateReportFromLoginfo("log");
 		generateReportFromLoginfo("log_yourkit");
+		generateReportFromLoginfo("naive_36");
+		generateReportFromLoginfo("log_13");
 	}
 }
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/GraphBuildTest.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/GraphBuildTest.java
new file mode 100644
index 0000000..7ecf31f
--- /dev/null
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/GraphBuildTest.java
@@ -0,0 +1,188 @@
+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 junit.framework.Assert;
+
+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 org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import edu.uci.ics.genomix.driver.Driver;
+import edu.uci.ics.genomix.driver.Driver.Plan;
+import edu.uci.ics.genomix.example.jobrun.TestUtils;
+import edu.uci.ics.genomix.job.GenomixJob;
+import edu.uci.ics.genomix.type.KmerBytesWritable;
+import edu.uci.ics.genomix.type.KmerCountValue;
+
+public class GraphBuildTest {
+	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 = "data/sequencefile/BridgePath";
+    private static final String HDFS_INPUT_PATH = "/BridgePath";
+    private static final String HDFS_OUTPUT_PATH = "/BridgePath_result";
+
+    private static final String DUMPED_RESULT = ACTUAL_RESULT_DIR + HDFS_OUTPUT_PATH + "/result.txt";
+    private static final String CONVERT_RESULT = DUMPED_RESULT + ".txt";
+    private static final String EXPECTED_PATH = "src/test/resources/expected/result2";
+    private static final String EXPECTED_REVERSE_PATH = "src/test/resources/expected/result_reverse";
+
+    private static final String HADOOP_CONF_PATH = ACTUAL_RESULT_DIR + File.separator + "conf.xml";
+    private MiniDFSCluster dfsCluster;
+
+    private JobConf conf = new JobConf();
+    private int numberOfNC = 2;
+    private int numPartitionPerMachine = 1;
+
+    private Driver driver;
+
+    @Before
+    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, 5);
+        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();
+    }
+
+    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 TestAll() throws Exception {
+        cleanUpReEntry();
+        TestHybridGroupby();
+        cleanUpReEntry();
+        TestPreClusterGroupby();
+    }
+
+    public void TestPreClusterGroupby() throws Exception {
+        conf.set(GenomixJob.GROUPBY_TYPE, "precluster");
+        System.err.println("Testing PreClusterGroupBy");
+        driver.runJob(new GenomixJob(conf), Plan.BUILD_DEBRUJIN_GRAPH, true);
+        Assert.assertEquals(true, checkResults(EXPECTED_PATH));
+    }
+    
+    public void TestHybridGroupby() throws Exception {
+        conf.set(GenomixJob.GROUPBY_TYPE, "hybrid");
+        System.err.println("Testing HybridGroupBy");
+        driver.runJob(new GenomixJob(conf), Plan.BUILD_DEBRUJIN_GRAPH, true);
+        Assert.assertEquals(true, checkResults(EXPECTED_PATH));
+    }
+
+    private boolean checkResults(String expectedPath) 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;
+    }
+
+    @After
+    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 8313ef3..353fc6d 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
@@ -19,8 +19,8 @@
 
 public class MergePathTest {
 	public static final String PATH_TO_TESTSTORE = "testcase/pathmerge/"; 
-	public static final String NAIVE_DATA_INPUT = "genomix_result/pathmerge/final_naive_infinite";
-	public static final String LOG_DATA_INPUT = "genomix_result/pathmerge/final_log_infinite";
+	public static final String NAIVE_DATA_INPUT = "genomix_result/pathmerge/naive_35";
