diff --git a/java/src/org/broadinstitute/sting/gatk/executive/MicroManager.java b/java/src/org/broadinstitute/sting/gatk/executive/MicroManager.java
index 362431efb..133b9c4c3 100644
--- a/java/src/org/broadinstitute/sting/gatk/executive/MicroManager.java
+++ b/java/src/org/broadinstitute/sting/gatk/executive/MicroManager.java
@@ -103,6 +103,7 @@ public class MicroManager {
             throw new RuntimeException( ex );
         }
 
+        walker.initialize();
         Object accumulator = ((LocusWalker<?,?>)walker).reduceInit();
 
         for(Shard shard: shardStrategy) {