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 2c85e42..eae94cb 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
@@ -83,12 +83,12 @@
     private static void generateP4ForMergeGraphJob(String jobName, String outputPath) throws IOException {
         PregelixJob job = new PregelixJob(jobName);
         job.setVertexClass(P4ForPathMergeVertex.class);
-        job.setVertexInputFormatClass(NaiveAlgorithmForPathMergeInputFormat.class); //DataCleanInputFormat
+        job.setVertexInputFormatClass(DataCleanInputFormat.class); //NaiveAlgorithmForPathMergeInputFormat //
         job.setVertexOutputFormatClass(DataCleanOutputFormat.class);
         job.setDynamicVertexValueSize(true);
         job.setOutputKeyClass(PositionWritable.class);
         job.setOutputValueClass(VertexValueWritable.class);
-        job.getConfiguration().setInt(P4ForPathMergeVertex.KMER_SIZE, 3);
+        job.getConfiguration().setInt(P4ForPathMergeVertex.KMER_SIZE, 5);
         job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
     }
 
@@ -100,7 +100,7 @@
     private static void generateTipAddGraphJob(String jobName, String outputPath) throws IOException {
         PregelixJob job = new PregelixJob(jobName);
         job.setVertexClass(TipAddVertex.class);
-        job.setVertexInputFormatClass(NaiveAlgorithmForPathMergeInputFormat.class);
+        job.setVertexInputFormatClass(DataCleanOutputFormat.class);
         job.setVertexOutputFormatClass(DataCleanOutputFormat.class);
         job.setDynamicVertexValueSize(true);
         job.setOutputKeyClass(PositionWritable.class);
@@ -117,12 +117,12 @@
     private static void generateTipRemoveGraphJob(String jobName, String outputPath) throws IOException {
         PregelixJob job = new PregelixJob(jobName);
         job.setVertexClass(TipRemoveVertex.class);
-        job.setVertexInputFormatClass(DataCleanInputFormat.class);
+        job.setVertexInputFormatClass(NaiveAlgorithmForPathMergeInputFormat.class);
         job.setVertexOutputFormatClass(DataCleanOutputFormat.class);
         job.setDynamicVertexValueSize(true);
         job.setOutputKeyClass(PositionWritable.class);
         job.setOutputValueClass(VertexValueWritable.class);
-        job.getConfiguration().setInt(TipRemoveVertex.KMER_SIZE, 3);
+        job.getConfiguration().setInt(TipRemoveVertex.KMER_SIZE, 5);
         job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
     }
 
@@ -156,7 +156,7 @@
         job.setDynamicVertexValueSize(true);
         job.setOutputKeyClass(PositionWritable.class);
         job.setOutputValueClass(VertexValueWritable.class);
-        job.getConfiguration().setInt(TipRemoveVertex.KMER_SIZE, 3);
+        job.getConfiguration().setInt(TipRemoveVertex.KMER_SIZE, 5);
         job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
     }
 
@@ -185,12 +185,12 @@
     private static void generateBubbleMergeGraphJob(String jobName, String outputPath) throws IOException {
         PregelixJob job = new PregelixJob(jobName);
         job.setVertexClass(BubbleMergeVertex.class);
-        job.setVertexInputFormatClass(DataCleanInputFormat.class);
+        job.setVertexInputFormatClass(NaiveAlgorithmForPathMergeInputFormat.class);
         job.setVertexOutputFormatClass(DataCleanOutputFormat.class);
         job.setDynamicVertexValueSize(true);
         job.setOutputKeyClass(PositionWritable.class);
         job.setOutputValueClass(VertexValueWritable.class);
-        job.getConfiguration().setInt(BubbleMergeVertex.KMER_SIZE, 3);
+        job.getConfiguration().setInt(BubbleMergeVertex.KMER_SIZE, 5);
         job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
     }
 
