# CRITICAL ERROR: The directory provided for ChocoPhlAn does not contain files of the expected format (ie '^\[g\_\_\]\[s\_\_\]')

**URL:** <https://forum.biobakery.org/t/critical-error-the-directory-provided-for-chocophlan-does-not-contain-files-of-the-expected-format-ie-g-s/749>\
**Category:** HUMAnN\
**Created:** [July 22, 2020, 4:23am UTC](https://forum.biobakery.org/t/critical-error-the-directory-provided-for-chocophlan-does-not-contain-files-of-the-expected-format-ie-g-s/749 "2020-07-22T04:23:37Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![wenping](https://avatars.discourse-cdn.com/v4/letter/w/e56c9b/32.png) [@wenping](https://forum.biobakery.org/u/wenping)\
**Post date:** [July 22, 2020, 4:23am UTC](https://forum.biobakery.org/t/critical-error-the-directory-provided-for-chocophlan-does-not-contain-files-of-the-expected-format-ie-g-s/749/1 "2020-07-22T04:23:37Z")

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hi Franzosa,  
I downloaded the newest database of ChocoPhlan and installed humann3. When I run humann as following, some error occured:

(py37) [wenping@localhost data]$ humann --input /data/liying\_metagenome/clean\_data\_ly/SRR5130527.fastq --output try\_humann --bypass-translated-search  
Creating output directory: /data/try\_humann  
Output files will be written to: /data/try\_humann  
Removing spaces from identifiers in input file …

CRITICAL ERROR: The directory provided for ChocoPhlAn does not contain files of the expected format (ie ‘^[g\_\_][s\_\_]’).

can you know how to fix the error?

wenping

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**Author:** ![lauren.j.mciver](https://avatars.discourse-cdn.com/v4/letter/l/f05b48/32.png) [@lauren.j.mciver](https://forum.biobakery.org/u/lauren.j.mciver)\
**Post date:** [July 22, 2020, 3:40pm UTC](https://forum.biobakery.org/t/critical-error-the-directory-provided-for-chocophlan-does-not-contain-files-of-the-expected-format-ie-g-s/749/2 "2020-07-22T15:40:49Z")

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Hi Wenping,

It looks like the location set in your config for the nucleotide database does not contain files of the expected format. Would you run the humann\_config command? It will print the folder that you have set to contain the directory for the ChocoPhlAn files (the nucleotide database). Those files should be named something with “g\_\_” (genus) and “s\_\_” (species) in the name. If the folder location needs to change you can also use the humann\_config command or set the new folder location when running HUMAnN with `--nucleotide-database <NEW_LOCATION>`.

```auto
# print the current config settings
$ humann_config --print
HUMAnN Configuration ( Section : Name = Value )
output_format : remove_stratified_output = False
output_format : output_max_decimals = 10
alignment_settings : prescreen_threshold = 0.01
alignment_settings : evalue_threshold = 1.0
alignment_settings : identity_threshold = 50.0
database_folders : nucleotide = data/chocophlan_DEMO

```

```auto
# update the config setting
$ humann_config --update database_folders nucleotide $NEW_LOCATION 

```

Thanks!  
Lauren

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<div class="post-metadata">

**Author:** ![wenping](https://avatars.discourse-cdn.com/v4/letter/w/e56c9b/32.png) [@wenping](https://forum.biobakery.org/u/wenping)\
**Post date:** [July 23, 2020, 12:36am UTC](https://forum.biobakery.org/t/critical-error-the-directory-provided-for-chocophlan-does-not-contain-files-of-the-expected-format-ie-g-s/749/3 "2020-07-23T00:36:43Z")

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Hi Lauren,  
It works.  
Thank you very much!  
Wenping

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<div class="post-metadata">

**Author:** ![nick-youngblut](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/nick-youngblut/32/528_2.png) [@nick-youngblut](https://forum.biobakery.org/u/nick-youngblut)\
**Post date:** [May 4, 2023, 12:28am UTC](https://forum.biobakery.org/t/critical-error-the-directory-provided-for-chocophlan-does-not-contain-files-of-the-expected-format-ie-g-s/749/4 "2023-05-04T00:28:28Z")

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In regards to this error:

```auto
CRITICAL ERROR: The directory provided for ChocoPhlAn does not contain files of the expected format (ie '^[g__][s__]').

```

`full_chocophlan.v201901_v31.tar.gz` contains the following file: `alaS.centroids.v201901_v31.ffn.gz`, which in not formatted like all of the other 12772 genome files in the database.

Should `alaS.centroids.v201901_v31.ffn.gz` be removed from `full_chocophlan.v201901_v31.tar.gz`, or is the `^[g__][s__]` format not actually needed for all genome files?