diff --git a/runBWA.sh b/runBWA.sh
index 47cf2ed..4d796b2 100755
--- a/runBWA.sh
+++ b/runBWA.sh
@@ -9,6 +9,6 @@ THREADS="16"
 READ1="$2"
 READ2="$3"
 SAM=$(basename ${READ1%.*} | cut -f 1-2 -d "_")
-bwa mem -M -x ont2d -t ${THREADS} ${REF} ${READ1} ${READ2} > ${SAM}.sam
+bwa mem -M -t ${THREADS} ${REF} ${READ1} ${READ2} > ${SAM}.sam
 samtools view --threads 16 -b -o ${SAM}.bam ${SAM}.sam
 samtools sort -m 8G -o ${SAM}_sorted.bam -T ${SAM}_temp --threads 16 ${SAM}.bam