diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h4/MergePathsH4.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h4/MergePathsH4.java
index c8cfe6d..69af73d 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h4/MergePathsH4.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h4/MergePathsH4.java
@@ -327,6 +327,10 @@
                 }
             }
         }
+
+        public void close() throws IOException {
+            mos.close();
+        }
     }
 
     /*
@@ -360,10 +364,15 @@
         		PositionWritable.class, MessageWritableNodeWithFlag.class);
         
         FileSystem dfs = FileSystem.get(conf); 
-        dfs.delete(outputPath, true); // clean output dir
+        // clean output dirs
+        dfs.delete(outputPath, true);
+        dfs.delete(new Path(toMergeOutput), true);
+        dfs.delete(new Path(completeOutput), true);
+        dfs.delete(new Path(updatesOutput), true);
+
         RunningJob job = JobClient.runJob(conf);
         
-        // move the tmp outputs to the arg-spec'ed dirs
+        // move the tmp outputs to the arg-spec'ed dirs. If there is no such dir, create an empty one to simplify downstream processing
         if (!dfs.rename(new Path(outputPath + File.separator +  MergePathsH4Reducer.TO_MERGE_OUTPUT), new Path(toMergeOutput))) {
             dfs.mkdirs(new Path(toMergeOutput));
         }
@@ -378,14 +387,13 @@
     }
 
     @Override
-    public int run(String[] arg0) throws Exception {
-        // TODO Auto-generated method stub
-        return 0;
+    public int run(String[] args) throws Exception {
+        int res = ToolRunner.run(new Configuration(), new MergePathsH4(), args);
+        return res;
     }
 
     public static void main(String[] args) throws Exception {
         int res = ToolRunner.run(new Configuration(), new MergePathsH4(), args);
-        System.out.println("Ran the job fine!");
         System.exit(res);
     }
 }
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h4/MergePathsH4Driver.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h4/MergePathsH4Driver.java
index f8cabee..72be4b5 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h4/MergePathsH4Driver.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h4/MergePathsH4Driver.java
@@ -21,6 +21,7 @@
 import org.apache.hadoop.fs.Path;
 import org.apache.hadoop.fs.PathFilter;
 import org.apache.hadoop.mapred.JobConf;
+import org.apache.tools.ant.util.IdentityMapper;
 import org.kohsuke.args4j.CmdLineParser;
 import org.kohsuke.args4j.Option;
 
@@ -29,130 +30,131 @@
 @SuppressWarnings("deprecation")
 public class MergePathsH4Driver {
 
-	private static final String TO_MERGE = "toMerge";
-	private static final String COMPLETE = "complete";
-	private static final String UPDATES = "updates";
-	private String mergeOutput;
-	private String completeOutput;
-	private String updatesOutput;
+    private static final String TO_MERGE = "toMerge";
+    private static final String COMPLETE = "complete";
+    private static final String UPDATES = "updates";
+    private String mergeOutput;
+    private String completeOutput;
+    private String updatesOutput;
 
-	private void setOutputPaths(String basePath, int mergeIteration) {
-		basePath = basePath.replaceAll("/$", ""); // strip trailing slash
-		mergeOutput = basePath + "_" + TO_MERGE + "_i" + mergeIteration;
-		completeOutput = basePath + "_" + COMPLETE + "_i" + mergeIteration;
-		updatesOutput = basePath + "_" + UPDATES + "_i" + mergeIteration;
-	}
+    private void setOutputPaths(String basePath, int mergeIteration) {
+        basePath = basePath.replaceAll("/$", ""); // strip trailing slash
+        mergeOutput = basePath + "_" + TO_MERGE + "_i" + mergeIteration;
+        completeOutput = basePath + "_" + COMPLETE + "_i" + mergeIteration;
+        updatesOutput = basePath + "_" + UPDATES + "_i" + mergeIteration;
+    }
 
-	private static class Options {
-		@Option(name = "-inputpath", usage = "the input path", required = true)
-		public String inputPath;
+    private static class Options {
+        @Option(name = "-inputpath", usage = "the input path", required = true)
+        public String inputPath;
 
-		@Option(name = "-outputpath", usage = "the output path", required = true)
-		public String outputPath;
+        @Option(name = "-outputpath", usage = "the output path", required = true)
+        public String outputPath;
 
-		@Option(name = "-mergeresultpath", usage = "the merging results path", required = true)
-		public String mergeResultPath;
+        @Option(name = "-mergeresultpath", usage = "the merging results path", required = true)
+        public String mergeResultPath;
 
