diff --git a/playground/java/src/org/broadinstitute/sting/atk/AnalysisTK.java b/playground/java/src/org/broadinstitute/sting/atk/AnalysisTK.java
index bb9e0e3c1..86ac6ba49 100644
--- a/playground/java/src/org/broadinstitute/sting/atk/AnalysisTK.java
+++ b/playground/java/src/org/broadinstitute/sting/atk/AnalysisTK.java
@@ -75,7 +75,6 @@ public class AnalysisTK extends CommandLineProgram {
         }
 
         this.engine = new TraversalEngine(INPUT_FILE, REF_FILE_ARG, rods);
-        engine.initialize(ENABLED_THREADED_IO.toLowerCase().equals("true"));
         //engine.testReference();
 
         ValidationStringency strictness;
@@ -97,6 +96,8 @@ public class AnalysisTK extends CommandLineProgram {
         engine.setDebugging(! ( DEBUGGING_STR == null || DEBUGGING_STR.toLowerCase().equals("true")));
         engine.setMaxReads(Integer.parseInt(MAX_READS_ARG));
 
+        engine.initialize(ENABLED_THREADED_IO.toLowerCase().equals("true"));
+
         if ( REGION_STR != null ) {
             engine.setLocation(REGION_STR);
         }