diff --git a/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentParser.java b/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentParser.java
index c88b7d235..baba87ea0 100644
--- a/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentParser.java
+++ b/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentParser.java
@@ -280,7 +280,7 @@ public class ArgumentParser {
         OurPosixParser parser = new OurPosixParser();
 
         try {
-            parser.parse(m_options, args, !allowIncomplete);
+            parser.parse(m_options, args, false);
         }
         catch( ParseException e ) {
             boolean isIncomplete = e instanceof MissingArgumentException ||