diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/ThresHolder.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/ThresHolder.java
index ebe2192b4..a6cbc1da3 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/ThresHolder.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/ThresHolder.java
@@ -116,7 +116,7 @@ final class ThresHolder {
     @Argument(fullName = "quality_status_threshold", shortName = "stQ", doc = "The proportion of the loci needed for calling POOR_QUALITY", required = false)
     public double qualityStatusThreshold = 0.50;
 
-    @Output(fullName = "missing_intervals", shortName = "missing", doc ="Produces a file with the intervals that don't pass filters", required = false)
+    @Output(fullName = "missing_intervals", shortName = "missing", defaultToStdout = false, doc ="Produces a file with the intervals that don't pass filters", required = false)
     public PrintStream missingTargets = null;
 
     public final List<Metric> locusMetricList = new LinkedList<Metric>();