+	public static final String LOG_DATA_INPUT = "genomix_result/pathmerge/log_12";
 	public static final String TEXT_OUTPUT = PATH_TO_TESTSTORE + "textfile";
 	public static final String CHAIN_OUTPUT = PATH_TO_TESTSTORE + "chain";
 	
@@ -38,8 +38,8 @@
 		FileUtils.cleanDirectory(new File(CHAIN_OUTPUT));
 		generateTextFromPathmergeResult(NAIVE_DATA_INPUT, TEXT_OUTPUT, "/naive");
 		generateTextFromPathmergeResult(LOG_DATA_INPUT, TEXT_OUTPUT, "/log");
-		generateSpecificLengthChainFromNaivePathmergeResult(NAIVE_DATA_INPUT, CHAIN_OUTPUT, maxLength);
-		generateSpecificLengthChainFromLogPathmergeResult(LOG_DATA_INPUT, CHAIN_OUTPUT, maxLength);
+		//generateSpecificLengthChainFromNaivePathmergeResult(NAIVE_DATA_INPUT, CHAIN_OUTPUT, maxLength);
+		//generateSpecificLengthChainFromLogPathmergeResult(LOG_DATA_INPUT, CHAIN_OUTPUT, maxLength);
 	} 
 	
 	public static void generateTextFromPathmergeResult(String input, String outputDir, String fileName) throws IOException{
@@ -56,7 +56,8 @@
 				if (key == null || value == null){
 					break;
 				}
-				if(value.getLengthOfMergeChain() != -1){
+				if(value.getLengthOfMergeChain() != -1
+						&& value.getState() == State.FINAL_VERTEX){
 					bw.write(value.getLengthOfMergeChain() + "\t" +
 							value.getMergeChain().toString() + "\t" +
 							GeneCode.getSymbolFromBitMap(value.getAdjMap()));
@@ -99,7 +100,7 @@
 		BufferedWriter bw = new BufferedWriter(new FileWriter(new File(output + "/log")));
 		Configuration conf = new Configuration();
 		FileSystem fileSys = FileSystem.get(conf);
-		for(int i = 0; i < 2; i++){
+		for(int i = 0; i < nc; i++){
 			Path path = new Path(input + "/part-" + i);
 			SequenceFile.Reader reader = new SequenceFile.Reader(fileSys, path, conf);
 			KmerBytesWritable key = new KmerBytesWritable(kmerSize);
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
new file mode 100644
index 0000000..8191496
--- /dev/null
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/PathMergeSmallTestCase.java
@@ -0,0 +1,125 @@
+/*
+ * Copyright 2009-2010 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.pregelix.pathmerge;
+
+import java.io.File;
+
+import junit.framework.TestCase;
+
+import org.apache.hadoop.fs.FileSystem;
+import org.apache.hadoop.fs.Path;
+import org.apache.hadoop.mapreduce.lib.input.FileInputFormat;
+import org.apache.hadoop.mapreduce.lib.output.FileOutputFormat;
+import org.junit.Test;
+
+import edu.uci.ics.genomix.pregelix.example.util.TestUtils;
+import edu.uci.ics.pregelix.api.job.PregelixJob;
+import edu.uci.ics.pregelix.core.base.IDriver.Plan;
+import edu.uci.ics.pregelix.core.driver.Driver;
+import edu.uci.ics.pregelix.core.util.PregelixHyracksIntegrationUtil;
+
+public class PathMergeSmallTestCase extends TestCase {
+    private static String HDFS_INPUTPATH = "/BridgePath";
+    private static String HDFS_OUTPUTPAH = "/resultBridgePath";
+
+    /*private static String HDFS_INPUTPATH2 = "/CyclePath";
+    private static String HDFS_OUTPUTPAH2 = "/resultCyclePath";
+
+    private static String HDFS_INPUTPATH3 = "/LongPath";
+    private static String HDFS_OUTPUTPAH3 = "/resultLongPath";
+
+    private static String HDFS_INPUTPATH4 = "/Path";
+    private static String HDFS_OUTPUTPAH4 = "/resultPath";
+
+    private static String HDFS_INPUTPATH5 = "/SimplePath";
+    private static String HDFS_OUTPUTPAH5 = "/resultSimplePath";
+    
+    private static String HDFS_INPUTPATH6 = "/SinglePath";
+    private static String HDFS_OUTPUTPAH6 = "/resultSinglePath";
+    