-		@Option(name = "-num-reducers", usage = "the number of reducers", required = true)
-		public int numReducers;
+        @Option(name = "-num-reducers", usage = "the number of reducers", required = true)
+        public int numReducers;
 
-		@Option(name = "-kmer-size", usage = "the size of kmer", required = true)
-		public int sizeKmer;
+        @Option(name = "-kmer-size", usage = "the size of kmer", required = true)
+        public int sizeKmer;
 
-		@Option(name = "-merge-rounds", usage = "the maximum number of rounds to merge", required = false)
-		public int mergeRound;
+        @Option(name = "-merge-rounds", usage = "the maximum number of rounds to merge", required = false)
+        public int mergeRound;
 
-		@Option(name = "-hadoop-conf", usage = "an (optional) hadoop configuration xml", required = false)
-		public String hadoopConf;
+        @Option(name = "-hadoop-conf", usage = "an (optional) hadoop configuration xml", required = false)
+        public String hadoopConf;
 
-	}
+    }
 
-	/*
-	 * Main driver for path merging. Given a graph, this driver runs
-	 * PathNodeInitial to ID heads and tails, then does up to @mergeRound
-	 * iterations of path merging. Updates during the merge are batch-processed
-	 * at the end in a final update job.
-	 */
-	public void run(String inputGraphPath, String outputGraphPath,
-			int numReducers, int sizeKmer, int mergeRound,
-			String defaultConfPath, JobConf defaultConf) throws IOException {
-		JobConf baseConf = defaultConf == null ? new JobConf() : defaultConf;
-		if (defaultConfPath != null) {
-			baseConf.addResource(new Path(defaultConfPath));
-		}
-		baseConf.setNumReduceTasks(numReducers);
-		baseConf.setInt("sizeKmer", sizeKmer);
-		FileSystem dfs = FileSystem.get(baseConf);
+    /*
+     * Main driver for path merging. Given a graph, this driver runs
+     * PathNodeInitial to ID heads and tails, then does up to @mergeRound
+     * iterations of path merging. Updates during the merge are batch-processed
+     * at the end in a final update job.
+     */
+    public void run(String inputGraphPath, String outputGraphPath, int numReducers, int sizeKmer, int mergeRound,
+            String defaultConfPath, JobConf defaultConf) throws IOException {
+        JobConf baseConf = defaultConf == null ? new JobConf() : defaultConf;
+        if (defaultConfPath != null) {
+            baseConf.addResource(new Path(defaultConfPath));
+        }
+        baseConf.setNumReduceTasks(numReducers);
+        baseConf.setInt("sizeKmer", sizeKmer);
+        FileSystem dfs = FileSystem.get(baseConf);
 
-		int iMerge = 0;
+        int iMerge = 0;
 
-		// identify head and tail nodes with pathnode initial
-		PathNodeInitial inith4 = new PathNodeInitial();
-		setOutputPaths(inputGraphPath, iMerge);
-		String prevToMergeOutput = inputGraphPath;
-		inith4.run(prevToMergeOutput, mergeOutput, completeOutput, baseConf);
+        // identify head and tail nodes with pathnode initial
+        PathNodeInitial inith4 = new PathNodeInitial();
+        setOutputPaths(inputGraphPath, iMerge);
+        String prevToMergeOutput = inputGraphPath;
+        System.out.println("initial run.  toMerge: " + mergeOutput + ", complete: " + completeOutput);
+        inith4.run(prevToMergeOutput, mergeOutput, completeOutput, baseConf);
+        dfs.copyToLocalFile(new Path(mergeOutput), new Path("initial-toMerge"));
+        dfs.copyToLocalFile(new Path(completeOutput), new Path("initial-complete"));
 
