From 7858ffec320a646eabc4aae5da9dda39530bc45e Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 4 Aug 2010 20:40:28 +0000
Subject: [PATCH] Spit out the error in the warning message so that Sendu can
 tell me what his problem is

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3942 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../variantrecalibration/GenerateVariantClustersWalker.java     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java
index 21c5f7853..211882ab2 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java
@@ -244,7 +244,7 @@ public class GenerateVariantClustersWalker extends RodWalker<ExpandingArrayList<
             try {
                 Runtime.getRuntime().exec( rScriptCommandLine );
             } catch ( IOException e ) {
-                Utils.warnUser("Unable to execute the RScript command.  While not critical to the calculations themselves, the script outputs a report that is extremely useful for confirming that the clustering proceded as expected.  We highly recommend trying to rerun the script manually if possible.");
+                Utils.warnUser("Unable to execute the RScript command because of [" + e.getMessage() + "].  While not critical to the calculations themselves, the script outputs a report that is extremely useful for confirming that the clustering proceded as expected.  We highly recommend trying to rerun the script manually if possible.");
             }
         }
     }