diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
index 127f2991608612f105fcfe81e3cea2048262f1b4..59dfa9d8593f25d09a4deb5785807d594f733544 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
@@ -9,6 +9,8 @@ trait BiopetJavaCommandLineFunction extends JavaCommandLineFunction with BiopetC
   javaGCHeapFreeLimit = config("java_gc_heap_freelimit")
   javaGCTimeLimit = config("java_gc_timelimit")
 
+  override def javaOpts = super.javaOpts + optional("-Dscala.concurrent.context.numThreads=", threads, spaceSeparated = false, escape = false)
+
   override def afterGraph {
     memoryLimit = config("memory_limit")
   }