diff --git a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
index 3a8431dca..de7439b85 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
@@ -293,9 +293,11 @@ public class GenomeAnalysisEngine {
         // create the output streams
         initializeOutputStreams(microScheduler.getOutputTracker());
 
-        logger.info("Creating shard strategy for " + readsDataSource.getReaderIDs().size() + " BAM files");
+        // Initializing the shard iterator / BAM schedule might take some time, so let the user know vaguely what's going on
+        logger.info("Preparing for traversal" +
+                    (readsDataSource.getReaderIDs().size() > 0 ? String.format(" over %d BAM files", readsDataSource.getReaderIDs().size()) : ""));
         Iterable<Shard> shardStrategy = getShardStrategy(readsDataSource,microScheduler.getReference(),intervals);
-        logger.info("Done creating shard strategy");
+        logger.info("Done preparing for traversal");
 
         // execute the microscheduler, storing the results
         return microScheduler.execute(this.walker, shardStrategy);
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShardBalancer.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShardBalancer.java
index 7772dbc1f..dc1b80efd 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShardBalancer.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShardBalancer.java
@@ -177,7 +177,9 @@ public class ReadShardBalancer extends ShardBalancer {
                 currentContigFilePointer = null;
                 List<FilePointer> nextContigFilePointers = new ArrayList<FilePointer>();
 
-                logger.info("Loading BAM index data for next contig");
+                if ( filePointers.hasNext() ) {
+                    logger.info("Loading BAM index data");
+                }
 
                 while ( filePointers.hasNext() ) {
 
@@ -215,8 +217,8 @@ public class ReadShardBalancer extends ShardBalancer {
                 }
 
                 if ( currentContigFilePointer != null ) {
-                    logger.info("Done loading BAM index data for next contig");
-                    logger.debug(String.format("Next contig FilePointer: %s", currentContigFilePointer));
+                    logger.info("Done loading BAM index data");
+                    logger.debug(String.format("Next FilePointer: %s", currentContigFilePointer));
                 }
             }