+    private static String HDFS_INPUTPATH7 = "/TreePath";
+    private static String HDFS_OUTPUTPAH7 = "/resultTreePath";*/
+
+    private final PregelixJob job;
+    private final String resultFileDir;
+    private final String jobFile;
+    private final Driver driver = new Driver(this.getClass());
+    private final FileSystem dfs;
+
+    public PathMergeSmallTestCase(String hadoopConfPath, String jobName, String jobFile, String resultFile,
+            FileSystem dfs) throws Exception {
+        super("test");
+        this.jobFile = jobFile;
+        this.job = new PregelixJob("test");
+        this.job.getConfiguration().addResource(new Path(jobFile));
+        this.job.getConfiguration().addResource(new Path(hadoopConfPath));
+        Path[] inputPaths = FileInputFormat.getInputPaths(job);
+        if (inputPaths[0].toString().endsWith(HDFS_INPUTPATH)) {
+            FileInputFormat.setInputPaths(job, HDFS_INPUTPATH);
+            FileOutputFormat.setOutputPath(job, new Path(HDFS_OUTPUTPAH));
+        } 
+        /*else if (inputPaths[0].toString().endsWith(HDFS_INPUTPATH2)) {
+            FileInputFormat.setInputPaths(job, HDFS_INPUTPATH2);
+            FileOutputFormat.setOutputPath(job, new Path(HDFS_OUTPUTPAH2));
+        } else if (inputPaths[0].toString().endsWith(HDFS_INPUTPATH3)) {
+            FileInputFormat.setInputPaths(job, HDFS_INPUTPATH3);
+            FileOutputFormat.setOutputPath(job, new Path(HDFS_OUTPUTPAH3));
+        } else if (inputPaths[0].toString().endsWith(HDFS_INPUTPATH4)) {
+            FileInputFormat.setInputPaths(job, HDFS_INPUTPATH4);
+            FileOutputFormat.setOutputPath(job, new Path(HDFS_OUTPUTPAH4));
+        } else if (inputPaths[0].toString().endsWith(HDFS_INPUTPATH5)) {
+            FileInputFormat.setInputPaths(job, HDFS_INPUTPATH5);
+            FileOutputFormat.setOutputPath(job, new Path(HDFS_OUTPUTPAH5));
+        } else if (inputPaths[0].toString().endsWith(HDFS_INPUTPATH6)) {
+            FileInputFormat.setInputPaths(job, HDFS_INPUTPATH6);
+            FileOutputFormat.setOutputPath(job, new Path(HDFS_OUTPUTPAH6));
+        } else if (inputPaths[0].toString().endsWith(HDFS_INPUTPATH7)) {
+            FileInputFormat.setInputPaths(job, HDFS_INPUTPATH7);
+            FileOutputFormat.setOutputPath(job, new Path(HDFS_OUTPUTPAH7));
+        }*/
+        job.setJobName(jobName);
+        this.resultFileDir = resultFile;
+        this.dfs = dfs;
+    }
+
+    private void waitawhile() throws InterruptedException {
+        synchronized (this) {
+            this.wait(20);
+        }
+    }
+
+    @Test
+    public void test() throws Exception {
+        setUp();
+        Plan[] plans = new Plan[] { Plan.OUTER_JOIN };
+        for (Plan plan : plans) {
+            driver.runJob(job, plan, PregelixHyracksIntegrationUtil.CC_HOST,
+                    PregelixHyracksIntegrationUtil.TEST_HYRACKS_CC_CLIENT_PORT, false);
+        }
+        compareResults();
+        tearDown();
+        waitawhile();
+    }
+
+    private void compareResults() throws Exception {
+        dfs.copyToLocalFile(FileOutputFormat.getOutputPath(job), new Path(resultFileDir));
+        //TestUtils.compareWithResultDir(new File(expectedFileDir), new File(resultFileDir));
+    }
+
+    public String toString() {
+        return jobFile;
+    }
+}
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
new file mode 100644
index 0000000..5329515
--- /dev/null
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/PathMergeSmallTestSuite.java
