diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/BaseTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/BaseTest.java
index 1c78574df..b8d60cf53 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/BaseTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/BaseTest.java
@@ -87,9 +87,6 @@ public abstract class BaseTest {
     /** our log, which we want to capture anything from org.broadinstitute.sting */
     public static final Logger logger = CommandLineUtils.getStingLogger();
 
-    private static final String CURRENT_DIRECTORY = System.getProperty("user.dir");
-    public static final String baseDirectory = System.getProperty("basedir", CURRENT_DIRECTORY) + "/";
-
     public static final String hg18Reference = "/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta";
     public static final String hg19Reference = "/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta";
     public static final String b36KGReference = "/humgen/1kg/reference/human_b36_both.fasta";
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MD5DB.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MD5DB.java
index 218906fdd..81c532434 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MD5DB.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MD5DB.java
@@ -49,7 +49,7 @@ public class MD5DB {
      */
     private static final int MAX_RECORDS_TO_READ = 1000000;
     private static final int MAX_RAW_DIFFS_TO_SUMMARIZE = -1;
-    public static final String LOCAL_MD5_DB_DIR = BaseTest.baseDirectory + "integrationtests";
+    public static final String LOCAL_MD5_DB_DIR = "integrationtests";
     public static final String GLOBAL_MD5_DB_DIR = "/humgen/gsa-hpprojects/GATK/data/integrationtests";
 
     // tracking and emitting a data file of origina and new md5s
@@ -95,7 +95,7 @@ public class MD5DB {
         File dir = new File(LOCAL_MD5_DB_DIR);
         if ( ! dir.exists() ) {
             System.out.printf("##### Creating MD5 db %s%n", LOCAL_MD5_DB_DIR);
-            if ( ! dir.mkdirs() ) {
+            if ( ! dir.mkdir() ) {
                 // Need to check AGAIN whether the dir exists, because we might be doing multi-process parallelism
                 // within the same working directory, and another GATK instance may have come along and created the
                 // directory between the calls to exists() and mkdir() above.