diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala
index f8b684e1ed8971b81ac7783f08d73cae24389fc4..d32eb27a3d782189bdbd623eee3d17f375b2d139 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala
@@ -269,7 +269,7 @@ class Tophat(val root: Configurable) extends BiopetCommandLineFunction with Refe
     if (bowtie1 && !new File(bowtie_index).getParentFile.list().toList
       .filter(_.startsWith(new File(bowtie_index).getName)).exists(_.endsWith(".bt2")))
       throw new IllegalArgumentException("No bowtie1 index found for tophat")
-    else if (new File(bowtie_index).getParentFile.list().toList
+    else if (!new File(bowtie_index).getParentFile.list().toList
       .filter(_.startsWith(new File(bowtie_index).getName)).exists(_.endsWith(".ebwt")))
       throw new IllegalArgumentException("No bowtie2 index found for tophat")
   }