# Metaphlan results as input on Humann

**URL:** <https://forum.biobakery.org/t/metaphlan-results-as-input-on-humann/3325>\
**Category:** HUMAnN\
**Created:** [March 18, 2022, 1:54am UTC](https://forum.biobakery.org/t/metaphlan-results-as-input-on-humann/3325 "2022-03-18T01:54:44Z")\
**Posts on this page:** 2\
**Page:** 1

<div class="post-metadata">

**Author:** ![wusan1234](https://avatars.discourse-cdn.com/v4/letter/w/85e7bf/32.png) [@wusan1234](https://forum.biobakery.org/u/wusan1234)\
**Post date:** [March 18, 2022, 1:54am UTC](https://forum.biobakery.org/t/metaphlan-results-as-input-on-humann/3325/1 "2022-03-18T01:54:44Z")

</div>

Hi dears,  
For some reasons, all my metagenome data had generated firstly by Metaphlan and now I want to run with humann. I browsed forum and found some related topics like:

1. [Humann 3.0 and bowtie metaphlan output](https://forum.biobakery.org/t/humann-3-0-and-bowtie-metaphlan-output/1049)
2. [Input Specification if Pre-Existing MetaPhlAn Files](https://forum.biobakery.org/t/input-specification-if-pre-existing-metaphlan-files/2096)
3. [Question about using MetaPhlAn3 output as input for HUMAnN3](https://forum.biobakery.org/t/question-about-using-metaphlan3-output-as-input-for-humann3/1444)

I had bowtie & sam files from metaphlan and the I used

```auto
humann -i $sample_sam -o $sample_out --threads 45 --taxonomic-profile $sample_metaphlan.txt --input-format sam

```

generated results with something like “UNMAPPED 0.0000000000 UNINTEGRATED 0.0000000000”

Now I have to run humann with raw input fasta file. So the bowtie & sam files from metaphlan have not useful for humann in any way？

Sincerely,

Louie

---

<div class="post-metadata">

**Author:** ![franzosa](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/franzosa/32/3511_2.png) [@franzosa](https://forum.biobakery.org/u/franzosa)\
**Post date:** [March 25, 2022, 3:23pm UTC](https://forum.biobakery.org/t/metaphlan-results-as-input-on-humann/3325/2 "2022-03-25T15:23:05Z")

</div>

If you’ve already run MetaPhlAn on your samples you can skip that step in HUMAnN by passing the existing taxonomic profile to HUMAnN via the `--taxonomic-profile` flag. You would pass your input reads and specify an output folder as normal.