diff --git a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/pmcommon/GenomixMiniClusterTest.java b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/pmcommon/GenomixMiniClusterTest.java
deleted file mode 100644
index 544f5fc..0000000
--- a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/pmcommon/GenomixMiniClusterTest.java
+++ /dev/null
@@ -1,192 +0,0 @@
-package edu.uci.ics.genomix.hadoop.pmcommon;
-
-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 java.util.ArrayList;
-
-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.io.Writable;
-import org.apache.hadoop.mapred.JobConf;
-import org.apache.hadoop.mapred.MiniMRCluster;
-import org.junit.After;
-import org.junit.Before;
-
-import edu.uci.ics.genomix.hyracks.driver.Driver;
-import edu.uci.ics.genomix.hyracks.job.GenomixJobConf;
-import edu.uci.ics.genomix.hyracks.test.TestUtils;
-import edu.uci.ics.hyracks.hdfs.utils.HyracksUtils;
-
-/*
- * A base class providing most of the boilerplate for Genomix-based tests
- */
-@SuppressWarnings("deprecation")
-public class GenomixMiniClusterTest {
-    protected int KMER_LENGTH = 5;
-    protected int READ_LENGTH = 8;
-    
-    // subclass should modify this to include the HDFS directories that should be cleaned up
-    protected ArrayList<String> HDFS_PATHS = new ArrayList<String>();
-
-    protected String EXPECTED_ROOT = "src/test/resources/expected/";
-    protected String ACTUAL_ROOT = "src/test/resources/actual/";
-    
-    protected String HADOOP_CONF_ROOT = "src/test/resources/hadoop/conf/";
-    
-    protected MiniDFSCluster dfsCluster;
-    protected JobConf conf = new JobConf();
-    protected int numberOfNC = 1;
-    protected int numPartitionPerMachine = 1;
-    protected Driver driver;
-
-    protected Writable key;
-    protected Writable value;
-    protected MiniMRCluster mrCluster;
-
-
-    @Before
-    public void setUp() throws Exception {
-        cleanupStores();
-        HyracksUtils.init();
-        FileUtils.forceMkdir(new File(ACTUAL_ROOT));
-        FileUtils.cleanDirectory(new File(ACTUAL_ROOT));
-        startHDFS();
-
-        conf.setInt(GenomixJobConf.KMER_LENGTH, KMER_LENGTH);
-        conf.setInt(GenomixJobConf.READ_LENGTH, READ_LENGTH);
-        driver = new Driver(HyracksUtils.CC_HOST,
-                HyracksUtils.TEST_HYRACKS_CC_CLIENT_PORT, numPartitionPerMachine);
-    }
-    
-    /*
-     * Merge and copy a DFS directory to a local destination, converting to text if necessary. 
-     * Also locally store the binary-formatted result if available.
