diff --git a/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala b/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
index 6d8f340b6e2aa2341b7bc8a1cebaf102056e41e6..52d47ccb01ae50142d89b945a746a22dae3d95eb 100644
--- a/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
+++ b/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
@@ -99,7 +99,13 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
     beforeGraph()
     internalBeforeGraph()
 
-    if (jobOutputFile != null) this.commandDirectory = this.jobOutputFile.getAbsoluteFile.getParentFile
+    if (jobOutputFile != null) {
+      this.commandDirectory = this.jobOutputFile.getAbsoluteFile.getParentFile
+      this match {
+        case s: ScatterGatherableFunction => s.scatterGatherDirectory = new File(this.commandDirectory, ".scatter")
+        case _                            =>
+      }
+    }
 
     super.freezeFieldValues()
   }