@@ -203,7 +203,7 @@
         //genNaiveAlgorithmForMergeGraph();
         //genLogAlgorithmForMergeGraph();
         //genP3ForMergeGraph();
-        genTipAddGraph();
+        //genTipAddGraph();
         genTipRemoveGraph();
         genBridgeAddGraph();
         genBridgeRemoveGraph();
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BridgeRemoveSmallTestSuite.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BridgeRemoveSmallTestSuite.java
index 5b641ff..397c514 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BridgeRemoveSmallTestSuite.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BridgeRemoveSmallTestSuite.java
@@ -43,26 +43,15 @@
 public class BridgeRemoveSmallTestSuite extends TestSuite {
     private static final Logger LOGGER = Logger.getLogger(BridgeRemoveSmallTestSuite.class.getName());
 
-    public static final String PreFix = "data/input"; //"graphbuildresult";
+    public static final String PreFix = "data/actual"; //"graphbuildresult";
     public static final String[] TestDir = { PreFix + File.separator
-    + "pathmerge_tip"};/*, PreFix + File.separator
-            /*+ "CyclePath"};, PreFix + File.separator
-            + "SimplePath", PreFix + File.separator
-            + "SinglePath", PreFix + File.separator
-            + "TreePath"};*/
-           /* + "2", PreFix + File.separator + "3", PreFix + File.separator + "4", PreFix + File.separator + "5",
-            PreFix + File.separator + "6", PreFix + File.separator + "7", PreFix + File.separator + "8",
-            PreFix + File.separator + "9", PreFix + File.separator + "TwoKmer", PreFix + File.separator + "ThreeKmer",
-            PreFix + File.separator + "SinglePath", PreFix + File.separator + "SimplePath",
-            PreFix + File.separator + "Path", PreFix + File.separator + "BridgePath",
-            PreFix + File.separator + "CyclePath", PreFix + File.separator + "RingPath",
-            PreFix + File.separator + "LongPath", PreFix + File.separator + "TreePath" };*/
-    private static final String ACTUAL_RESULT_DIR = "actual";
+    + "pathmerge/P4ForMergeGraph/bin/tworeads"};
+    private static final String ACTUAL_RESULT_DIR = "data/actual/bridgeremove";
     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_ONLY = "src/test/resources/only.txt";
+    private static final String PATH_TO_ONLY = "src/test/resources/only_bridgeremove.txt";
 
     public static final String HDFS_INPUTPATH = "/PathTestSet";
 
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BubbleMergeSmallTestSuite.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BubbleMergeSmallTestSuite.java
index 9e98cb6..a94d31c 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BubbleMergeSmallTestSuite.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BubbleMergeSmallTestSuite.java
@@ -45,24 +45,13 @@
 
     public static final String PreFix = "data/input"; //"graphbuildresult";
     public static final String[] TestDir = { PreFix + File.separator
-    + "pathmerge"};/*, PreFix + File.separator
-            /*+ "CyclePath"};, PreFix + File.separator
-            + "SimplePath", PreFix + File.separator
-            + "SinglePath", PreFix + File.separator
-            + "TreePath"};*/
-           /* + "2", PreFix + File.separator + "3", PreFix + File.separator + "4", PreFix + File.separator + "5",
-            PreFix + File.separator + "6", PreFix + File.separator + "7", PreFix + File.separator + "8",
-            PreFix + File.separator + "9", PreFix + File.separator + "TwoKmer", PreFix + File.separator + "ThreeKmer",
-            PreFix + File.separator + "SinglePath", PreFix + File.separator + "SimplePath",
-            PreFix + File.separator + "Path", PreFix + File.separator + "BridgePath",
-            PreFix + File.separator + "CyclePath", PreFix + File.separator + "RingPath",
-            PreFix + File.separator + "LongPath", PreFix + File.separator + "TreePath" };*/
-    private static final String ACTUAL_RESULT_DIR = "actual";
+    + "graphs/bubblemerge/fr_bubble"};
+    private static final String ACTUAL_RESULT_DIR = "data/actual/bubblemerge";
     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_ONLY = "src/test/resources/only.txt";
+    private static final String PATH_TO_ONLY = "src/test/resources/only_bubblemerge.txt";
 
     public static final String HDFS_INPUTPATH = "/PathTestSet";
 
