diff --git a/java/src/org/broadinstitute/sting/secondarybase/AnnotateSecondaryBase.java b/java/src/org/broadinstitute/sting/secondarybase/AnnotateSecondaryBase.java
index 03d94a298..010455ce7 100755
--- a/java/src/org/broadinstitute/sting/secondarybase/AnnotateSecondaryBase.java
+++ b/java/src/org/broadinstitute/sting/secondarybase/AnnotateSecondaryBase.java
@@ -60,9 +60,6 @@ public class AnnotateSecondaryBase extends CommandLineProgram {
         while ((rr = iparser.next()) != null) {
             FourProbRead fpr = model.call(rr);
 
-            System.out.println(rr.getSequenceAsString());
-            System.out.println(fpr.getPrimaryBaseSequence());
-
             SAMRecord sr = constructSAMRecord(rr, fpr, sfh, RUN_BARCODE);
             sfw.addAlignment(sr);
         }