Hi there I'm trying to follow the instructions here

https://www.htslib.org/workflow/fastq.html

However when I get to the second step and input:

samtools fixmate -O bam,level=1 -m my.sam fixmate.bam

It tells me that level is an unknown option.

I tried stripping that part of the command so it ran

samtools fixmate -O -m my.sam fixmate.bam

However it just tells me:

Usage: samtools fixmate <in.nameSrt.bam> <out.nameSrt.bam>
Options:
  -r           Remove unmapped reads and secondary alignments
  -p           Disable FR proper pair check
  -c           Add template cigar ct tag
      --input-fmt-option OPT[=VAL]
               Specify a single input file format option in the form
               of OPTION or OPTION=VALUE
  -O, --output-fmt FORMAT[,OPT[=VAL]]...
               Specify output format (SAM, BAM, CRAM)
      --output-fmt-option OPT[=VAL]
               Specify a single output file format option in the form
               of OPTION or OPTION=VALUE
      --reference FILE
               Reference sequence FASTA FILE [null]

As elsewhere in samtools, use '-' as the filename for stdin/stdout. The input
file must be grouped by read name (e.g. sorted by name). Coordinated sorted
input is not accepted.

I tried transposing the -O and -m switches out of desperation but that doesn't run either.

Does anybody perhaps know what I'm doing wrong? Thanks