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/PathMergeSmallTestSuite.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/PathMergeSmallTestSuite.java
index 44d24d6..79a13b3 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/PathMergeSmallTestSuite.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/PathMergeSmallTestSuite.java
@@ -43,10 +43,13 @@
 public class PathMergeSmallTestSuite extends TestSuite {
     private static final Logger LOGGER = Logger.getLogger(PathMergeSmallTestSuite.class.getName());
 
-    public static final String PreFix = "data/PathTestSet_bidirection"; //"graphbuildresult";
+    public static final String PreFix = "data/actual"; //"graphbuildresult";
     public static final String[] TestDir = { PreFix + File.separator
-    + "tworeads_6"};/*
-    + "2", PreFix + File.separator
+    + "bubblemerge/BubbleMergeGraph/bin/small_bubble"};
+    //+ "tipremove/TipRemoveGraph/bin/fr_with_tip"};
+    //+ "graphs/pathmerge/singleread"};
+    //+ "bridgeadd/BridgeAddGraph/bin/tworeads"};
+    /*+ "2", PreFix + File.separator
     + "3", PreFix + File.separator
     + "4", PreFix + File.separator
     + "5", PreFix + File.separator
@@ -54,21 +57,8 @@
     + "7", PreFix + File.separator
     + "8", PreFix + File.separator
     + "9", PreFix + File.separator
-    + "tworeads"}; 
-    /*+ "tipremove/TipRemoveGraph/bin/tworeads"};
-    + "bridgeadd/BridgeAddGraph/bin/tworeads"};, PreFix + File.separator
-    + "tipadd/TipAddGraph/bin/read"}, PreFix + File.separator
-            /*+ "CyclePath"};, PreFix + File.separator
-            + "SimplePath", PreFix + File.separator
-            + "SinglePath", PreFix + File.separator
-            + "TreePath"};*/
-           /* + "2", PreFix + File.separator + "3", PreFix + File.separator + "4", PreFix + File.separator + "5",
-            PreFix + File.separator + "6", PreFix + File.separator + "7", PreFix + File.separator + "8",
-            PreFix + File.separator + "9", PreFix + File.separator + "TwoKmer", PreFix + File.separator + "ThreeKmer",
-            PreFix + File.separator + "SinglePath", PreFix + File.separator + "SimplePath",
-            PreFix + File.separator + "Path", PreFix + File.separator + "BridgePath",
-            PreFix + File.separator + "CyclePath", PreFix + File.separator + "RingPath",
-            PreFix + File.separator + "LongPath", PreFix + File.separator + "TreePath" };*/
+    + "tworeads3", PreFix + File.separator
+    + "tworeads_6"};*/
     private static final String ACTUAL_RESULT_DIR = "data/actual/pathmerge";
     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";
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/TipRemoveSmallTestSuite.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/TipRemoveSmallTestSuite.java
index e174bd9..def24e4 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/TipRemoveSmallTestSuite.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/TipRemoveSmallTestSuite.java
@@ -43,20 +43,10 @@
 public class TipRemoveSmallTestSuite extends TestSuite {
     private static final Logger LOGGER = Logger.getLogger(TipRemoveSmallTestSuite.class.getName());
     //P4ForMergeGraph/bin/read
-    public static final String PreFix = "data/actual"; //"graphbuildresult";
+    public static final String PreFix = "data/input"; //"graphbuildresult";
     public static final String[] TestDir = { PreFix + File.separator
-    + "bridgeadd/BridgeAddGraph/bin/tworeads"};/*, PreFix + File.separator
-            /*+ "CyclePath"};, PreFix + File.separator
-            + "SimplePath", PreFix + File.separator
-            + "SinglePath", PreFix + File.separator
-            + "TreePath"};*/
-           /* + "2", PreFix + File.separator + "3", PreFix + File.separator + "4", PreFix + File.separator + "5",
-            PreFix + File.separator + "6", PreFix + File.separator + "7", PreFix + File.separator + "8",
-            PreFix + File.separator + "9", PreFix + File.separator + "TwoKmer", PreFix + File.separator + "ThreeKmer",
-            PreFix + File.separator + "SinglePath", PreFix + File.separator + "SimplePath",
-            PreFix + File.separator + "Path", PreFix + File.separator + "BridgePath",
-            PreFix + File.separator + "CyclePath", PreFix + File.separator + "RingPath",
-            PreFix + File.separator + "LongPath", PreFix + File.separator + "TreePath" };*/
+    + "graphs/tipremove/fr_with_tip"};
+    //+ "bridgeadd/BridgeAddGraph/bin/tworeads"};
     private static final String ACTUAL_RESULT_DIR = "data/actual/tipremove";
     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";
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/graphbuilding/JobRunStepByStepTest.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/graphbuilding/JobRunStepByStepTest.java
index cc9e2d2..3531ec1 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/graphbuilding/JobRunStepByStepTest.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/graphbuilding/JobRunStepByStepTest.java
@@ -50,7 +50,7 @@
     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 DATA_INPUT_PATH = "data/input/singleread";
+    private static final String DATA_INPUT_PATH = "data/graphbuild.test/tworead3.txt";
     private static final String HDFS_INPUT_PATH = "/webmap";
     private static final String HDFS_OUTPUT_PATH = "/webmap_result";
 
