From d7090ef1586d87b4574e8f6d0057a29648e9ba2f Mon Sep 17 00:00:00 2001
From: Ron Levine <rlevine@broadinstitute.org>
Date: Fri, 21 Oct 2016 13:01:07 -0400
Subject: [PATCH] Write saved WARN messages to stderr instead of stdout

---
 .../gatk/utils/commandline/CommandLineProgram.java          | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/CommandLineProgram.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/CommandLineProgram.java
index 4f5afcc08..0cb132bd6 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/CommandLineProgram.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/CommandLineProgram.java
@@ -363,10 +363,10 @@ public abstract class CommandLineProgram {
      * @param listAppender  Appender for saving logging messages to a list
      */
     private static void printDoneAndLogMessages(final ListAppender listAppender) {
-        System.out.println("------------------------------------------------------------------------------------------");
-        System.out.print("Done. ");
+        System.err.println("------------------------------------------------------------------------------------------");
+        System.err.print("Done. ");
         listAppender.write();
-        System.out.println("------------------------------------------------------------------------------------------");
+        System.err.println("------------------------------------------------------------------------------------------");
     }
 
     /**