# What metaphlan 4.1 output shoud I use as input for humann 3.9? **URL:** \ **Category:** HUMAnN\ **Created:** [May 15, 2024, 7:57am UTC](https://forum.biobakery.org/t/what-metaphlan-4-1-output-shoud-i-use-as-input-for-humann-3-9/7051 "2024-05-15T07:57:51Z")\ **Posts on this page:** 2\ **Page:** 1
**Author:** ![Francesco\_Pantini](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/francesco_pantini/32/2856_2.png) [@Francesco\_Pantini](https://forum.biobakery.org/u/Francesco_Pantini)\ **Post date:** [May 15, 2024, 7:57am UTC](https://forum.biobakery.org/t/what-metaphlan-4-1-output-shoud-i-use-as-input-for-humann-3-9/7051/1 "2024-05-15T07:57:51Z")
Greetings, I’m a student and I’m currently trying to use humann3.9 with the metaphlan4.1 output but I’m a little bit stuck cause with both the biom and the sam the humann gives me only UNMAPPED. I know that there is also the possibility to use the humann with fastq but i need to maintain the two programs separated. The thing i wanna ask is, what is the optimal metaphlan output to give to the humann? Thank you for your patience and have a nice week. ---
**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:** [June 20, 2024, 8:53pm UTC](https://forum.biobakery.org/t/what-metaphlan-4-1-output-shoud-i-use-as-input-for-humann-3-9/7051/2 "2024-06-20T20:53:05Z")
If you’re running MetaPhlAn outside of HUMAnN, then you need to pass the default taxonomic profile MetaPhlAn creates to HUMAnN via the `--taxonomic-profile` flag. HUMAnN will _also_ need the input reads used to generate that profile as its own `--input`. The taxonomic profile will be functioning as a guide in this case for putting together a relevant pangenome database to map the reads against.