diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/CommandLineUtils.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/CommandLineUtils.java
index ddedda054..cb9a781c3 100644
--- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/CommandLineUtils.java
+++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/CommandLineUtils.java
@@ -173,7 +173,7 @@ public class CommandLineUtils {
         }
         // Extracted from BasicConfigurator.configure(), but only applied to the Sting logger.
         Logger.getRootLogger().addAppender(new ConsoleAppender(
-                    new PatternLayout(PatternLayout.TTCC_CONVERSION_PATTERN)));
+                    new PatternLayout(PatternLayout.TTCC_CONVERSION_PATTERN), ConsoleAppender.SYSTEM_ERR));
     }
 
     /**