# Update HUMAnN for MetaPhlAn 4.2 compatability

**URL:** <https://forum.biobakery.org/t/update-humann-for-metaphlan-4-2-compatability/8117>\
**Category:** Feature/Pull Request\
**Created:** [June 7, 2025, 7:11am UTC](https://forum.biobakery.org/t/update-humann-for-metaphlan-4-2-compatability/8117 "2025-06-07T07:11:28Z")\
**Posts on this page:** 4\
**Page:** 1

<div class="post-metadata">

**Author:** ![zzkt](https://avatars.discourse-cdn.com/v4/letter/z/e8c25b/32.png) [@zzkt](https://forum.biobakery.org/u/zzkt)\
**Post date:** [June 7, 2025, 7:11am UTC](https://forum.biobakery.org/t/update-humann-for-metaphlan-4-2-compatability/8117/1 "2025-06-07T07:11:28Z")

</div>

I’ve recently upgraded to humann v3.9 & MetaPhlAn version 4.2.2 and it appears that the way MetaPhlAn handles map files has changed, so the ‘–bowtie2out’ arg is now ‘–mapout’ (as mentioned in the [release announcement](https://forum.biobakery.org/t/metaphlan-4-2-2-release-initial-long-read-sequencing-support-and-database-update/8109))

An example PR at [Update for MetaPhlAn 4.2 compatability by zzkt · Pull Request #67 · biobakery/humann · GitHub](https://github.com/biobakery/humann/pull/67)

---

<div class="post-metadata">

**Author:** ![zzkt](https://avatars.discourse-cdn.com/v4/letter/z/e8c25b/32.png) [@zzkt](https://forum.biobakery.org/u/zzkt)\
**Post date:** [June 11, 2025, 6:52am UTC](https://forum.biobakery.org/t/update-humann-for-metaphlan-4-2-compatability/8117/2 "2025-06-11T06:52:09Z")

</div>

The same issue is present in HUMAnN 4.0.0a1

---

<div class="post-metadata">

**Author:** ![jordan.valdez](https://avatars.discourse-cdn.com/v4/letter/j/4bbf92/32.png) [@jordan.valdez](https://forum.biobakery.org/u/jordan.valdez)\
**Post date:** [June 14, 2025, 4:17pm UTC](https://forum.biobakery.org/t/update-humann-for-metaphlan-4-2-compatability/8117/3 "2025-06-14T16:17:57Z")

</div>

I also am having compatibility issues with HUMAnN v4.0.0.alpha.1 and MetaPhlAn 4.2.2 as a result of --bowtie2out no longer being an arguement. Any suggestions on how to address this?

---

<div class="post-metadata">

**Author:** ![zzkt](https://avatars.discourse-cdn.com/v4/letter/z/e8c25b/32.png) [@zzkt](https://forum.biobakery.org/u/zzkt)\
**Post date:** [June 16, 2025, 5:34pm UTC](https://forum.biobakery.org/t/update-humann-for-metaphlan-4-2-compatability/8117/4 "2025-06-16T17:34:41Z")

</div>

You can try patching a local copy of HUMAnN to use the new arg prefix (specifics [here](https://github.com/biobakery/humann/pull/67/files)). It should still pass all the tests run by `humann_test` and `humann_test --run-functional-tests-tools`.

Seems to work as expected so far…