diff --git a/src/main/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBImport.java b/src/main/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBImport.java
index 783b520f272..b42d728f0f2 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBImport.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBImport.java
@@ -394,7 +394,7 @@ public final class GenomicsDBImport extends GATKTool {
 
     //executor service used when vcfInitializerThreads > 1
     private ExecutorService inputPreloadExecutorService;
-    
+
     /**
      * Get the largest interval per contig that contains the intervals specified on the command line.
      * @param getIntervals intervals to be transformed
diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/PileupSparkIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/PileupSparkIntegrationTest.java
index 4af39b776ac..98995ad319a 100644
--- a/src/test/java/org/broadinstitute/hellbender/tools/spark/PileupSparkIntegrationTest.java
+++ b/src/test/java/org/broadinstitute/hellbender/tools/spark/PileupSparkIntegrationTest.java
@@ -25,9 +25,15 @@ public Object[][] shuffleParameters() {
         return new Object[][] { { false }, { true } };
     }
 
+    private File createAndDeleteTempFile() {
+        final File out = IOUtils.createTempFile("out", ".txt");
+        out.delete();
+        return out;
+    }
+    
     @Test(dataProvider = "shuffle")
     public void testSimplePileup(boolean useShuffle) throws Exception {
-        final File out = createTempFile();
+        final File out = createAndDeleteTempFile();
         final ArgumentsBuilder args = new ArgumentsBuilder();
         args.addRaw("--input");
         args.addRaw(NA12878_20_21_WGS_bam);
@@ -47,7 +53,7 @@ public void testSimplePileup(boolean useShuffle) throws Exception {
 
     @Test(dataProvider = "shuffle")
     public void testVerbosePileup(boolean useShuffle) throws Exception {
-        final File out = createTempFile();
+        final File out = createAndDeleteTempFile();
         final ArgumentsBuilder args = new ArgumentsBuilder();
         args.addRaw("--input");
         args.addRaw(NA12878_20_21_WGS_bam);
@@ -68,7 +74,7 @@ public void testVerbosePileup(boolean useShuffle) throws Exception {
 
     @Test(dataProvider = "shuffle")
     public void testFeaturesPileup(boolean useShuffle) throws Exception {
-        final File out = createTempFile();
+        final File out = createAndDeleteTempFile();
         final ArgumentsBuilder args = new ArgumentsBuilder();
         args.addRaw("--input");
         args.addRaw(NA12878_20_21_WGS_bam);
@@ -89,7 +95,7 @@ public void testFeaturesPileup(boolean useShuffle) throws Exception {
 
     @Test(dataProvider = "shuffle")
     public void testInsertLengthPileup(boolean useShuffle) throws Exception {
-        final File out = createTempFile();
+        final File out = createAndDeleteTempFile();
         final ArgumentsBuilder args = new ArgumentsBuilder();
         args.addRaw("--input");
         args.addRaw(NA12878_20_21_WGS_bam);
@@ -122,7 +128,7 @@ public void testFeaturesPileupHdfs(boolean useShuffle) throws Exception {
             cluster.getFileSystem().copyFromLocalFile(new Path(dbsnp_138_b37_20_21_vcf), vcfPath);
             cluster.getFileSystem().copyFromLocalFile(new Path(dbsnp_138_b37_20_21_vcf + ".idx"), idxPath);
 
-            final File out = createTempFile();
+            final File out = createAndDeleteTempFile();
             final ArgumentsBuilder args = new ArgumentsBuilder();
             args.addRaw("--input");
             args.addRaw(NA12878_20_21_WGS_bam);
diff --git a/src/testUtils/java/org/broadinstitute/hellbender/testutils/BaseTest.java b/src/testUtils/java/org/broadinstitute/hellbender/testutils/BaseTest.java
index 988a6f8cc3c..aacf175b33e 100644
--- a/src/testUtils/java/org/broadinstitute/hellbender/testutils/BaseTest.java
+++ b/src/testUtils/java/org/broadinstitute/hellbender/testutils/BaseTest.java
@@ -353,6 +353,15 @@ public static File createTempDir(final String prefix){
         return IOUtils.createTempDir(prefix);
     }
 
+    /**
+     * Creates an empty temp directory which will be deleted on exit after tests are complete
+     *
+     * @return an empty directory will be deleted after the program exits
+     */
+    public static File createTempDir(){
+        return createTempDir("tmp");
+    }
+
     /**
      * Log this message so that it shows up inline during output as well as in html reports
      */