Biobakery workflows Strainphlan

Infrastructure and utilities bioBakery workflows
1

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

2

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