diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java b/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java
index 10a90684f..edfed5e50 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java
@@ -284,7 +284,7 @@ public class ReferenceOrderedData<ROD extends ReferenceOrderedDatum> implements
                 }
                 catch( MalformedGenomeLocException ex ) {
                     if( firstFailure ) {
-                        Utils.warnUser("Failed to parse contig on line '" + line + "'.  Skipping ahead to the next recognized GenomeLoc.");
+                        Utils.warnUser("Failed to parse contig on line '" + line + "'.  The reason given was: " + ex.getMessage() + " Skipping ahead to the next recognized GenomeLoc. ");
                         firstFailure = false;
                     }
                     if( !parser.hasNext() )
diff --git a/java/src/org/broadinstitute/sting/utils/GenomeLoc.java b/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
index b872f9da7..e6b0a39d1 100644
--- a/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
+++ b/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
@@ -137,7 +137,7 @@ public class GenomeLoc implements Comparable<GenomeLoc>, Cloneable {
      */
     public static GenomeLoc parseGenomeLoc( final String contig, long start, long stop ) {
         if( !isContigValid(contig) )
-            throw new MalformedGenomeLocException("Contig " + contig + " is not within installed in the GATK sequence dictionary derived from the reference.");
+            throw new MalformedGenomeLocException("Contig " + contig + " does not match any contig in the GATK sequence dictionary derived from the reference.");
         return new GenomeLoc(contig,start,stop);
     }
 
@@ -198,7 +198,7 @@ public class GenomeLoc implements Comparable<GenomeLoc>, Cloneable {
         }
 
         if( !isContigValid(contig) )
-            throw new MalformedGenomeLocException("Contig " + contig + " is not within installed in the GATK sequence dictionary derived from the reference.");
+            throw new MalformedGenomeLocException("Contig " + contig + " does not match any contig in the GATK sequence dictionary derived from the reference.");
 
         GenomeLoc loc = parseGenomeLoc(contig,start,stop);
  //       System.out.printf("  => Parsed location '%s' into %s%n", str, loc);
diff --git a/java/src/org/broadinstitute/sting/utils/Utils.java b/java/src/org/broadinstitute/sting/utils/Utils.java
index a47ce0ab3..933a681c0 100755
--- a/java/src/org/broadinstitute/sting/utils/Utils.java
+++ b/java/src/org/broadinstitute/sting/utils/Utils.java
@@ -29,7 +29,7 @@ public class Utils {
         logger.warn(String.format("********************************************************************************"));
         logger.warn(String.format("* WARNING:"));
         logger.warn(String.format("*"));
-        logger.warn(String.format("* %s", msg));
+        prettyPrintWarningMessage(msg);
         logger.warn(String.format("********************************************************************************"));
     }
 
@@ -43,6 +43,22 @@ public class Utils {
         throw new RuntimeException(msg);
     }
 
+    /**
+     * pretty print the warning message supplied
+     * @param message the message
+     */
+    private static void prettyPrintWarningMessage(String message) {
+        StringBuilder builder = new StringBuilder(message);
+        while (builder.length() > 70) {
+            int space = builder.lastIndexOf(" ", 70);
+            if (space <= 0) space = 70;
+            logger.warn(String.format("* %s", builder.substring(0,space)));
+            builder.delete(0,space + 1);
+        }
+        logger.warn(String.format("* %s", builder));
+    }
+
+
     public static SAMFileWriter createSAMFileWriterWithCompression(SAMFileHeader header, boolean presorted, String file, int compression) {
         if (file.endsWith(".bam"))
             return new SAMFileWriterFactory().makeBAMWriter(header, presorted, new File(file), compression);