diff --git a/genomix/genomix-pregelix/src/test/resources/jobs/BridgeRemoveGraph.xml b/genomix/genomix-pregelix/src/test/resources/jobs/BridgeRemoveGraph.xml
index b36258a..f9b801a 100644
--- a/genomix/genomix-pregelix/src/test/resources/jobs/BridgeRemoveGraph.xml
+++ b/genomix/genomix-pregelix/src/test/resources/jobs/BridgeRemoveGraph.xml
@@ -96,7 +96,7 @@
 <property><name>io.sort.mb</name><value>100</value></property>
 <property><name>mapred.local.dir</name><value>${hadoop.tmp.dir}/mapred/local</value></property>
 <property><name>io.sort.factor</name><value>10</value></property>
-<property><name>BasicPathMergeVertex.kmerSize</name><value>3</value></property>
+<property><name>BasicPathMergeVertex.kmerSize</name><value>5</value></property>
 <property><name>mapred.task.profile</name><value>false</value></property>
 <property><name>job.end.retry.interval</name><value>30000</value></property>
 <property><name>mapred.tasktracker.procfsbasedprocesstree.sleeptime-before-sigkill</name><value>5000</value></property>
diff --git a/genomix/genomix-pregelix/src/test/resources/jobs/BubbleMergeGraph.xml b/genomix/genomix-pregelix/src/test/resources/jobs/BubbleMergeGraph.xml
index 1b5cf0c..605a004 100644
--- a/genomix/genomix-pregelix/src/test/resources/jobs/BubbleMergeGraph.xml
+++ b/genomix/genomix-pregelix/src/test/resources/jobs/BubbleMergeGraph.xml
@@ -99,7 +99,7 @@
 <property><name>mapred.task.profile</name><value>false</value></property>
 <property><name>job.end.retry.interval</name><value>30000</value></property>
 <property><name>mapred.tasktracker.procfsbasedprocesstree.sleeptime-before-sigkill</name><value>5000</value></property>
-<property><name>BubbleMergeVertex.kmerSize</name><value>3</value></property>
+<property><name>BubbleMergeVertex.kmerSize</name><value>5</value></property>
 <property><name>mapred.jobtracker.completeuserjobs.maximum</name><value>100</value></property>
 <property><name>mapred.task.profile.reduces</name><value>0-2</value></property>
 <property><name>webinterface.private.actions</name><value>false</value></property>
@@ -122,7 +122,7 @@
 <property><name>mapred.map.tasks.speculative.execution</name><value>true</value></property>
 <property><name>mapred.inmem.merge.threshold</name><value>1000</value></property>
 <property><name>hadoop.logfile.size</name><value>10000000</value></property>
-<property><name>pregelix.vertexInputFormatClass</name><value>edu.uci.ics.genomix.pregelix.format.DataCleanInputFormat</value></property>
+<property><name>pregelix.vertexInputFormatClass</name><value>edu.uci.ics.genomix.pregelix.format.NaiveAlgorithmForPathMergeInputFormat</value></property>
 <property><name>mapred.job.queue.name</name><value>default</value></property>
 <property><name>mapred.job.tracker.persist.jobstatus.active</name><value>false</value></property>
 <property><name>pregelix.incStateLength</name><value>true</value></property>
diff --git a/genomix/genomix-pregelix/src/test/resources/jobs/P4ForMergeGraph.xml b/genomix/genomix-pregelix/src/test/resources/jobs/P4ForMergeGraph.xml
index ae0dc7e..5ef1509 100644
--- a/genomix/genomix-pregelix/src/test/resources/jobs/P4ForMergeGraph.xml
+++ b/genomix/genomix-pregelix/src/test/resources/jobs/P4ForMergeGraph.xml
@@ -96,7 +96,7 @@
 <property><name>io.sort.mb</name><value>100</value></property>
