diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/driver/Driver.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/driver/Driver.java
deleted file mode 100644
index 4c24919..0000000
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/driver/Driver.java
+++ /dev/null
@@ -1,172 +0,0 @@
-/*
- * 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.driver;
-
-import java.net.URL;
-import java.util.EnumSet;
-import java.util.Map;
-
-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.job.GenomixJobConf;
-import edu.uci.ics.genomix.hyracks.job.JobGen;
-import edu.uci.ics.genomix.hyracks.job.JobGenBrujinGraph;
-import edu.uci.ics.genomix.hyracks.job.JobGenCheckReader;
-import edu.uci.ics.genomix.hyracks.job.JobGenCreateKmerInfo;
-import edu.uci.ics.genomix.hyracks.job.JobGenGroupbyReadID;
-import edu.uci.ics.genomix.hyracks.job.JobGenMapKmerToRead;
-import edu.uci.ics.genomix.hyracks.job.JobGenUnMerged;
-import edu.uci.ics.hyracks.api.client.HyracksConnection;
-import edu.uci.ics.hyracks.api.client.IHyracksClientConnection;
-import edu.uci.ics.hyracks.api.client.NodeControllerInfo;
-import edu.uci.ics.hyracks.api.exceptions.HyracksException;
-import edu.uci.ics.hyracks.api.job.JobFlag;
-import edu.uci.ics.hyracks.api.job.JobId;
-import edu.uci.ics.hyracks.api.job.JobSpecification;
-import edu.uci.ics.hyracks.hdfs.scheduler.Scheduler;
-
-public class Driver {
-    public static enum Plan {
-        CHECK_KMERREADER,
-        OUTPUT_KMERHASHTABLE,
-        OUTPUT_MAP_KMER_TO_READ,
-        OUTPUT_GROUPBY_READID,
-        BUILD_DEBRUJIN_GRAPH,
-        BUILD_UNMERGED_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);
-            scheduler = new Scheduler(hcc.getNodeControllerInfos());
-        } catch (Exception e) {
-            throw new HyracksException(e);
-        }
-        this.numPartitionPerMachine = numPartitionPerMachine;
-    }
-
-    public void runJob(GenomixJobConf job) throws HyracksException {
-        runJob(job, Plan.BUILD_DEBRUJIN_GRAPH, false);
-    }
-
-    public void runJob(GenomixJobConf job, Plan planChoice, boolean profiling) throws HyracksException {
-        /** add hadoop configurations */
-        URL hadoopCore = job.getClass().getClassLoader().getResource("core-site.xml");
-        job.addResource(hadoopCore);
-        URL hadoopMapRed = job.getClass().getClassLoader().getResource("mapred-site.xml");
-        job.addResource(hadoopMapRed);
-        URL hadoopHdfs = job.getClass().getClassLoader().getResource("hdfs-site.xml");
-        job.addResource(hadoopHdfs);
-
-        LOG.info("job started");
-        long start = System.currentTimeMillis();
-        long end = start;
-        long time = 0;
-
-        this.profiling = profiling;
-        try {
-            Map<String, NodeControllerInfo> ncMap = hcc.getNodeControllerInfos();
-            LOG.info("ncmap:" + ncMap.size() + " " + ncMap.keySet().toString());
-            switch (planChoice) {
-                case BUILD_DEBRUJIN_GRAPH:
-                default:
-                    jobGen = new JobGenBrujinGraph(job, scheduler, ncMap, numPartitionPerMachine);
-                    break;
-                case OUTPUT_KMERHASHTABLE:
-                    jobGen = new JobGenCreateKmerInfo(job, scheduler, ncMap, numPartitionPerMachine);
-                    break;
-                case OUTPUT_MAP_KMER_TO_READ:
-                    jobGen = new JobGenMapKmerToRead(job, scheduler, ncMap, numPartitionPerMachine);
-                    break;
-                case OUTPUT_GROUPBY_READID:
-                    jobGen = new JobGenGroupbyReadID(job, scheduler, ncMap, numPartitionPerMachine);
-                    break;
-                case CHECK_KMERREADER:
-                    jobGen = new JobGenCheckReader(job, scheduler, ncMap, numPartitionPerMachine);
-                    break;
-                case BUILD_UNMERGED_GRAPH:
-                    jobGen = new JobGenUnMerged(job, scheduler, ncMap, numPartitionPerMachine);
-            }
-
-            start = System.currentTimeMillis();
-            run(jobGen);
-            end = System.currentTimeMillis();
-            time = end - start;
-            LOG.info("result writing finished " + time + "ms");
-            LOG.info("job finished");
-        } catch (Exception e) {
-            throw new HyracksException(e);
-        }
-    }
-
-    private void run(JobGen jobGen) throws Exception {
-        try {
-            JobSpecification createJob = jobGen.generateJob();
-            execute(createJob);
-        } catch (Exception e) {
-            e.printStackTrace();
-            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);
-    }
-}