@@ -0,0 +1,235 @@
+/*
+ * Copyright 2009-2010 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.pregelix.pathmerge;
+
+import java.io.BufferedReader;
+import java.io.DataOutputStream;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.logging.Logger;
+
+import junit.framework.Test;
+import junit.framework.TestResult;
+import junit.framework.TestSuite;
+
+import org.apache.commons.io.FileUtils;
+import org.apache.hadoop.conf.Configuration;
+import org.apache.hadoop.fs.FileSystem;
+import org.apache.hadoop.fs.Path;
+import org.apache.hadoop.hdfs.MiniDFSCluster;
+import org.apache.hadoop.mapred.JobConf;
+
+import edu.uci.ics.pregelix.core.jobgen.clusterconfig.ClusterConfig;
+import edu.uci.ics.pregelix.core.util.PregelixHyracksIntegrationUtil;
+
+@SuppressWarnings("deprecation")
+public class PathMergeSmallTestSuite extends TestSuite {
+    private static final Logger LOGGER = Logger.getLogger(PathMergeSmallTestSuite.class.getName());
+
+    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";
+    private static final String PATH_TO_CLUSTER_PROPERTIES = "src/test/resources/cluster/cluster.properties";
+    private static final String PATH_TO_JOBS = "src/test/resources/jobs/";
+    private static final String PATH_TO_IGNORE = "src/test/resources/ignore.txt";
+    private static final String PATH_TO_ONLY = "src/test/resources/only.txt";
+
+    private static final String DATA_PATH = "data/input/BridgePath";
+    private static final String HDFS_PATH = "/BridgePath/";
+
+    /*private static final String DATA_PATH2 = "data/sequencefile/CyclePath";
+    private static final String HDFS_PATH2 = "/CyclePath/";
+
+    private static final String DATA_PATH3 = "data/sequencefile/LongPath";
+    private static final String HDFS_PATH3 = "/LongPath/";
+
+    private static final String DATA_PATH4 = "data/sequencefile/Path";
+    private static final String HDFS_PATH4 = "/Path/";
+
+    private static final String DATA_PATH5 = "data/sequencefile/SimplePath";
+    private static final String HDFS_PATH5 = "/SimplePath/";
+    
+    private static final String DATA_PATH6 = "data/sequencefile/SinglePath";
+    private static final String HDFS_PATH6 = "/SinglePath/";
+    
+    private static final String DATA_PATH7 = "data/sequencefile/TreePath";
+    private static final String HDFS_PATH7 = "/TreePath/";*/
+
+    private static final String HADOOP_CONF_PATH = ACTUAL_RESULT_DIR + File.separator + "conf.xml";
+    private MiniDFSCluster dfsCluster;
+
+    private JobConf conf = new JobConf();
+    private int numberOfNC = 1;
+
+    public void setUp() throws Exception {
+        ClusterConfig.setStorePath(PATH_TO_CLUSTER_STORE);
+        ClusterConfig.setClusterPropertiesPath(PATH_TO_CLUSTER_PROPERTIES);
+        cleanupStores();
+        PregelixHyracksIntegrationUtil.init("src/test/resources/topology.xml");
+        LOGGER.info("Hyracks mini-cluster started");
+        FileUtils.forceMkdir(new File(ACTUAL_RESULT_DIR));
+        FileUtils.cleanDirectory(new File(ACTUAL_RESULT_DIR));
+        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"));
+        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_PATH);
+        dfs.mkdirs(dest);
+        dfs.copyFromLocalFile(src, dest);
+
+        /*src = new Path(DATA_PATH2);
+        dest = new Path(HDFS_PATH2);
+        dfs.mkdirs(dest);
+        dfs.copyFromLocalFile(src, dest);
+
+        src = new Path(DATA_PATH3);
+        dest = new Path(HDFS_PATH3);
+        dfs.mkdirs(dest);
+        dfs.copyFromLocalFile(src, dest);
+