-		// several iterations of merging
-		MergePathsH4 merger = new MergePathsH4();
-		for (iMerge = 1; iMerge <= mergeRound; iMerge++) {
-			prevToMergeOutput = mergeOutput;
-			setOutputPaths(inputGraphPath, iMerge);
-			merger.run(prevToMergeOutput, mergeOutput, completeOutput,
-					updatesOutput, baseConf);
-			if (dfs.listStatus(new Path(mergeOutput)).length == 0) {
-				// no output from previous run-- we are done!
-				break;
-			}
-		}
+        // several iterations of merging
+        MergePathsH4 merger = new MergePathsH4();
+        for (iMerge = 1; iMerge <= mergeRound; iMerge++) {
+            prevToMergeOutput = mergeOutput;
+            setOutputPaths(inputGraphPath, iMerge);
+            merger.run(prevToMergeOutput, mergeOutput, completeOutput, updatesOutput, baseConf);
+            dfs.copyToLocalFile(new Path(mergeOutput), new Path("i" + iMerge +"-toMerge"));
+            dfs.copyToLocalFile(new Path(completeOutput), new Path("i" + iMerge +"-complete"));
+            dfs.copyToLocalFile(new Path(updatesOutput), new Path("i" + iMerge +"-updates"));
+            
+            if (dfs.listStatus(new Path(mergeOutput)) == null || dfs.listStatus(new Path(mergeOutput)).length == 0) {
+                // no output from previous run-- we are done!
+                break;
+            }
+        }
+        
+        // finally, combine all the completed paths and update messages to
+        // create a single merged graph output
+        dfs.delete(new Path(outputGraphPath), true); // clear any previous
+                                                     // output
+        // use all the "complete" and "update" outputs in addition to the final
+        // (possibly empty) toMerge directories
+        // as input to the final update step. This builds a comma-delim'ed
+        // String of said files.
+        final String lastMergeOutput = mergeOutput;
+        PathFilter updateFilter = new PathFilter() {
+            @Override
+            public boolean accept(Path arg0) {
+                String path = arg0.toString();
+                System.out.println("equals last: " + path + " vs " + lastMergeOutput + " = " + path.endsWith(lastMergeOutput));
+                return (path.matches(".*" + COMPLETE + "_i\\d+$") || path.matches(".*" + UPDATES + "_i\\d+$") || path.endsWith(lastMergeOutput));
+            }
+        };
+        StringBuilder sb = new StringBuilder();
+        String delim = "";
+        for (FileStatus file : dfs.globStatus(new Path(inputGraphPath.replaceAll("/$",  "") + "*"), updateFilter)) {
+            sb.append(delim).append(file.getPath());
+            delim = ",";
+        }
+        String finalInputs = sb.toString();
+        System.out.println("This is the final sacrifice: " + finalInputs);
+        // TODO run the update iteration
+    }
 
-		// finally, combine all the completed paths and update messages to
-		// create a single merged graph output
-		dfs.delete(new Path(outputGraphPath), true); // clear any previous
-														// output
-		// use all the "complete" and "update" outputs in addition to the final
-		// (possibly empty) toMerge directories
-		// as input to the final update step. This builds a comma-delim'ed
-		// String of said files.
-		final String lastMergeOutput = mergeOutput;
-		PathFilter updateFilter = new PathFilter() {
-			@Override
-			public boolean accept(Path arg0) {
-				String path = arg0.toString();
-				return path.contains(COMPLETE + "_i")
-						|| path.contains(UPDATES + "_i")
-						|| path.equals(lastMergeOutput);
-			}
-		};
-		StringBuilder sb = new StringBuilder();
-		String delim = "";
-		for (FileStatus file : dfs.globStatus(new Path("*"), updateFilter)) {
-			sb.append(delim).append(file);
-			delim = ",";
-		}
-		String finalInputs = sb.toString();
-		// TODO run the update iteration
-	}
+    public void run(String inputPath, String outputGraphPath, int numReducers, int sizeKmer, int mergeRound,
+            String defaultConfPath) throws IOException {
+        run(inputPath, outputGraphPath, numReducers, sizeKmer, mergeRound, defaultConfPath, null);
+    }
 
-	public void run(String inputPath, String outputGraphPath, int numReducers,
-			int sizeKmer, int mergeRound, String defaultConfPath)
-			throws IOException {
-		run(inputPath, outputGraphPath, numReducers, sizeKmer, mergeRound,
-				defaultConfPath, null);
-	}
+    public void run(String inputPath, String outputGraphPath, int numReducers, int sizeKmer, int mergeRound,
+            JobConf defaultConf) throws IOException {
+        run(inputPath, outputGraphPath, numReducers, sizeKmer, mergeRound, null, defaultConf);
+    }
 
