diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h3/MergePathsH3.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h3/MergePathsH3.java
index 38dde9d..c2b0e52 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h3/MergePathsH3.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h3/MergePathsH3.java
@@ -40,6 +40,7 @@
         public static final byte IS_HEAD = 1 << 3;
         public static final byte IS_TAIL = 1 << 4;
         public static final byte IS_PSEUDOHEAD = 1 << 5;
+        public static final byte IS_COMPLETE = 1 << 6;
 
         public static String getFlagAsString(byte code) {
             // TODO: allow multiple flags to be set
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/pmcommon/PathNodeInitial.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/pmcommon/PathNodeInitial.java
index c8386ea..5fbf33f 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/pmcommon/PathNodeInitial.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/pmcommon/PathNodeInitial.java
@@ -34,6 +34,7 @@
 import org.apache.hadoop.mapred.RunningJob;
 import org.apache.hadoop.mapred.SequenceFileInputFormat;
 import org.apache.hadoop.mapred.SequenceFileOutputFormat;
+import org.apache.hadoop.mapred.lib.MultipleOutputs;
 import org.apache.hadoop.util.Tool;
 import org.apache.hadoop.util.ToolRunner;
 
@@ -126,27 +127,34 @@
                         output.collect(outputKey, outputValue);
                     }
                 }
+                // push this non-path node to the "complete" output
+                outputValue.set((byte) (MessageFlag.FROM_SELF | MessageFlag.IS_COMPLETE), key);
+                output.collect(key.getNodeID(), outputValue);
             }
         }
     }
 
     public static class PathNodeInitialReducer extends MapReduceBase implements
             Reducer<PositionWritable, MessageWritableNodeWithFlag, PositionWritable, MessageWritableNodeWithFlag> {
-
+        private MultipleOutputs mos;
+        private static final String COMPLETE_OUTPUT = "complete";
         private int KMER_SIZE;
         private MessageWritableNodeWithFlag inputValue;
         private MessageWritableNodeWithFlag outputValue;
         private NodeWritable nodeToKeep;
         private int count;
         private byte flag;
+        private boolean isComplete;
 
         public void configure(JobConf conf) {
+            mos = new MultipleOutputs(conf);
             KMER_SIZE = conf.getInt("sizeKmer", 0);
             inputValue = new MessageWritableNodeWithFlag(KMER_SIZE);
             outputValue = new MessageWritableNodeWithFlag(KMER_SIZE);
             nodeToKeep = new NodeWritable(KMER_SIZE);
         }
 
+        @SuppressWarnings("unchecked")
         @Override
         public void reduce(PositionWritable key, Iterator<MessageWritableNodeWithFlag> values,
                 OutputCollector<PositionWritable, MessageWritableNodeWithFlag> output, Reporter reporter)
@@ -155,19 +163,28 @@
             inputValue.set(values.next());
             if (!values.hasNext()) {
                 if ((inputValue.getFlag() & MessageFlag.FROM_SELF) > 0) {
-                    // FROM_SELF => need to keep this PATH node
-                    output.collect(key, inputValue);
+                    if ((inputValue.getFlag() & MessageFlag.IS_COMPLETE) > 0) {
+                        // non-path node.  Store in "complete" output
+                        mos.getCollector(COMPLETE_OUTPUT, reporter).collect(key, inputValue);
+                    } else {
+                        // FROM_SELF => need to keep this PATH node
+                        output.collect(key, inputValue);
+                    }
                 }
             } else {
                 // multiple inputs => possible HEAD or TAIL to a path node. note if HEAD or TAIL node 
                 count = 0;
                 flag = MessageFlag.EMPTY_MESSAGE;
+                isComplete = false;
                 while (true) { // process values; break when no more
                     count++;
                     if ((inputValue.getFlag() & MessageFlag.FROM_SELF) > 0) {
                         // SELF -> keep this node
                         flag |= MessageFlag.FROM_SELF;
                         nodeToKeep.set(inputValue.getNode());
+                        if ((inputValue.getFlag() & MessageFlag.IS_COMPLETE) > 0) {
+                            isComplete = true;
+                        }
                     } else if ((inputValue.getFlag() & MessageFlag.FROM_SUCCESSOR) > 0) {
                         flag |= MessageFlag.IS_TAIL;
                     } else if ((inputValue.getFlag() & MessageFlag.FROM_PREDECESSOR) > 0) {
@@ -176,7 +193,7 @@
                     if (!values.hasNext()) {
                         break;
                     } else {
-                        inputValue = values.next();
+                        inputValue.set(values.next());
                     }
                 }
                 if (count < 2) {
@@ -184,20 +201,24 @@
                             + String.valueOf(count));
                 }
                 if ((flag & MessageFlag.FROM_SELF) > 0) {
-                    // only keep simple path nodes
-                    outputValue.set(flag, nodeToKeep);
-                    output.collect(key, outputValue);
-                    
-                    reporter.incrCounter("genomix", "path_nodes", 1);
-                    if ((flag & MessageFlag.IS_HEAD) > 0) {
-                        reporter.incrCounter("genomix", "path_nodes_heads", 1);
-                    }
-                    if ((flag & MessageFlag.IS_TAIL) > 0) {
-                        reporter.incrCounter("genomix", "path_nodes_tails", 1);
+                    if ((flag & MessageFlag.IS_COMPLETE) > 0) {
+                        // non-path node.  Store in "complete" output
+                        mos.getCollector(COMPLETE_OUTPUT, reporter).collect(key, inputValue);
+                    } else {
+                        // only keep simple path nodes
+                        outputValue.set(flag, nodeToKeep);
+                        output.collect(key, outputValue);
+
+                        reporter.incrCounter("genomix", "path_nodes", 1);
+                        if ((flag & MessageFlag.IS_HEAD) > 0) {
+                            reporter.incrCounter("genomix", "path_nodes_heads", 1);
+                        }
+                        if ((flag & MessageFlag.IS_TAIL) > 0) {
+                            reporter.incrCounter("genomix", "path_nodes_tails", 1);
+                        }
                     }
                 } else {
-                    // this is a non-path node.
-                    // TODO: keep this node in a "completed" reducer
+                    throw new IOException("No SELF node recieved in reduce! key=" + key.toString() + " flag=" + flag);
                 }
             }
         }