diff --git a/java/src/org/broadinstitute/sting/gatk/io/storage/OutputStreamStorage.java b/java/src/org/broadinstitute/sting/gatk/io/storage/OutputStreamStorage.java
index 8f71eaa57..002951b99 100644
--- a/java/src/org/broadinstitute/sting/gatk/io/storage/OutputStreamStorage.java
+++ b/java/src/org/broadinstitute/sting/gatk/io/storage/OutputStreamStorage.java
@@ -87,6 +87,11 @@ public class OutputStreamStorage extends OutputStream implements Storage<OutputS
      * @{inheritDoc}
      */
     public void close() {
+        // Don't close System.out or System.err; this'll cause trouble
+        // with subsequent code running in this VM.
+        if( outputStream == System.out || outputStream == System.err )
+            return;
+        
         try {
             outputStream.close();
         }
diff --git a/java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamStub.java b/java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamStub.java
index 5722d6ca2..5cf84c5a2 100644
--- a/java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamStub.java
+++ b/java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamStub.java
@@ -105,7 +105,7 @@ public class OutputStreamStub extends OutputStream implements Stub<OutputStream>
      * @{inheritDoc}
      */
     public void flush() throws IOException {
-        outputTracker.getStorage(this).close();
+        outputTracker.getStorage(this).flush();
     }
 
     /**