diff --git a/build.xml b/build.xml
index e2063ea45..7c14ba80d 100644
--- a/build.xml
+++ b/build.xml
@@ -199,7 +199,7 @@
     <target name="test.compile" depends="compile">
         <echo message="Sting: Compiling test cases!"/>
         <mkdir dir="${test.classes}"/>
-        <javac destdir="${test.classes}" debug="on" optimize="on">
+        <javac destdir="${test.classes}" debug="true" optimize="on">
             <src path="${test.sources}"/>
             <classpath>
                 <path refid="external.dependencies"/>
@@ -214,9 +214,8 @@
     <target name="test" depends="test.compile" description="Run unit tests">
         <mkdir dir="${report}"/>
         <echo message="Sting: Running test cases!"/>
-        <junit printsummary="yes" showoutput="yes" clonevm="yes" haltonfailure="yes">
-            <formatter type="plain"/>
-
+        <junit printsummary="yes" showoutput="yes" clonevm="yes" haltonfailure="yes" failureProperty="test.failure">
+            <formatter type="brief" usefile="false" />
             <classpath>
                 <path refid="external.dependencies"/>
                 <pathelement location="build"/>
@@ -227,9 +226,11 @@
             <batchtest fork="yes" todir="${report}">
                 <fileset dir="${test.classes}">
                     <include name="**/*.class"/>
+                    <exclude name="**/BaseTest.class"/>
                 </fileset>
             </batchtest>
         </junit>
+        <fail message="test failed" if="test.failure" />
 
     </target>
 
diff --git a/java/test/org/broadinstitute/sting/gatk/dataSources/shards/ShardStrategyFactoryTest.java b/java/test/org/broadinstitute/sting/gatk/dataSources/shards/ShardStrategyFactoryTest.java
index 9c06162c4..843c62aca 100755
--- a/java/test/org/broadinstitute/sting/gatk/dataSources/shards/ShardStrategyFactoryTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/dataSources/shards/ShardStrategyFactoryTest.java
@@ -4,6 +4,7 @@ import static junit.framework.Assert.assertEquals;
 import static junit.framework.Assert.fail;
 import net.sf.samtools.SAMSequenceDictionary;
 import net.sf.samtools.SAMSequenceRecord;
+import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.utils.FastaSequenceFile2;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.junit.*;
@@ -37,7 +38,7 @@ import java.util.ArrayList;
  * <p/>
  * A descriptions should go here. Blame aaron if it's missing.
  */
-public class ShardStrategyFactoryTest {
+public class ShardStrategyFactoryTest extends BaseTest {
 
     private static FastaSequenceFile2 seq;
 
@@ -47,7 +48,7 @@ public class ShardStrategyFactoryTest {
      */
     @BeforeClass
     public static void doBeforeAnyTests() {
-        seq = new FastaSequenceFile2(new File("/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta"));
+        seq = new FastaSequenceFile2(new File(seqLocation + "/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta"));
     }
 
     /**
@@ -117,17 +118,17 @@ public class ShardStrategyFactoryTest {
         int size = 10000;
         int location = 1;
         GenomeLoc.setupRefContigOrdering(dic);
-        System.err.println("done to sleep");
+        logger.debug("done to sleep");
         // keep track of the number of genome locs we build
         int genomeLocs = 0;
         ArrayList<GenomeLoc> locations = new ArrayList<GenomeLoc>();
-        System.err.println("done to sleep2");
+        logger.debug("done to sleep2");
         try {
             while (location + size < stop) {
-            System.err.println("s = " + s.getSequenceName() + " " + location + " " + size);
+            logger.debug("s = " + s.getSequenceName() + " " + location + " " + size);
             // lets make up some fake locations
             GenomeLoc gl = new GenomeLoc(s.getSequenceName(), location, location + size - 1);
-            System.err.println("loc = " + location);
+            logger.debug("loc = " + location);
 
             // let's move the location up, with a size space
             location += (size * 2);
@@ -141,18 +142,18 @@ public class ShardStrategyFactoryTest {
         } catch (Exception e) {
             e.printStackTrace();
         }
-        System.err.println("Location count = " + genomeLocs);
+        logger.debug("Location count = " + genomeLocs);
         ShardStrategy strategy = ShardStrategyFactory.shatter(ShardStrategyFactory.SHATTER_STRATEGY.LINEAR, seq.getSequenceDictionary(), 5000, locations);
         int shardCount = 0;
         try {
             for (Shard sh : strategy) {
                 GenomeLoc l = sh.getGenomeLoc();
 
