diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/DiagnoseTargets.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/DiagnoseTargets.java
index a3ac21ae0..4bd08294b 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/DiagnoseTargets.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/DiagnoseTargets.java
@@ -65,8 +65,7 @@ import org.broadinstitute.variant.variantcontext.*;
 import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
 import org.broadinstitute.variant.vcf.*;
 
-import java.io.FileWriter;
-import java.io.IOException;
+import java.io.PrintStream;
 import java.util.*;
 
 /**
@@ -200,11 +199,7 @@ public class DiagnoseTargets extends LocusWalker<Long, Long> {
         }
 
         if (thresholds.missingTargets != null) {
-            try {
-                thresholds.missingTargets.close();
-            } catch (IOException e) {
-                e.printStackTrace();
-            }
+            thresholds.missingTargets.close();
         }
     }
 
@@ -326,13 +321,9 @@ public class DiagnoseTargets extends LocusWalker<Long, Long> {
         }
     }
 
-    private void outputMissingInterval(final String contig, final int start, final int stop){
-        final FileWriter out = thresholds.missingTargets;
-        try {
-            out.write(String.format("%s:%d-%d\n", contig, start, stop));
-        } catch (IOException e) {
-            e.printStackTrace();
-        }
+    private void outputMissingInterval(final String contig, final int start, final int stop) {
+        final PrintStream out = thresholds.missingTargets;
+            out.println(String.format("%s:%d-%d", contig, start, stop));
     }
 
     /**
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 8c5a75148..ebe2192b4 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
@@ -49,7 +49,7 @@ package org.broadinstitute.sting.gatk.walkers.diagnostics.diagnosetargets;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 
-import java.io.FileWriter;
+import java.io.PrintStream;
 import java.util.LinkedList;
 import java.util.List;
 
@@ -117,7 +117,7 @@ final class ThresHolder {
     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)
-    public FileWriter missingTargets = null;
+    public PrintStream missingTargets = null;
 
     public final List<Metric> locusMetricList = new LinkedList<Metric>();
     public final List<Metric> sampleMetricList = new LinkedList<Metric>();