-     */
-    protected void copyResultsToLocal(String hdfsSrcDir, String localDestFile, Configuration conf) throws IOException {
-        String fileFormat = conf.get(GenomixJobConf.OUTPUT_FORMAT);
-        if (GenomixJobConf.OUTPUT_FORMAT_TEXT.equalsIgnoreCase(fileFormat)) {
-            // for text files, just concatenate them together
-            FileUtil.copyMerge(FileSystem.get(conf), new Path(hdfsSrcDir),
-                    FileSystem.getLocal(new Configuration()), new Path(localDestFile),
-                    false, conf, null);
-        } else {
-            // file is binary
-            // merge and store the binary format
-//            FileUtil.copyMerge(FileSystem.get(conf), new Path(hdfsSrcDir),
-//                    FileSystem.getLocal(new Configuration()), new Path(localDestFile + ".bin"),
-//                    false, conf, null);
-            // load the Node's and write them out as text locally
-            FileSystem lfs = FileSystem.getLocal(new Configuration());
-            lfs.mkdirs(new Path(localDestFile).getParent());
-            File filePathTo = new File(localDestFile);
-            BufferedWriter bw = new BufferedWriter(new FileWriter(filePathTo));
-            FileSystem dfs = FileSystem.get(conf);
-            SequenceFile.Reader reader = new SequenceFile.Reader(dfs, new Path(hdfsSrcDir + "part-0"), conf);
-            SequenceFile.Writer writer = new SequenceFile.Writer(lfs, new JobConf(), new Path(localDestFile + ".bin"), reader.getKeyClass(), reader.getValueClass());
-            
-            for (int i=0; i < java.lang.Integer.MAX_VALUE; i++) {
-                Path path = new Path(hdfsSrcDir + "part-" + i);
-                if (!dfs.exists(path)) {
-                    break;
-                }
-                if (dfs.getFileStatus(path).getLen() == 0) {
-                    continue;
-                }
-                reader = new SequenceFile.Reader(dfs, path, 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();
-                    writer.append(key, value);
-                    
-                }
-                reader.close();
-            }
-            writer.close();
-            bw.close();
-        }
-
-    }
-    
-    protected boolean checkResults(String expectedPath, String actualPath, int[] poslistField) throws Exception {
-        File dumped = new File(actualPath); 
-        if (poslistField != null) {
-            TestUtils.compareWithUnSortedPosition(new File(expectedPath), dumped, poslistField);
-        } else {
-            TestUtils.compareWithSortedResult(new File(expectedPath), dumped);
-        }
-        return true;
-    }
-
-    protected void cleanupStores() throws IOException {
-        FileUtils.forceMkdir(new File("teststore"));
-        FileUtils.forceMkdir(new File("build"));
-        FileUtils.cleanDirectory(new File("teststore"));
-        FileUtils.cleanDirectory(new File("build"));
-    }
-
-    protected void startHDFS() throws IOException {
-        conf.addResource(new Path(HADOOP_CONF_ROOT + "core-site.xml"));
-        conf.addResource(new Path(HADOOP_CONF_ROOT + "mapred-site.xml"));
-        conf.addResource(new Path(HADOOP_CONF_ROOT + "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);
-        //mrCluster = new MiniMRCluster(4, dfsCluster.getFileSystem().getUri().toString(), 2);
-        
-        DataOutputStream confOutput = new DataOutputStream(new FileOutputStream(new File(ACTUAL_ROOT + "conf.xml")));
-        conf.writeXml(confOutput);
-        confOutput.close();
-    }
-    
-    protected void copyLocalToDFS(String localSrc, String hdfsDest) throws IOException {
-        FileSystem dfs = FileSystem.get(conf);
-        Path src = new Path(localSrc);
-        Path dest = new Path(hdfsDest);
-        dfs.mkdirs(dest);
-        dfs.copyFromLocalFile(src, dest);
-    }
-    
-    /*
-     * Remove the local "actual" folder and any hdfs folders in use by this test
-     */
-    public void cleanUpOutput() throws IOException {
-        // local cleanup
-        FileSystem lfs = FileSystem.getLocal(new Configuration());
-        if (lfs.exists(new Path(ACTUAL_ROOT))) {
-            lfs.delete(new Path(ACTUAL_ROOT), true);
-        }
-        // dfs cleanup
-        FileSystem dfs = FileSystem.get(conf);
-        for (String path : HDFS_PATHS) {
-            if (dfs.exists(new Path(path))) {
-                dfs.delete(new Path(path), true);
-            }
-        }
-    }
-
-    @After
-    public void tearDown() throws Exception {
-        HyracksUtils.deinit();
-        cleanupHDFS();
-    }
-
-    protected void cleanupHDFS() throws Exception {
-        dfsCluster.shutdown();
-        //mrCluster.shutdown();
-    }
-}
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 871b094..3e9a098 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
@@ -18,7 +18,6 @@
 import org.apache.hadoop.util.ReflectionUtils;
 import org.junit.Test;
 
-import edu.uci.ics.genomix.hadoop.utils.TestUtils;
 @SuppressWarnings("deprecation")
 
 public class NewGraphBuildingTest {