-                System.err.println("Shard start: " + l.getStart() + " stop " + l.getStop() + " contig " + l.getContig());
+                logger.debug("Shard start: " + l.getStart() + " stop " + l.getStop() + " contig " + l.getContig());
                 shardCount++;
             }
 
-             System.err.println("Shard count = " + shardCount); 
+             logger.debug("Shard count = " + shardCount); 
             assertEquals(shardCount, genomeLocs * 2);
 
         } catch (Exception e) {
diff --git a/java/test/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMBAMDataSourceTest.java b/java/test/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMBAMDataSourceTest.java
index e38794e46..2172b986a 100755
--- a/java/test/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMBAMDataSourceTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMBAMDataSourceTest.java
@@ -2,6 +2,7 @@ package org.broadinstitute.sting.gatk.dataSources.simpleDataSources;
 
 import static junit.framework.Assert.fail;
 import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.gatk.dataSources.shards.Shard;
 import org.broadinstitute.sting.gatk.dataSources.shards.ShardStrategy;
 import org.broadinstitute.sting.gatk.dataSources.shards.ShardStrategyFactory;
@@ -42,7 +43,7 @@ import java.util.List;
  * <p/>
  * A descriptions should go here. Blame aaron if it's missing.
  */
-public class SAMBAMDataSourceTest {
+public class SAMBAMDataSourceTest extends BaseTest {
 
     private List<String> fl;
     private FastaSequenceFile2 seq;
@@ -57,7 +58,7 @@ public class SAMBAMDataSourceTest {
         fl = new ArrayList<String>();
 
         // sequence
-        seq = new FastaSequenceFile2(new File("/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta"));
+        seq = new FastaSequenceFile2(new File(seqLocation + "/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta"));
         GenomeLoc.setupRefContigOrdering(seq.getSequenceDictionary());
     }
 
@@ -81,7 +82,7 @@ public class SAMBAMDataSourceTest {
         int count = 0;
 
         // setup the data
-        fl.add("/humgen/gsa-scr1/aaron/stink/NA12892.bam");
+        fl.add(oneKGLocation + "/pilot3/sams/NA12892.bam");
 
 
         try {
@@ -90,8 +91,8 @@ public class SAMBAMDataSourceTest {
                 int readCount = 0;
                 count++;
 
-                System.out.println("Start : " + sh.getGenomeLoc().getStart() + " stop : " + sh.getGenomeLoc().getStop() + " contig " + sh.getGenomeLoc().getContig());
-                System.out.println("count = " + count);
+                logger.debug("Start : " + sh.getGenomeLoc().getStart() + " stop : " + sh.getGenomeLoc().getStop() + " contig " + sh.getGenomeLoc().getContig());
+                logger.debug("count = " + count);
                 MergingSamRecordIterator2 datum = data.seek(sh.getGenomeLoc());
 
                 // for the first couple of shards make sure we can see the reads
@@ -118,7 +119,7 @@ public class SAMBAMDataSourceTest {
 
 
         // setup the test files
-        fl.add("/seq/dirseq/analysis/cancer_exome/sams/TCGA-06-0188.aligned.duplicates_marked.bam");
+        fl.add(seqLocation + "/dirseq/analysis/cancer_exome/sams/TCGA-06-0188.aligned.duplicates_marked.bam");
 
         ArrayList<Integer> readcountPerShard = new ArrayList<Integer>();
         ArrayList<Integer> readcountPerShard2 = new ArrayList<Integer>();
@@ -143,7 +144,7 @@ public class SAMBAMDataSourceTest {
 
                 }
                 readcountPerShard.add(readCount);
-                System.out.println("read count = " + readCount);
+                logger.debug("read count = " + readCount);
                 datum.close();
             }
         }
@@ -155,13 +156,13 @@ public class SAMBAMDataSourceTest {
 
