diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java
index 7e39d2658..cb03d4c61 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java
@@ -228,14 +228,12 @@ public class ValidationAmplicons extends RodWalker<Integer,Integer> {
     }
 
     public void onTraversalDone(Integer fin ) {
-        if(aligner != null)
-            aligner.close();
-
         validateSequence();
         if ( doNotUseBWA ) {
             lowerRepeats();
         } else {
             lowerNonUniqueSegments();
+            aligner.close();
         }
         print();
     }