diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
index b87e3cb1ec19fc84b6b4852e525e2d18f03d4e77..e732c1023de5f713f4c21ed366da68eddc825285 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
@@ -59,7 +59,7 @@ class RunGubbins(val root: Configurable) extends BiopetCommandLineFunction {
       ".filtered_polymorphic_sites.fasta",
       ".filtered_polymorphic_sites.phylip",
       ".final_tree.tre")
-    for (t <- out) outputFiles ::= new File(outputDirectory + File.separator + prefix + t)
+    for (t <- out) outputFiles ::= new File(outputDirectory + File.separator + prefix.getOrElse("gubbins") + t)
   }
 
   def cmdLine = required("cd", outputDirectory) + " && " + required(executable) +