         // setup the data and the counter before our second run
         fl.clear();
-        fl.add("/seq/dirseq/analysis/cancer_exome/sams/TCGA-06-0188-01A-01W.aligned.duplicates_marked.bam");
-        fl.add("/seq/dirseq/analysis/cancer_exome/sams/TCGA-06-0188-10B-01W.aligned.duplicates_marked.bam");
+        fl.add(seqLocation + "/dirseq/analysis/cancer_exome/sams/TCGA-06-0188-01A-01W.aligned.duplicates_marked.bam");
+        fl.add(seqLocation + "/dirseq/analysis/cancer_exome/sams/TCGA-06-0188-10B-01W.aligned.duplicates_marked.bam");
         count = 0;
         // the sharding strat.
         strat = ShardStrategyFactory.shatter(ShardStrategyFactory.SHATTER_STRATEGY.LINEAR, seq.getSequenceDictionary(), 100000);
 
-        System.err.println("Pile two:");
+        logger.debug("Pile two:");
         try {
             SAMBAMDataSource data = new SAMBAMDataSource(fl);
             for (Shard sh : strat) {
@@ -180,7 +181,7 @@ public class SAMBAMDataSourceTest {
                 }
 
                 readcountPerShard2.add(readCount);
-                System.out.println("read count = " + readCount);
+                logger.debug("read count = " + readCount);
                 datum.close();
             }
         }
diff --git a/java/test/org/broadinstitute/sting/utils/FastaSequenceFile2Test.java b/java/test/org/broadinstitute/sting/utils/FastaSequenceFile2Test.java
index d5e55a5ef..2c220a1ae 100755
--- a/java/test/org/broadinstitute/sting/utils/FastaSequenceFile2Test.java
+++ b/java/test/org/broadinstitute/sting/utils/FastaSequenceFile2Test.java
@@ -1,12 +1,11 @@
 package org.broadinstitute.sting.utils;
 
-import org.junit.*;
-import org.apache.log4j.BasicConfigurator;
-
-import java.io.File;
-
 import edu.mit.broad.picard.reference.ReferenceSequence;
 import net.sf.samtools.util.StringUtil;
+import org.broadinstitute.sting.BaseTest;
+import org.junit.*;
+
+import java.io.File;
 
 /**
  * Created by IntelliJ IDEA.
@@ -14,9 +13,9 @@ import net.sf.samtools.util.StringUtil;
  * Date: Apr 11, 2009
  * Time: 2:32:52 PM
  */
-public class FastaSequenceFile2Test {
+public class FastaSequenceFile2Test extends BaseTest {
 
-    private final String sequenceFileName = "/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta";
+    private static String sequenceFileName;
     private FastaSequenceFile2 sequenceFile = null;
 
     private final String firstBasesOfChrM = "GATCACAGGTCTATCACCCT";
@@ -25,7 +24,7 @@ public class FastaSequenceFile2Test {
 
     @BeforeClass
     public static void initialize() {
-        BasicConfigurator.configure();
+         sequenceFileName = seqLocation + "/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta";
     }
 
     @Before
@@ -116,6 +115,7 @@ public class FastaSequenceFile2Test {
 
         try {
             startTime = System.currentTimeMillis();
+            boolean success = sequenceFile.seekToContig("absent");
         }
         finally {
             endTime = System.currentTimeMillis();
diff --git a/java/test/org/broadinstitute/sting/utils/cmdLine/ArgumentParserTest.java b/java/test/org/broadinstitute/sting/utils/cmdLine/ArgumentParserTest.java
index d4e89bb83..f7c10cfa7 100644
--- a/java/test/org/broadinstitute/sting/utils/cmdLine/ArgumentParserTest.java
+++ b/java/test/org/broadinstitute/sting/utils/cmdLine/ArgumentParserTest.java
@@ -7,6 +7,7 @@ package org.broadinstitute.sting.utils.cmdLine;
 import org.junit.*;
 import static org.junit.Assert.*;
 import org.apache.commons.cli.ParseException;
+import org.broadinstitute.sting.BaseTest;
 
 /**
  * The ArgumentParserTest test class.  In JUnit 4, you don't have to extent the
@@ -24,7 +25,7 @@ import org.apache.commons.cli.ParseException;
  * <p/>
  * You should use the methods like
  */
-public class ArgumentParserTest {
+public class ArgumentParserTest extends BaseTest {
 
     // our argument parser
     private ArgumentParser m_parser = null;