# bowtie2 not available while running MetaPhlan2 and Humann2

**URL:** https://help.galaxyproject.org/t/bowtie2-not-available-while-running-metaphlan2-and-humann2/11369
**Category:** usegalaxy.org support
**Tags:** metagenomics, server-open-issue, humann
**Created:** [December 27, 2023, 8:17pm UTC](https://help.galaxyproject.org/t/bowtie2-not-available-while-running-metaphlan2-and-humann2/11369 "2023-12-27T20:17:31Z")
**Posts on this page:** 2
**Page:** 1

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### Author: ![hussnain](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/hussnain/32/5017_2.png) [@hussnain](https://help.galaxyproject.org/u/hussnain)
#### Post date: [December 27, 2023, 8:17pm UTC](https://help.galaxyproject.org/t/bowtie2-not-available-while-running-metaphlan2-and-humann2/11369/1 "2023-12-27T20:17:31Z")

</div>

Hi there.

I have been facing this issue on both, .ORG and .BE, servers for more than a week now. It was working fine before that. I am trying to run MetaPhlan2 (MetaPhlan on .org) and getting the following error:

```auto
/srv/galaxy/shared/etc/dependencies/miniconda3/envs/mulled-v1-c5867e29ea0fba532ec8dc4a557d8798445dccb6ecf21f67e09143751a79b65d/bin/bowtie2-align-s: /srv/galaxy/shared/etc/dependencies/miniconda3/envs/mulled-v1-c5867e29ea0fba532ec8dc4a557d8798445dccb6ecf21f67e09143751a79b65d/bin/../lib/libstdc++.so.6: version `CXXABI_1.3.13' not found (required by /lib64/libtbb.so.2)
(ERR): Description of arguments failed!
Exiting now ...
Error while running bowtie2.

```

The error for Humann2 is:

```auto
CRITICAL ERROR: Can not call software version for bowtie2

```

I thought there was a problem with my data and flow, so I produced this error by following the flow and data on this [tutorial](https://training.galaxyproject.org/training-material/topics/metagenomics/tutorials/general-tutorial/tutorial.html#shotgun-metagenomics-data).

I would highly appreciate your help.  
Hussnain

---

<div class="post-metadata">

### Author: ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)
#### Post date: [January 10, 2024, 12:13am UTC](https://help.galaxyproject.org/t/bowtie2-not-available-while-running-metaphlan2-and-humann2/11369/2 "2024-01-10T00:13:41Z")

</div>

> [@hussnain](#):
>
> MetaPhlan2

Yes, there are some known issues with the indexes. Details → [https://github.com/galaxyproject/usegalaxy-tools/issues/649](https://github.com/galaxyproject/usegalaxy-tools/issues/649)

Try running the tools at [UseGalaxy.eu](http://UseGalaxy.eu) instead for now.