From ed50814ccba7fe72f296c466e0abf64d7923c51d Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Wed, 21 Nov 2012 15:57:05 -0500
Subject: [PATCH] Finally found a case where user errors were being masked
 behind other errors and could debug.  It turns out that the
 checkForMaskedUserErrors() method needs to run recursively over all levels
 (calling exception.getCause()) to check for the original cause.

---
 .../sting/gatk/CommandLineGATK.java           | 21 ++++++++++++-------
 1 file changed, 13 insertions(+), 8 deletions(-)

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());
     }
 
     /**