diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala
index f9d1dd1467630060f9cb162511eddf9044fec8a3..00904552adbaa21985d96c5090e5c2f24eb629d2 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala
@@ -11,7 +11,7 @@ class HaplotypeCaller(val root: Configurable) extends org.broadinstitute.gatk.qu
     if (config.contains("scattercount")) scatterCount = config("scattercount")
     if (config.contains("dbsnp")) this.dbsnp = config("dbsnp")
     this.sample_ploidy = config("ploidy")
-    nct = config("threads", default = 3)
+    nct = config("threads", default = 1)
     bamOutput = config("bamOutput")
     memoryLimit = Option(nct.getOrElse(1) * 2)
     if (config.contains("allSitePLs")) this.allSitePLs = config("allSitePLs")
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala
index 96cc081492fd65b350d8f28b2e75e7d776779811..75105f1b200592926c1461b9722ad0a5a35b6a7c 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala
@@ -10,7 +10,7 @@ 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 = 3)
+    nct = config("threads", default = 1)
     memoryLimit = Option(nct.getOrElse(1) * 2)
     if (config.contains("allSitePLs")) this.allSitePLs = config("allSitePLs")
     if (config.contains("output_mode")) {