Error: The sam file is not sorted properly on positions

[iranianuser]

Hello I m using methylkit on bismark alignment files. I used the command below and used the bam output from bismark alignment process: methRaw = processBismarkAln( location = "/media/genome2/SP PHD U3/vahedi/802/SRR4298802_1_val_1_bismark_bt2_pe.bam", sample.id="Cancer_802", assembly = "hg38", treatment = (1), read.context = "CpG") I have 3 cancerous samples and 1 control but first I test just one of my samples. I got this Error :The sam file is not sorted properly on positions: chr: 11 pos: 36283681 is followed by chr: 11 pos: 36283418 You can sort the file in unix-like machines using: grep -v \'^[[:space:]]*\@\' test.sam | sort -k3,3 -k4,4n > test.sorted.sam

what can I do to solve this problem??

thanks alot