diff --git a/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java b/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java
index feae86587..09b5af034 100755
--- a/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java
+++ b/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java
@@ -118,8 +118,8 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar
         if (!( walker instanceof TreeReducible ))
             throw new IllegalArgumentException("The GATK can currently run in parallel only with TreeReducible walkers");
 
+        traversalEngine.startTimers();
         ReduceTree reduceTree = new ReduceTree(this);
-
         initializeWalker(walker);
 
         for (Shard shard : shardStrategy)
diff --git a/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java b/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java
index 23e4b575e..1da0cdeed 100644
--- a/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java
+++ b/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java
@@ -45,6 +45,7 @@ public class LinearMicroScheduler extends MicroScheduler {
      * @param shardStrategy A strategy for sharding the data.
      */
     public Object execute(Walker walker, ShardStrategy shardStrategy) {
+        traversalEngine.startTimers();
         walker.initialize();
         Accumulator accumulator = Accumulator.create(engine,walker);
 
diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
index fb13a8dab..ea1e6d4fe 100755
--- a/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
@@ -96,10 +96,15 @@ public abstract class TraversalEngine<M,T,WalkerType extends Walker<M,T>,Provide
         if (mustPrint || nRecords == 1 || nRecords % N_RECORDS_TO_PRINT == 0 || maxElapsedIntervalForPrinting(curTime)) {
             this.lastProgressPrintTime = curTime;
             final double secsPer1MReads = (elapsed * 1000000.0) / nRecords;
-            if (loc != null)
-                logger.info(String.format("[PROGRESS] Traversed to %s, processing %,d %s in %.2f secs (%.2f secs per 1M %s)", loc, nRecords, getTraversalType(), elapsed, secsPer1MReads, getTraversalType()));
-            else
-                logger.info(String.format("[PROGRESS] Traversed %,d %s in %.2f secs (%.2f secs per 1M %s)", nRecords, getTraversalType(), elapsed, secsPer1MReads, getTraversalType()));
+
+            if ( nRecords == 1 )
+                logger.info("[INITIALIZATION COMPLETE; TRAVERSAL STARTING]");
+            else {
+                if (loc != null)
+                    logger.info(String.format("[PROGRESS] Traversed to %s, processing %,d %s in %.2f secs (%.2f secs per 1M %s)", loc, nRecords, getTraversalType(), elapsed, secsPer1MReads, getTraversalType()));
+                else
+                    logger.info(String.format("[PROGRESS] Traversed %,d %s in %.2f secs (%.2f secs per 1M %s)", nRecords, getTraversalType(), elapsed, secsPer1MReads, getTraversalType()));
+            }
         }   
     }
 
@@ -135,6 +140,12 @@ public abstract class TraversalEngine<M,T,WalkerType extends Walker<M,T>,Provide
      */
     public void initialize(GenomeAnalysisEngine engine) {
         this.engine = engine;
+    }
+
+    /**
+     * Should be called to indicate that we're going to process records and the timer should start ticking
+     */
+    public void startTimers() {
         lastProgressPrintTime = startTime = System.currentTimeMillis();
     }