diff --git a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala
index 18b4f06414cdfa4b1fb781de46fbf43cbf15fc78..9521e9ea0f0d09b49690a9f6ea977f13a6eb3b8d 100644
--- a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala
+++ b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala
@@ -41,7 +41,7 @@ class HaplotypeCaller(val root: Configurable) extends org.broadinstitute.gatk.qu
       threads = 1
       logger.warn("BamOutput is on, nct/threads is forced to set on 1, this option is only for debug")
     }
-    nct = Some(threads)
+    nct = Some(getThreads(1))
     memoryLimit = Option(memoryLimit.getOrElse(2.0) * nct.getOrElse(1))
   }
 
diff --git a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala
index 684c2123a56be28ef3a327ad3102d05bb808033a..599ffa170519c17d7b3e35e14783ad75e208dadb 100644
--- a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala
+++ b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala
@@ -15,7 +15,7 @@ class UnifiedGenotyper(val root: Configurable) extends org.broadinstitute.gatk.q
     if (config.contains("scattercount")) scatterCount = config("scattercount")
     if (config.contains("dbsnp")) this.dbsnp = config("dbsnp")
     this.sample_ploidy = config("ploidy")
-    nct = config("threads", default = 1)
+    nct = Some(getThreads(1))
     memoryLimit = Option(nct.getOrElse(1) * 2)
     if (config.contains("allSitePLs")) this.allSitePLs = config("allSitePLs")
     if (config.contains("output_mode")) {