diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/ThreadLocalOutputTracker.java b/public/java/src/org/broadinstitute/sting/gatk/io/ThreadLocalOutputTracker.java
index 999deddd1..636787c69 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/io/ThreadLocalOutputTracker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/io/ThreadLocalOutputTracker.java
@@ -119,7 +119,7 @@ public class ThreadLocalOutputTracker extends OutputTracker {
 
         try {
             tempFile = File.createTempFile( stub.getClass().getName(), null );
-            tempFile.deleteOnExit();
+            //tempFile.deleteOnExit();
         }
         catch( IOException ex ) {
             throw new UserException.BadTmpDir("Unable to create temporary file for stub: " + stub.getClass().getName() );
diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java b/public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java
index 161179f84..72f8581dd 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java
@@ -194,6 +194,9 @@ public class VariantContextWriterStorage implements Storage<VariantContextWriter
             }
 
             source.close();
+            file.delete(); // this should be last to aid in debugging when the process fails
+        } catch (UserException e) {
+            throw new ReviewedStingException("BUG: intermediate file " + file + " is malformed, got error while reading", e);
         } catch (IOException e) {
             throw new UserException.CouldNotReadInputFile(file, "Error reading file in VCFWriterStorage: ", e);
         }