diff --git a/public/java/src/org/broadinstitute/sting/utils/nanoScheduler/NanoScheduler.java b/public/java/src/org/broadinstitute/sting/utils/nanoScheduler/NanoScheduler.java
index 4f9fedce3..89e44ce93 100644
--- a/public/java/src/org/broadinstitute/sting/utils/nanoScheduler/NanoScheduler.java
+++ b/public/java/src/org/broadinstitute/sting/utils/nanoScheduler/NanoScheduler.java
@@ -51,7 +51,8 @@ public class NanoScheduler<InputType, MapType, ReduceType> {
 
     final int bufferSize;
     final int nThreads;
-    final ExecutorService executor;
+    final ExecutorService inputExecutor;
+    final ExecutorService mapExecutor;
     boolean shutdown = false;
     boolean debug = false;
 
@@ -75,7 +76,8 @@ public class NanoScheduler<InputType, MapType, ReduceType> {
 
         this.bufferSize = bufferSize;
         this.nThreads = nThreads;
-        this.executor = nThreads == 1 ? null : Executors.newFixedThreadPool(nThreads-1);
+        this.mapExecutor = nThreads == 1 ? null : Executors.newFixedThreadPool(nThreads-1);
+        this.inputExecutor = Executors.newSingleThreadExecutor();
 
         // start timing the time spent outside of the nanoScheduler
         outsideSchedulerTimer.start();
@@ -107,10 +109,10 @@ public class NanoScheduler<InputType, MapType, ReduceType> {
     public void shutdown() {
         outsideSchedulerTimer.stop();
 
-        if ( executor != null ) {
-            final List<Runnable> remaining = executor.shutdownNow();
+        if ( mapExecutor != null ) {
+            final List<Runnable> remaining = mapExecutor.shutdownNow();
             if ( ! remaining.isEmpty() )
-                throw new IllegalStateException("Remaining tasks found in the executor, unexpected behavior!");
+                throw new IllegalStateException("Remaining tasks found in the mapExecutor, unexpected behavior!");
         }
         shutdown = true;
 
@@ -236,8 +238,8 @@ public class NanoScheduler<InputType, MapType, ReduceType> {
         boolean done = false;
 
         final BlockingQueue<InputDatum> inputQueue = new LinkedBlockingDeque<InputDatum>(bufferSize);
-        final InputProducer inputProducer = new InputProducer(inputReader, inputQueue);
-        inputProducer.start();
+
+        inputExecutor.submit(new InputProducer(inputReader, inputQueue));
 
         while ( ! done ) {
             try {
@@ -247,7 +249,7 @@ public class NanoScheduler<InputType, MapType, ReduceType> {
 
                 if ( ! inputs.isEmpty() ) {
                     // send jobs for map
-                    final Queue<Future<MapType>> mapQueue = submitMapJobs(map, executor, inputs);
+                    final Queue<Future<MapType>> mapQueue = submitMapJobs(map, mapExecutor, inputs);
 
                     // send off the reduce job, and block until we get at least one reduce result
                     sum = reduceSerial(reduce, mapQueue, sum);
@@ -311,7 +313,7 @@ public class NanoScheduler<InputType, MapType, ReduceType> {
         return new Pair<List<InputType>, Boolean>(inputs, done);
     }
 
-    private class InputProducer extends Thread {
+    private class InputProducer implements Runnable {
         final Iterator<InputType> inputReader;
         final BlockingQueue<InputDatum> outputQueue;