+        src = new Path(DATA_PATH4);
+        dest = new Path(HDFS_PATH4);
+        dfs.mkdirs(dest);
+        dfs.copyFromLocalFile(src, dest);
+
+        src = new Path(DATA_PATH5);
+        dest = new Path(HDFS_PATH5);
+        dfs.mkdirs(dest);
+        dfs.copyFromLocalFile(src, dest);
+        
+        src = new Path(DATA_PATH6);
+        dest = new Path(HDFS_PATH6);
+        dfs.mkdirs(dest);
+        dfs.copyFromLocalFile(src, dest);
+        
+        src = new Path(DATA_PATH7);
+        dest = new Path(HDFS_PATH7);
+        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();
+    }
+
+    /**
+     * cleanup hdfs cluster
+     */
+    private void cleanupHDFS() throws Exception {
+        dfsCluster.shutdown();
+    }
+
+    public void tearDown() throws Exception {
+        PregelixHyracksIntegrationUtil.deinit();
+        LOGGER.info("Hyracks mini-cluster shut down");
+        cleanupHDFS();
+    }
+
+    public static Test suite() throws Exception {
+        List<String> ignores = getFileList(PATH_TO_IGNORE);
+        List<String> onlys = getFileList(PATH_TO_ONLY);
+        File testData = new File(PATH_TO_JOBS);
+        File[] queries = testData.listFiles();
+        PathMergeSmallTestSuite testSuite = new PathMergeSmallTestSuite();
+        testSuite.setUp();
+        boolean onlyEnabled = false;
+        FileSystem dfs = FileSystem.get(testSuite.conf);
+
+        if (onlys.size() > 0) {
+            onlyEnabled = true;
+        }
+        for (File qFile : queries) {
+            if (isInList(ignores, qFile.getName()))
+                continue;
+
+            if (qFile.isFile()) {
+                if (onlyEnabled && !isInList(onlys, qFile.getName())) {
+                    continue;
+                } else {
+                    String resultFileName = ACTUAL_RESULT_DIR + File.separator + jobExtToResExt(qFile.getName());
+                    testSuite.addTest(new PathMergeSmallTestCase(HADOOP_CONF_PATH, qFile.getName(), qFile.getAbsolutePath()
+                            .toString(), resultFileName, dfs));
+                }
+            }
+        }
+        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);
+        }
+    }
+
+    protected static List<String> getFileList(String ignorePath) throws FileNotFoundException, IOException {
+        BufferedReader reader = new BufferedReader(new FileReader(ignorePath));
+        String s = null;
+        List<String> ignores = new ArrayList<String>();
+        while ((s = reader.readLine()) != null) {
+            ignores.add(s);
+        }
+        reader.close();
+        return ignores;
+    }
+
+    private static String jobExtToResExt(String fname) {
+        int dot = fname.lastIndexOf('.');
+        return fname.substring(0, dot);
+    }
+
+    private static boolean isInList(List<String> onlys, String name) {
+        for (String only : onlys)
+            if (name.indexOf(only) >= 0)
+                return true;
+        return false;
+    }
+
+}
diff --git a/genomix/genomix-pregelix/src/test/resources/cluster/cluster.properties b/genomix/genomix-pregelix/src/test/resources/cluster/cluster.properties
index 14f8bd4..d0722ce 100644
--- a/genomix/genomix-pregelix/src/test/resources/cluster/cluster.properties
+++ b/genomix/genomix-pregelix/src/test/resources/cluster/cluster.properties
@@ -20,7 +20,7 @@
 NCLOGS_DIR=$NCTMP_DIR/logs
 
 #Comma separated I/O directories for the spilling of external sort
-IO_DIRS="/tmp/t3,/tmp/t4"
+IO_DIRS="/tmp/t3"
 
 #The JAVA_HOME
 JAVA_HOME=$JAVA_HOME