-	public void run(String inputPath, String outputGraphPath, int numReducers,
-			int sizeKmer, int mergeRound, JobConf defaultConf)
-			throws IOException {
-		run(inputPath, outputGraphPath, numReducers, sizeKmer, mergeRound,
-				null, defaultConf);
-	}
-
-	public static void main(String[] args) throws Exception {
-		Options options = new Options();
-		CmdLineParser parser = new CmdLineParser(options);
-		parser.parseArgument(args);
-		MergePathsH4Driver driver = new MergePathsH4Driver();
-		driver.run(options.inputPath, options.outputPath, options.numReducers,
-				options.sizeKmer, options.mergeRound, null, null);
-	}
+    public static void main(String[] args) throws Exception {
+        Options options = new Options();
+        CmdLineParser parser = new CmdLineParser(options);
+        parser.parseArgument(args);
+        MergePathsH4Driver driver = new MergePathsH4Driver();
+        driver.run(options.inputPath, options.outputPath, options.numReducers, options.sizeKmer, options.mergeRound,
+                null, null);
+    }
 }
diff --git a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h4/TestPathMergeH4.java b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h4/TestPathMergeH4.java
index 667c4b1..45a2d0a 100644
--- a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h4/TestPathMergeH4.java
+++ b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h4/TestPathMergeH4.java
@@ -1,5 +1,6 @@
 package edu.uci.ics.genomix.hadoop.graphclean.mergepaths.h4;
 
+import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Arrays;
 
@@ -24,6 +25,8 @@
     protected final String GRAPHBUILD = "/01-graphbuild/";
     protected final String MERGED = "/02-pathmerge/";
     
+    protected final String ACTUAL = "src/test/resources/actual/";
+    
     protected final boolean regenerateGraph = true;
     
     {
@@ -37,22 +40,27 @@
     @Test
     public void TestMergeOneIteration() throws Exception {
         cleanUpOutput();
-        if (regenerateGraph) {
-            copyLocalToDFS(LOCAL_SEQUENCE_FILE, SEQUENCE);
-            buildGraph();
-            copyLocalToDFS(ACTUAL_ROOT + GRAPHBUILD + ".bindir", GRAPHBUILD);
-        } else {
-            copyLocalToDFS(EXPECTED_ROOT + GRAPHBUILD + ".bindir", GRAPHBUILD);
-        }
+        prepareGraph();
         
         MergePathsH4Driver h4 = new MergePathsH4Driver();
-        h4.run(GRAPHBUILD, MERGED, 2, KMER_LENGTH, 1, conf);
+        h4.run(GRAPHBUILD, MERGED, 2, KMER_LENGTH, 5, conf);
         copyResultsToLocal(MERGED, ACTUAL_ROOT + MERGED, false, conf);
     }
 
+//    @Test
+    public void testPathNode() throws IOException {
+        cleanUpOutput();
+        prepareGraph();
+
+        // identify head and tail nodes with pathnode initial
+        PathNodeInitial inith4 = new PathNodeInitial();
+        inith4.run(GRAPHBUILD, "/toMerge", "/completed", conf);
+    }
+    
+    
 
 
-    public void buildGraph() throws Exception {
+    public void buildGraph() throws IOException {
         JobConf buildConf = new JobConf(conf);  // use a separate conf so we don't interfere with other jobs 
         FileInputFormat.setInputPaths(buildConf, SEQUENCE);
         FileOutputFormat.setOutputPath(buildConf, new Path(GRAPHBUILD));
@@ -63,4 +71,14 @@
         boolean resultsAreText = false;
         copyResultsToLocal(GRAPHBUILD, ACTUAL_ROOT + GRAPHBUILD, resultsAreText, buildConf);
     }
+    
+    private void prepareGraph() throws IOException {
+        if (regenerateGraph) {
+            copyLocalToDFS(LOCAL_SEQUENCE_FILE, SEQUENCE);
+            buildGraph();
+            copyLocalToDFS(ACTUAL_ROOT + GRAPHBUILD + ".bindir", GRAPHBUILD);
+        } else {
+            copyLocalToDFS(EXPECTED_ROOT + GRAPHBUILD + ".bindir", GRAPHBUILD);
+        }
+    }
 }
diff --git a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/pmcommon/HadoopMiniClusterTest.java b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/pmcommon/HadoopMiniClusterTest.java
index 2cd3b53..9a113f1 100644
--- a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/pmcommon/HadoopMiniClusterTest.java
+++ b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/pmcommon/HadoopMiniClusterTest.java
@@ -94,6 +94,9 @@
             FileSystem lfs = FileSystem.getLocal(new Configuration());
             lfs.mkdirs(new Path(localDestFile).getParent());
             File filePathTo = new File(localDestFile);
+            if (filePathTo.exists() && filePathTo.isDirectory()) {
+                filePathTo = new File(localDestFile + "/data");
+            }
             BufferedWriter bw = new BufferedWriter(new FileWriter(filePathTo));
             SequenceFile.Reader reader = new SequenceFile.Reader(dfs, validFile.getPath(), conf);
             SequenceFile.Writer writer = new SequenceFile.Writer(lfs, new JobConf(), new Path(localDestFile