diff --git a/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java b/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
index bc4c181be..870492e42 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
@@ -35,6 +35,7 @@ import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
 import org.broadinstitute.sting.gatk.refdata.tracks.FeatureManager;
 import org.broadinstitute.sting.gatk.walkers.Attribution;
 import org.broadinstitute.sting.gatk.walkers.Walker;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.help.*;
 import org.broadinstitute.sting.utils.text.TextFormattingUtils;
@@ -120,9 +121,13 @@ public class CommandLineGATK extends CommandLineExecutable {
         if ( message.indexOf("Too many open files") != -1 )
             exitSystemWithUserError(new UserException.TooManyOpenFiles());
 
-        // Malformed BAM looks like a SAM file
+        // malformed BAM looks like a SAM file
         if ( message.indexOf("Cannot use index file with textual SAM file") != -1 )
             exitSystemWithSamError(t);
+
+        // can't close tribble index when writing
+        if ( message.indexOf("Unable to close index for") != -1 )
+            exitSystemWithUserError(new UserException(t.getCause().getMessage()));
     }
 
     /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java b/public/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java
index 9920213a3..bb0344848 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java
@@ -6,11 +6,11 @@ import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider;
 import org.broadinstitute.sting.gatk.datasources.reads.Shard;
 import org.broadinstitute.sting.gatk.io.ThreadLocalOutputTracker;
 import org.broadinstitute.sting.gatk.traversals.TraversalEngine;
-import org.broadinstitute.sting.gatk.walkers.LocusWalker;
 import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.util.concurrent.Callable;
+import java.util.concurrent.ExecutionException;
 /**
  * User: hanna
  * Date: Apr 29, 2009
@@ -79,6 +79,10 @@ public class ShardTraverser implements Callable {
             microScheduler.reportShardTraverseTime(endTime-startTime);
 
             return accumulator;
+        } catch(Throwable t) {
+            // Notify that an exception has occurred
+            microScheduler.handleException(new ExecutionException(t));
+            throw new RuntimeException(t);
         } finally {
             synchronized(this) {
                 complete = true;