diff --git a/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java b/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java
index 44f3730c6..543d2f6d9 100755
--- a/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java
+++ b/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java
@@ -52,6 +52,11 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar
     private final Queue<Shard> traverseTasks = new LinkedList<Shard>();
     private final Queue<TreeReduceTask> reduceTasks = new LinkedList<TreeReduceTask>();
 
+    /**
+     * An exception that's occurred in this traversal.  If null, no exception has occurred.
+     */
+    private Throwable error = null;
+
     /**
      * Keep a queue of shard traversals, and constantly monitor it to see what output
      * merge tasks remain.
@@ -126,6 +131,10 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar
         totalTraversals = traverseTasks.size();
 
         while (isShardTraversePending() || isTreeReducePending()) {
+            // Check for errors during execution.
+            if(hasTraversalErrorOccurred())
+                throw new StingException("An error has occurred during the traversal.",getTraversalError());
+
             // Too many files sitting around taking up space?  Merge them.
             if (isMergeLimitExceeded())
                 mergeExistingOutput(false);
@@ -343,6 +352,27 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar
         return reducer;
     }
 
+    /**
+     * Detects whether an execution error has occurred.
+     * @return True if an error has occurred.  False otherwise.
+     */
+    private synchronized boolean hasTraversalErrorOccurred() {
+        return error != null;
+    }
+
+    private synchronized Throwable getTraversalError() {
+        if(!hasTraversalErrorOccurred())
+            throw new StingException("User has attempted to retrieve a traversal error when none exists");
+        return error;
+    }
+
+    /**
+     * Allows other threads to notify of an error during traversal.
+     */
+    protected synchronized void notifyOfTraversalError(Throwable error) {
+        this.error = error;    
+    }
+
 
     /** A small wrapper class that provides the TreeReducer interface along with the FutureTask semantics. */
     private class TreeReduceTask extends FutureTask {
diff --git a/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java b/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java
index 40d194341..cf110d1e2 100755
--- a/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java
+++ b/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java
@@ -81,6 +81,11 @@ public class ShardTraverser implements Callable {
 
             return accumulator;
         }
+        catch(Throwable t) {
+            // Notify that an exception has occurred and rethrow it.
+            microScheduler.notifyOfTraversalError(t);
+            throw new StingException("An error has occurred during traversal",t);
+        }
         finally {
             synchronized(this) {
                 complete = true;
diff --git a/java/src/org/broadinstitute/sting/gatk/executive/TreeReducer.java b/java/src/org/broadinstitute/sting/gatk/executive/TreeReducer.java
index 4ea2ee447..5b49f762d 100755
--- a/java/src/org/broadinstitute/sting/gatk/executive/TreeReducer.java
+++ b/java/src/org/broadinstitute/sting/gatk/executive/TreeReducer.java
@@ -1,6 +1,7 @@
 package org.broadinstitute.sting.gatk.executive;
 
 import org.broadinstitute.sting.gatk.walkers.TreeReducible;
+import org.broadinstitute.sting.utils.StingException;
 
 import java.util.concurrent.Callable;
 import java.util.concurrent.Future;
@@ -88,10 +89,12 @@ public class TreeReducer implements Callable {
                 result = walker.treeReduce( lhs.get(), rhs.get() );
         }
         catch( InterruptedException ex ) {
-            throw new RuntimeException("Hierarchical reduce interrupted", ex);
+            microScheduler.notifyOfTraversalError(ex);
+            throw new StingException("Hierarchical reduce interrupted", ex);
         }
         catch( ExecutionException ex ) {
-            throw new RuntimeException("Hierarchical reduce failed", ex);
+            microScheduler.notifyOfTraversalError(ex);
+            throw new StingException("Hierarchical reduce failed", ex);
         }
 
         long endTime = System.currentTimeMillis();