diff --git a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
index b9e44d87b..b8a7334b3 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
@@ -307,7 +307,7 @@ public class GATKArgumentCollection {
      * the benefit of not requiring X times as much memory per thread as data threads do, but rather
      * only a constant overhead.
      */
-    @Argument(fullName="num_cpu_threads_per_data_thread", shortName = "cnt", doc="How many CPU threads should be allocated per data thread to running this analysis?", required = false)
+    @Argument(fullName="num_cpu_threads_per_data_thread", shortName = "nct", doc="How many CPU threads should be allocated per data thread to running this analysis?", required = false)
     public int numberOfCPUThreadsPerDataThread = 1;
 
     @Argument(fullName="num_io_threads", shortName = "nit", doc="How many of the given threads should be allocated to IO", required = false)
diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java b/public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java
index 1da712e8a..46d6b5882 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java
@@ -117,7 +117,7 @@ public abstract class MicroScheduler implements MicroSchedulerMBean {
             }
         } else {
             if ( threadAllocation.getNumCPUThreadsPerDataThread() > 1 && ! (walker instanceof NanoSchedulable) )
-                throw badNT("cnt", engine, walker);
+                throw badNT("nct", engine, walker);
             return new LinearMicroScheduler(engine, walker, reads, reference, rods, threadAllocation);
         }
     }
diff --git a/public/java/test/org/broadinstitute/sting/WalkerTest.java b/public/java/test/org/broadinstitute/sting/WalkerTest.java
index bcfd00aed..fa9f9e8a7 100755
--- a/public/java/test/org/broadinstitute/sting/WalkerTest.java
+++ b/public/java/test/org/broadinstitute/sting/WalkerTest.java
@@ -280,11 +280,11 @@ public class WalkerTest extends BaseTest {
             results = executeTest(name + "-nt-" + nt, spec);
         }
 
-        for ( int cnt : cpuThreads ) {
-            if ( cnt != 1 ) {
-                String extra = " -cnt " + cnt;
+        for ( int nct : cpuThreads ) {
+            if ( nct != 1 ) {
+                String extra = " -nct " + nct;
                 spec.args = originalArgs + extra;
-                results = executeTest(name + "-cnt-" + cnt, spec);
+                results = executeTest(name + "-cnt-" + nct, spec);
             }
         }