Metaphlan cli docs

Microbial community profiling MetaPhlAn
1

I’m using MetaPhlAn version 4.0.3 (24 Oct 2022) and noticed a couple of unclear aspects on the cli docs:

marker_table

 --nreads NUMBER_OF_READS
                        The total number of reads in the original metagenome. It is used only when 
                        -t marker_table is specified for normalizing the length-normalized counts 
                        with the metagenome size as well. No normalization applied if --nreads is not 
                        specified

…but I’m guessing that -t marker_table should be -t marker_ab_table.

–nreads

  --nreads NUMBER_OF_READS
                        The total number of reads in the original metagenome. It is used only when 
                        -t marker_table is specified for normalizing the length-normalized counts 
                        with the metagenome size as well. No normalization applied if --nreads is not 
                        specified

Specifically: It is used only when -t marker_table is specified, but the docs at MetaPhlAn 4 · biobakery/MetaPhlAn Wiki · GitHub state:

If you want to estimate the unknown fraction of a metagenome and your input file is a SAM file, remember to specify the metagenome size using --nreads

…with no mention of -t marker_(ab)_table

–samout

  -s sam_output_file, --samout sam_output_file
                        The sam output file

It is unclear from these docs on whether the sam output file is written by default, and if so, what is the default output file name.

2

Should I maybe move to this to a github issue?

3

Thanks for reporting this. In the latest version --nreads is only needed when using a sam file as input. if not specified, the sam file will only be stored as a temporal file discarded at the end of the execution. I will update the doc in the next version!

4

Thanks for clarifying and updating the docs!