# Biobakery workflows Strainphlan

**URL:** <https://forum.biobakery.org/t/biobakery-workflows-strainphlan/7398>\
**Category:** bioBakery workflows\
**Created:** [August 23, 2024, 9:08am UTC](https://forum.biobakery.org/t/biobakery-workflows-strainphlan/7398 "2024-08-23T09:08:31Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![imontero](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/imontero/32/3411_2.png) [@imontero](https://forum.biobakery.org/u/imontero)\
**Post date:** [August 23, 2024, 9:08am UTC](https://forum.biobakery.org/t/biobakery-workflows-strainphlan/7398/1 "2024-08-23T09:08:31Z")

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I reinstalled biobakery workflows last june using Conda instructions. Kneaddata, Metaphlan and Humann worked, but Strainphlan gives me an error

ERROR: Unable to find database STRAINPHLAN\_DB\_MARKERS. This is the folder containing the StrainPhlAN marker files. Unable to find in default install folders or with environment variables.

I have set conda env variables

BIOBAKERY\_WORKFLOWS\_DATABASES = /media/microviable/e/biobakery\_workflows\_databases  
KNEADDATA\_DB\_HUMAN\_GENOME = /media/microviable/e/biobakery\_workflows\_databases/kneaddata\_db\_human\_genome  
KNEADDATA\_DB\_RIBOSOMAL\_RNA = /media/microviable/e/biobakery\_workflows\_databases/kneaddata\_db\_human\_genome  
KNEADDATA\_DB\_HUMAN\_TRANSCRIPTOME = /media/microviable/e/biobakery\_workflows\_databases/kneaddata\_db\_human\_genome  
KNEADDATA\_DB\_MOUSE\_GENOME = /media/microviable/e/biobakery\_workflows\_databases/kneaddata\_db\_mouse\_genome  
STRAINPHLAN\_DB\_REFERENCE = /media/microviable/e/biobakery\_workflows\_databases/strainphlan\_db\_reference  
STRAINPHLAN\_DB\_MARKERS = /media/microviable/e/biobakery\_workflows\_databases/strainphlan\_db\_marker

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**Author:** ![smithhhlna](https://avatars.discourse-cdn.com/v4/letter/s/ecc23a/32.png) [@smithhhlna](https://forum.biobakery.org/u/smithhhlna)\
**Post date:** [September 5, 2024, 9:36am UTC](https://forum.biobakery.org/t/biobakery-workflows-strainphlan/7398/2 "2024-09-05T09:36:31Z")

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Hi,

I think you should try StrainPhlAn is unable to locate the marker database. Double check the path set for STRAINPHLAN DB MARKERS to ensure the folder exists and contains the necessary marker files. Also verify that the environment variable is correctly set in your active Conda environment and restart the session to apply any changes. You might also need to re download the StrainPhlAn marker files if they are missing or corrupted.

Thanks