 <property><name>mapred.local.dir</name><value>${hadoop.tmp.dir}/mapred/local</value></property>
 <property><name>io.sort.factor</name><value>10</value></property>
-<property><name>BasicPathMergeVertex.kmerSize</name><value>3</value></property>
+<property><name>BasicPathMergeVertex.kmerSize</name><value>5</value></property>
 <property><name>mapred.task.profile</name><value>false</value></property>
 <property><name>job.end.retry.interval</name><value>30000</value></property>
 <property><name>mapred.tasktracker.procfsbasedprocesstree.sleeptime-before-sigkill</name><value>5000</value></property>
@@ -122,7 +122,7 @@
 <property><name>mapred.map.tasks.speculative.execution</name><value>true</value></property>
 <property><name>mapred.inmem.merge.threshold</name><value>1000</value></property>
 <property><name>hadoop.logfile.size</name><value>10000000</value></property>
-<property><name>pregelix.vertexInputFormatClass</name><value>edu.uci.ics.genomix.pregelix.format.NaiveAlgorithmForPathMergeInputFormat</value></property>
+<property><name>pregelix.vertexInputFormatClass</name><value>edu.uci.ics.genomix.pregelix.format.DataCleanInputFormat</value></property>
 <property><name>mapred.job.queue.name</name><value>default</value></property>
 <property><name>mapred.job.tracker.persist.jobstatus.active</name><value>false</value></property>
 <property><name>pregelix.incStateLength</name><value>true</value></property>
diff --git a/genomix/genomix-pregelix/src/test/resources/jobs/TipRemoveGraph.xml b/genomix/genomix-pregelix/src/test/resources/jobs/TipRemoveGraph.xml
index 1fcacc9..588cc9f 100644
--- a/genomix/genomix-pregelix/src/test/resources/jobs/TipRemoveGraph.xml
+++ b/genomix/genomix-pregelix/src/test/resources/jobs/TipRemoveGraph.xml
@@ -96,7 +96,7 @@
 <property><name>io.sort.mb</name><value>100</value></property>
 <property><name>mapred.local.dir</name><value>${hadoop.tmp.dir}/mapred/local</value></property>
 <property><name>io.sort.factor</name><value>10</value></property>
-<property><name>BasicPathMergeVertex.kmerSize</name><value>3</value></property>
+<property><name>BasicPathMergeVertex.kmerSize</name><value>5</value></property>
 <property><name>mapred.task.profile</name><value>false</value></property>
 <property><name>job.end.retry.interval</name><value>30000</value></property>
 <property><name>mapred.tasktracker.procfsbasedprocesstree.sleeptime-before-sigkill</name><value>5000</value></property>
@@ -122,7 +122,7 @@
 <property><name>mapred.map.tasks.speculative.execution</name><value>true</value></property>
 <property><name>mapred.inmem.merge.threshold</name><value>1000</value></property>
 <property><name>hadoop.logfile.size</name><value>10000000</value></property>
-<property><name>pregelix.vertexInputFormatClass</name><value>edu.uci.ics.genomix.pregelix.format.DataCleanInputFormat</value></property>
+<property><name>pregelix.vertexInputFormatClass</name><value>edu.uci.ics.genomix.pregelix.format.NaiveAlgorithmForPathMergeInputFormat</value></property>
 <property><name>mapred.job.queue.name</name><value>default</value></property>
 <property><name>mapred.job.tracker.persist.jobstatus.active</name><value>false</value></property>
 <property><name>pregelix.incStateLength</name><value>true</value></property>