and the command file content is #!/bin/bash -euo pipefail bwa mem \ -t 12 \ -M \ -R ‘@RG\tIDH3K4me2 WT t1 R2 T1\tSMH3K4me2_WT_t1_R2\tPLILLUMINA\tLBH3K4me2_WT_t1_R2_T1\tPU:1’ \ WholeGenomeFasta/genome.fa \ ChIPseq_H3K4me2_WT_t1_rep2_S26_R1_001.fastq.gz ChIPseq_H3K4me2_WT_t1_rep2_S26_R2_001.fastq.gz \ | samtools view -@ 12 -b -h -F 0x0100 -O BAM -o H3K4me2_WT_t1_R2_T1.Lb.bam -