diff --git a/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java b/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java
index 6119e20a6..77ac948e9 100644
--- a/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java
+++ b/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java
@@ -189,7 +189,8 @@ public class GATKExtensionsGenerator extends CommandLineProgram {
      */
     private static final List<String> gatkPackages = Arrays.asList(
             "org.broadinstitute.sting.gatk",
-            "org.broadinstitute.sting.analyzecovariates");
+            "org.broadinstitute.sting.analyzecovariates",
+            "");
 
     /**
      * Returns true if the class is part of the GATK.