# CRITICAL ERROR: The metaphlan2.py executable not found

**URL:** <https://forum.biobakery.org/t/critical-error-the-metaphlan2-py-executable-not-found/5099>\
**Category:** HUMAnN\
**Created:** [April 5, 2023, 6:50pm UTC](https://forum.biobakery.org/t/critical-error-the-metaphlan2-py-executable-not-found/5099 "2023-04-05T18:50:41Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![Sam\_Degregori](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/sam_degregori/32/1748_2.png) [@Sam\_Degregori](https://forum.biobakery.org/u/Sam_Degregori)\
**Post date:** [April 5, 2023, 6:50pm UTC](https://forum.biobakery.org/t/critical-error-the-metaphlan2-py-executable-not-found/5099/1 "2023-04-05T18:50:41Z")

</div>

Hi all,

I am trying to run humann2 and get this error:

> (primate) root@DESKTOP-J59VIIJ:/mnt/c/Users/samde/gutmicrobiome# humann2 --input primateFastq/kneadpaired/KIT\_HANDLER\_DN\_MG3\_D8.filt1\_kneaddata\_paired\_1.fastq --output humOut/KIT\_HANDLER\_DN\_MG3\_D8.filt1\_kneaddata\_paired\_1 --threads 3  
> Output files will be written to: /mnt/c/Users/samde/gutmicrobiome/humOut/KIT\_HANDLER\_DN\_MG3\_D8.filt1\_kneaddata\_paired\_1  
> CRITICAL ERROR: The metaphlan2.py executable can not be found. Please check the install.

There is a similar post saying to run `metaphlan2.py --version` But I just get command not found. I tried installing metaphlan2 and get a “biom-format” error:

> ```auto
> error: command 'gcc' failed: No such file or directory: 'gcc'
> 
> ```

[end of output]

> note: This error originates from a subprocess, and is likely not a problem with pip.  
> ERROR: Failed building wheel for biom-format  
> Failed to build biom-format  
> ERROR: Could not build wheels for biom-format, which is required to install pyproject.toml-based projects

And then I cannot install biom-format etiher… Have spent all day on this but no luck… Any ideas?? For context I am on a WSL system with Ubunutu downloaded. And currently in a conda environment where only pip installs have worked. Conda installs keep finding inconsistencies.  
Thanks!  
Sam