diff --git a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BaseCounter.scala b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BaseCounter.scala
index 014718a9bdd62f15b7f9faf9a78864d3e3644c5b..e9817cc90e2131820fd134383de2f1856cccfd18 100644
--- a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BaseCounter.scala
+++ b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BaseCounter.scala
@@ -57,7 +57,11 @@ object BaseCounter extends ToolCommand {
     //Sets picard logging level
     htsjdk.samtools.util.Log.setGlobalLogLevel(htsjdk.samtools.util.Log.LogLevel.valueOf(logger.getLevel.toString))
 
+    require(cmdArgs.outputDir.exists(), s"Output dir does not exist: ${cmdArgs.outputDir}")
+    require(cmdArgs.outputDir.isDirectory, s"Output dir is not a dir: ${cmdArgs.outputDir}")
+
     logger.info("Start reading RefFlat file")
+
     val bamReader = SamReaderFactory.makeDefault().open(cmdArgs.bamFile)
     val geneReader = GeneAnnotationReader.loadRefFlat(cmdArgs.refFlat, bamReader.getFileHeader.getSequenceDictionary)
     bamReader.close()