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 14d462518..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
@@ -233,6 +233,7 @@ public class ValidationAmplicons extends RodWalker<Integer,Integer> {
             lowerRepeats();
         } else {
             lowerNonUniqueSegments();
+            aligner.close();
         }
         print();
     }
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmpliconsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmpliconsIntegrationTest.java
index 6528f5795..95f4ac0ae 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmpliconsIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmpliconsIntegrationTest.java
@@ -14,7 +14,7 @@ import java.util.Arrays;
  */
 public class ValidationAmpliconsIntegrationTest extends WalkerTest {
 
-    @Test
+    @Test(enabled=true)
     public void testWikiExample() {
         String siteVCF = validationDataLocation + "sites_to_validate.vcf";
         String maskVCF = validationDataLocation + "amplicon_mask_sites.vcf";
@@ -27,7 +27,7 @@ public class ValidationAmpliconsIntegrationTest extends WalkerTest {
         executeTest("Test probes", spec);
     }
 
-    @Test
+    @Test(enabled=true)
     public void testWikiExampleNoBWA() {
         String siteVCF = validationDataLocation + "sites_to_validate.vcf";
         String maskVCF = validationDataLocation + "amplicon_mask_sites.vcf";
@@ -40,7 +40,7 @@ public class ValidationAmpliconsIntegrationTest extends WalkerTest {
         executeTest("Test probes", spec);
     }
 
-    @Test
+    @Test(enabled=true)
     public void testWikiExampleMonoFilter() {
         String siteVCF = validationDataLocation + "sites_to_validate.vcf";
         String maskVCF = validationDataLocation + "amplicon_mask_sites.vcf";