diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/AnalyzeCovariatesIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/AnalyzeCovariatesIntegrationTest.java
index 485e3ddda..4dd20fc47 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/AnalyzeCovariatesIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/AnalyzeCovariatesIntegrationTest.java
@@ -147,7 +147,6 @@ public class AnalyzeCovariatesIntegrationTest extends WalkerTest {
             throws IOException  {
 
         final File afterFile = new File(TEST_DATA_DIR,afterFileName);
-        afterFile.deleteOnExit();
         final WalkerTestSpec spec = new WalkerTestSpec(
                 buildCommandLine(null,"%s",true,true,afterFile),
                 1,UserException.IncompatibleRecalibrationTableParameters.class);