diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/RawBaseCounter.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/RawBaseCounter.scala
index efd7de06ed650af589b1a9932a18c62c33b5fdbc..8be307a9d1323f0252d5b7f2e24f52c07148adcc 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/RawBaseCounter.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/RawBaseCounter.scala
@@ -83,7 +83,7 @@ class RawBaseCounter(val root: Configurable) extends BiopetCommandLineFunction {
   }
 
   override def beforeGraph(): Unit = {
-    if (annotationBed != null) Logging.addError("Annotation BED must be supplied")
+    if (annotationBed == null) Logging.addError("Annotation BED must be supplied")
     require(output != null, "Output must be defined")
     require((mixedStrand && !distinctStrand) || (!mixedStrand && distinctStrand),
       "Invalid input BAM combinations for RawBaseCounter")