diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
index 878eedd21a0c65cfe6c15df6f95c140440619955..b706e6176cd898f9d4c742cb718e10ac5dffd066 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
@@ -206,6 +206,7 @@ object BastyGenerateFasta extends ToolCommand {
         for (c <- chunks.keySet.toList.sortWith(_ < _)) {
           writer.print(chunks(c)._1)
         }
+        writer.println()
         writer.close
       }
       if (cmdArgs.outputConsensusVariants != null) {
@@ -214,6 +215,7 @@ object BastyGenerateFasta extends ToolCommand {
         for (c <- chunks.keySet.toList.sortWith(_ < _)) {
           writer.print(chunks(c)._2)
         }
+        writer.println()
         writer.close
       }
     }