diff --git a/scala/src/org/broadinstitute/sting/queue/function/CommandLineFunction.scala b/scala/src/org/broadinstitute/sting/queue/function/CommandLineFunction.scala
index 6d0fd27ec..e2baeb7f6 100644
--- a/scala/src/org/broadinstitute/sting/queue/function/CommandLineFunction.scala
+++ b/scala/src/org/broadinstitute/sting/queue/function/CommandLineFunction.scala
@@ -170,7 +170,7 @@ trait CommandLineFunction extends QFunction with Logging {
         newFileExtension
       }
       case file: File => {
-        if (file.getClass == classOf[File])
+        if (file.getClass != classOf[File])
           throw new QException("Extensions of file must also extend with FileExtension so that the path can be modified.");
         val newFile = IOUtils.resetParent(tempDir, file)
         setFieldValue(field, newFile)