diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/CommandLineProgram.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/CommandLineProgram.java
index 8c7e11f35..8b1a390f4 100644
--- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/CommandLineProgram.java
+++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/CommandLineProgram.java
@@ -277,19 +277,19 @@ public abstract class CommandLineProgram {
         Level par;
         if (logging_level.toUpperCase().equals("DEBUG")) {
             par = Level.DEBUG;
-        } else if (logging_level.toUpperCase().equals("ERROR")) {
-            par = Level.ERROR;
-        } else if (logging_level.toUpperCase().equals("FATAL")) {
-            par = Level.FATAL;
         } else if (logging_level.toUpperCase().equals("INFO")) {
             par = Level.INFO;
         } else if (logging_level.toUpperCase().equals("WARN")) {
             par = Level.WARN;
+        } else if (logging_level.toUpperCase().equals("ERROR")) {
+            par = Level.ERROR;
+        } else if (logging_level.toUpperCase().equals("FATAL")) {
+            par = Level.FATAL;
         } else if (logging_level.toUpperCase().equals("OFF")) {
             par = Level.OFF;
         } else {
             // we don't understand the logging level, let's get out of here
-            throw new ArgumentException("Unable to match: " + logging_level + " to a logging level, make sure it's a valid level (INFO, DEBUG, ERROR, FATAL, OFF)");
+            throw new ArgumentException("Unable to match: " + logging_level + " to a logging level, make sure it's a valid level (DEBUG, INFO, WARN, ERROR, FATAL, OFF)");
         }
 
         Logger.getRootLogger().setLevel(par);
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));
     }
 
     /**