diff --git a/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java b/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java
index e1366e13e..fa9f7a645 100755
--- a/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java
+++ b/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java
@@ -142,6 +142,8 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar
 
         printOnTraversalDone(result);
 
+        getOutputTracker().close();
+
         return result;
     }
 
diff --git a/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java b/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java
index d525f3b7c..246472358 100644
--- a/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java
+++ b/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java
@@ -59,6 +59,8 @@ public class LinearMicroScheduler extends MicroScheduler {
 
         printOnTraversalDone(result);
 
+        getOutputTracker().close();
+
         return accumulator;
     }
 
diff --git a/java/src/org/broadinstitute/sting/gatk/io/OutputTracker.java b/java/src/org/broadinstitute/sting/gatk/io/OutputTracker.java
index 69a0be1f7..82c587d73 100755
--- a/java/src/org/broadinstitute/sting/gatk/io/OutputTracker.java
+++ b/java/src/org/broadinstitute/sting/gatk/io/OutputTracker.java
@@ -65,19 +65,16 @@ public abstract class OutputTracker {
         // Otherwise, initialize them separately.
         if( outFileName != null && outFileName.equals(errFileName) ) {
             outStub = errStub = new OutputStreamStub(new File(outFileName));
-            outStub.register(this);
-            outputs.put(outStub,null);
+            addOutput(outStub);
         }
         else {
             outStub = (outFileName != null) ? new OutputStreamStub(new File(outFileName))
                                             : new OutputStreamStub(System.out);
-            outStub.register(this);
-            outputs.put(outStub,null);
+            addOutput(outStub);
 
             errStub = (errFileName != null) ? new OutputStreamStub(new File(errFileName))
                                             : new OutputStreamStub(System.err);
-            errStub.register(this);
-            outputs.put(errStub,null);            
+            addOutput(errStub);
         }
     }
 
@@ -127,6 +124,20 @@ public abstract class OutputTracker {
         outputs.put(stub,null);
     }
 
+    /**
+     * Close down all existing output streams.
+     */
+    public void close() {
+        for( Stub stub: outputs.keySet() ) {
+            // If the stream hasn't yet been created, create it so that there's at least an empty file present.
+            if( outputs.get(stub) == null )
+                getTargetStream(stub);
+
+            // Close down the storage.
+            outputs.get(stub).close();
+        }
+    }
+
     /**
      * Collects the target stream for this data.
      * @param stub The stub for this stream.