diff --git a/scala/qscript/oneoffs/carneiro/dataProcessingV2.scala b/scala/qscript/oneoffs/carneiro/dataProcessingV2.scala
index 7665d1824..5b74c1534 100755
--- a/scala/qscript/oneoffs/carneiro/dataProcessingV2.scala
+++ b/scala/qscript/oneoffs/carneiro/dataProcessingV2.scala
@@ -442,7 +442,7 @@ class dataProcessingV2 extends QScript {
     @Input(doc="bwa alignment index file for 1st mating pair") var sai1 = inSai1
     @Input(doc="bwa alignment index file for 2nd mating pair") var sai2 = inSai2
     @Output(doc="output aligned bam file") var alignedBam = outBam
-    def commandLine = bwaPath + " samse " + reference + " " + sai1 + " " + sai2 + " " + bam + " -r " + readGroup + " > " + alignedBam
+    def commandLine = bwaPath + " sampe " + reference + " " + sai1 + " " + sai2 + " " + bam + " -r " + readGroup + " > " + alignedBam
     this.isIntermediate = true
     this.analysisName = queueLogDir + outBam + ".bwa_sam_pe"
     this.jobName = queueLogDir + outBam + ".bwa_sam_pe"
diff --git a/scala/qscript/oneoffs/carneiro/justClean.scala b/scala/qscript/oneoffs/carneiro/justClean.scala
index e2e8a7153..1ecc4bd5a 100755
--- a/scala/qscript/oneoffs/carneiro/justClean.scala
+++ b/scala/qscript/oneoffs/carneiro/justClean.scala
@@ -59,14 +59,14 @@ class justClean extends QScript {
     clean.reference_sequence = reference
     clean.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
     clean.rodBind :+= RodBind("indels", "VCF", indels)
-    clean.doNotUseSW = true
+    clean.doNotUseSW = false
     clean.compress = 0
-    clean.U = org.broadinstitute.sting.gatk.arguments.ValidationExclusion.TYPE.NO_READ_ORDER_VERIFICATION  // todo -- update clean with the last consensus between Tim, Matt and Eric. This is ugly!
+//    clean.U = org.broadinstitute.sting.gatk.arguments.ValidationExclusion.TYPE.NO_READ_ORDER_VERIFICATION  // todo -- update clean with the last consensus between Tim, Matt and Eric. This is ugly!
     clean.jobName = queueLogDir + outBam + ".clean"
     clean.jarFile = GATKjar
-    clean.memoryLimit = 12
+    clean.memoryLimit = 6
     clean.scatterCount = 84
 
-    add(clean);
+    add(target, clean);
   }
 }