diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/qc/TransferReadTags.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/qc/TransferReadTags.java
index 9421e35f21e..c5b263d58b8 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/qc/TransferReadTags.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/qc/TransferReadTags.java
@@ -94,7 +94,11 @@ public void onTraversalStart(){
         if (unmappedSamIterator.hasNext()){
             currentUnmappedRead = unmappedSamIterator.next();
         } else {
-            throw new UserException("unmapped sam iterator is empty.");
+            if (alignedSamIterator.hasNext()) {
+                throw new UserException("unmapped sam iterator is empty and aligned sam iterator is not.");
+            } else {
+                logger.warn("Input data contains no reads.  Output will also contain no reads.");
+            }
         }
 
         writer = createSAMWriter(new GATKPath(outSamFile.getAbsolutePath()), false);