diff --git a/tools/accel_align/accel_align.rule.snakefile b/tools/accel_align/accel_align.rule.snakefile
index e80bf361073438f95beea37653ab4026b7d0fdcc..4674556666cb67bc9ff0166fe2743773d02b7c7d 100755
--- a/tools/accel_align/accel_align.rule.snakefile
+++ b/tools/accel_align/accel_align.rule.snakefile
@@ -29,7 +29,7 @@ if config["SeOrPe"] == "PE":
             "-o {params.tmp_sam}  "
             "{params.indexPrefix} "
             "{input.read} {input.read2} 2> {log}; "
-            "samtools view -b {params.tmp_sam}/ 2>> {log} "
+            "samtools view -hb {params.tmp_sam} 2>> {log} "
             "| samtools sort -@ {threads} > {output.bam} 2>> {log} && "
             "samtools index -@ {threads} {output.bam} 2>> {log}; "
             "rm -f {params.tmp_sam} "
@@ -63,7 +63,7 @@ elif config["SeOrPe"] == "SE":
             "-o {params.tmp_sam} "
             "{params.indexPrefix} "
             "{input.read} 2> {log}; "
-            "| samtools view -b {params.tmp_sam} 2>> {log} "
+            "| samtools view -hb {params.tmp_sam} 2>> {log} "
             "| samtools sort -@ {threads} > {output.bam} 2>> {log} && "
             "samtools index -@ {threads} {output.bam} 2>> {log}; "
             "rm -f {params.tmp_sam} "