diff --git a/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java b/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
index e3cb441b2..bec67689b 100755
--- a/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
+++ b/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
@@ -2,9 +2,9 @@ package org.broadinstitute.sting.gatk;
 
 import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.utils.cmdLine.Argument;
 import org.broadinstitute.sting.utils.cmdLine.ArgumentCollection;
 import org.broadinstitute.sting.utils.cmdLine.CommandLineProgram;
-import org.broadinstitute.sting.gatk.GATKArgumentCollection;
 
 /**
  *
@@ -36,6 +36,9 @@ import org.broadinstitute.sting.gatk.GATKArgumentCollection;
  */
 public class CommandLineGATK extends CommandLineProgram {
 
+    @Argument(fullName = "analysis_type", shortName = "T", doc = "Type of analysis to run")
+    public String analysisName = null;
+
     @ArgumentCollection // our argument collection, the collection of command line args we accept
     public GATKArgumentCollection argCollection = new GATKArgumentCollection();
 
@@ -68,14 +71,16 @@ public class CommandLineGATK extends CommandLineProgram {
     protected int execute() {
         Walker<?, ?> mWalker = null;
         try {
-            mWalker = walkerManager.createWalkerByName(argCollection.analysisName);
+            mWalker = walkerManager.createWalkerByName(analysisName);
         } catch (InstantiationException ex) {
             throw new RuntimeException("Unable to instantiate walker.", ex);
         }
         catch (IllegalAccessException ex) {
             throw new RuntimeException("Unable to access walker", ex);
         }
+        loadArgumentsIntoObject(argCollection);
         loadArgumentsIntoObject(mWalker);
+        this.argCollection.analysisName = this.analysisName;
         try {
             GATKEngine = new GenomeAnalysisEngine(argCollection, mWalker);
         } catch (StingException exp) {
@@ -103,16 +108,20 @@ public class CommandLineGATK extends CommandLineProgram {
      */
     @Override
     protected Class[] getArgumentSources() {
-        loadArgumentsIntoObject(this.argCollection);
-        if (argCollection.analysisName == null)
+        try {
+            Thread.sleep(5000);
+        } catch (InterruptedException e) {
+            e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
+        }
+        if (analysisName == null)
             throw new IllegalArgumentException("Must provide analysis name");
 
         walkerManager = new WalkerManager(pluginPathName);
 
-        if (!walkerManager.doesWalkerExist(argCollection.analysisName))
+        if (!walkerManager.doesWalkerExist(analysisName))
             throw new IllegalArgumentException("Invalid analysis name");
 
-        return new Class[]{walkerManager.getWalkerClassByName(argCollection.analysisName)};
+        return new Class[]{walkerManager.getWalkerClassByName(analysisName)};
     }
 
     @Override
diff --git a/java/src/org/broadinstitute/sting/gatk/GATKArgumentCollection.java b/java/src/org/broadinstitute/sting/gatk/GATKArgumentCollection.java
index d9cfa1c4e..e0a8164e8 100755
--- a/java/src/org/broadinstitute/sting/gatk/GATKArgumentCollection.java
+++ b/java/src/org/broadinstitute/sting/gatk/GATKArgumentCollection.java
@@ -68,7 +68,6 @@ public class GATKArgumentCollection {
     public File referenceFile = null;
 
     @Element(required=false)
-    @Argument(fullName = "analysis_type", shortName = "T", doc = "Type of analysis to run")
     public String analysisName = null;
 
     // parameters and their defaults
diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
index bffd73974..7659c8a9e 100755
--- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
@@ -184,8 +184,7 @@ public class GenomeAnalysisEngine {
             microScheduler = MicroScheduler.create(my_walker, argCollection.samFiles, argCollection.referenceFile, rods, argCollection.numberOfThreads);
             engine = microScheduler.getTraversalEngine();
         }
-        else if (my_walker instanceof ReadWalker)
-        {
+        else if (my_walker instanceof ReadWalker) {
             if (argCollection.referenceFile == null)
                 Utils.scareUser(String.format("Locus-based traversals require a reference file but none was given"));
             microScheduler = MicroScheduler.create(my_walker, argCollection.samFiles, argCollection.referenceFile, rods, argCollection.numberOfThreads);
@@ -236,15 +235,17 @@ public class GenomeAnalysisEngine {
      * @return a list of genomeLoc representing the interval file
      */
     private List<GenomeLoc> setupIntervalRegion() {
-        List<GenomeLoc> locs;
-        if( new File(argCollection.intervals).exists() ) {
-            logger.info("Intervals argument specifies a file.  Loading intervals from file.");
-            return GenomeLoc.IntervalFileToList(argCollection.intervals);
-        }
-        else {
-            logger.info("Intervals argument does not specify a file.  Trying to parse it as a simple string.");
-            return GenomeLoc.parseGenomeLocs(argCollection.intervals);
+        List<GenomeLoc> locs = null;
+        if (argCollection.intervals != null) {
+            if (new File(argCollection.intervals).exists()) {
+                logger.info("Intervals argument specifies a file.  Loading intervals from file.");
+                locs = GenomeLoc.IntervalFileToList(argCollection.intervals);
+            } else {
+                logger.info("Intervals argument does not specify a file.  Trying to parse it as a simple string.");
+                locs = GenomeLoc.parseGenomeLocs(argCollection.intervals);
+            }
         }
+        return locs;
     }
 
     /**