diff --git a/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java b/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
index 0daad2c2b..4f9031329 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
@@ -118,17 +118,24 @@ public class CommandLineGATK extends CommandLineExecutable {
     public static final String DISK_QUOTA_EXCEEDED_ERROR = "Disk quota exceeded";
 
     private static void checkForMaskedUserErrors(final Throwable t) {
+        // masked out of memory error
+        if ( t instanceof OutOfMemoryError )
+            exitSystemWithUserError(new UserException.NotEnoughMemory());
+        // masked user error
+        if ( t instanceof UserException || t instanceof TribbleException )
+            exitSystemWithUserError(new UserException(t.getMessage()));
+
+        // no message means no masked error
         final String message = t.getMessage();
         if ( message == null )
             return;
 
-        // we know what to do about the common "Too many open files" error
+        // too many open files error
         if ( message.contains("Too many open files") )
             exitSystemWithUserError(new UserException.TooManyOpenFiles());
 
         // malformed BAM looks like a SAM file
-        if ( message.contains(PICARD_TEXT_SAM_FILE_ERROR_1) ||
-                message.contains(PICARD_TEXT_SAM_FILE_ERROR_2) )
+        if ( message.contains(PICARD_TEXT_SAM_FILE_ERROR_1) || message.contains(PICARD_TEXT_SAM_FILE_ERROR_2) )
             exitSystemWithSamError(t);
 
         // can't close tribble index when writing
@@ -138,12 +145,10 @@ public class CommandLineGATK extends CommandLineExecutable {
         // disk is full
         if ( message.contains(NO_SPACE_LEFT_ON_DEVICE_ERROR) || message.contains(DISK_QUOTA_EXCEEDED_ERROR) )
             exitSystemWithUserError(new UserException.NoSpaceOnDevice());
-        if ( t.getCause() != null && (t.getCause().getMessage().contains(NO_SPACE_LEFT_ON_DEVICE_ERROR) || t.getCause().getMessage().contains(DISK_QUOTA_EXCEEDED_ERROR)) )
-            exitSystemWithUserError(new UserException.NoSpaceOnDevice());
 
-        // masked out of memory error
-        if ( t.getCause() != null && t.getCause() instanceof OutOfMemoryError )
-            exitSystemWithUserError(new UserException.NotEnoughMemory());
+        // masked error wrapped in another one
+        if ( t.getCause() != null )
+            checkForMaskedUserErrors(t.getCause());
     }
 
     /**