# Metaphlan cli docs

**URL:** <https://forum.biobakery.org/t/metaphlan-cli-docs/4586>\
**Category:** MetaPhlAn\
**Created:** [January 2, 2023, 6:29pm UTC](https://forum.biobakery.org/t/metaphlan-cli-docs/4586 "2023-01-02T18:29:03Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![nick-youngblut](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/nick-youngblut/32/528_2.png) [@nick-youngblut](https://forum.biobakery.org/u/nick-youngblut)\
**Post date:** [January 2, 2023, 6:29pm UTC](https://forum.biobakery.org/t/metaphlan-cli-docs/4586/1 "2023-01-02T18:29:03Z")

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

## marker\_table

```auto
 --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

```auto
  --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](https://github.com/biobakery/MetaPhlAn/wiki/MetaPhlAn-4) 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

```auto
  -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.

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<div class="post-metadata">

**Author:** ![nick-youngblut](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/nick-youngblut/32/528_2.png) [@nick-youngblut](https://forum.biobakery.org/u/nick-youngblut)\
**Post date:** [January 16, 2023, 11:36pm UTC](https://forum.biobakery.org/t/metaphlan-cli-docs/4586/2 "2023-01-16T23:36:25Z")

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Should I maybe move to this to a [github issue](https://github.com/biobakery/MetaPhlAn/issues)?

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<div class="post-metadata">

**Author:** ![aitor.blancomiguez](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/aitor.blancomiguez/32/86_2.png) [@aitor.blancomiguez](https://forum.biobakery.org/u/aitor.blancomiguez)\
**Post date:** [January 17, 2023, 4:51pm UTC](https://forum.biobakery.org/t/metaphlan-cli-docs/4586/3 "2023-01-17T16:51:02Z")

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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!

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<div class="post-metadata">

**Author:** ![nick-youngblut](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/nick-youngblut/32/528_2.png) [@nick-youngblut](https://forum.biobakery.org/u/nick-youngblut)\
**Post date:** [January 18, 2023, 3:43pm UTC](https://forum.biobakery.org/t/metaphlan-cli-docs/4586/4 "2023-01-18T15:43:01Z")

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Thanks for clarifying and updating the docs!