The steps we followed:
conda create --name py377 python=3.7.7
conda activate py377
conda install -c biobakery biobakery_workflows
biobakery_workflows_databases --install wmgx
While trying to install the wmgx module, the system is throwing the below error. Seems like the error is coming from the bowtie2 module.
(py377) shekhar@shekhar-VirtualBox:~$ biobakery_workflows_databases --install wmgx
Installing humann utility mapping database
Download URL: http://huttenhower.sph.harvard.edu/humann2_data/full_mapping_v201901.tar.gz
Downloading file of size: 1.37 GB
1.37 GB 100.00 % 5.84 MB/sec 0 min -0 sec
Extracting: /home/shekhar/biobakery_workflows_databases/humann/full_mapping_v201901.tar.gz
Database installed: /home/shekhar/biobakery_workflows_databases/humann/utility_mapping
HUMAnN configuration file updated: database_folders : utility_mapping = /home/shekhar/biobakery_workflows_databases/humann/utility_mapping
Generating strainphlan fasta database
/home/shekhar/anaconda3/envs/py377/bin/bowtie2-inspect:24: DeprecationWarning: the imp module is deprecated in favour of importlib; see the module’s documentation for alternative uses
import imp
Could not locate a Bowtie index corresponding to basename “/home/shekhar/anaconda3/envs/py377/lib/python3.7/site-packages/metaphlan/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901”
Error: Encountered internal Bowtie 2 exception (#1)
Command: /home/shekhar/anaconda3/envs/py377/bin/bowtie2-inspect-s --wrapper basic-0 /home/shekhar/anaconda3/envs/py377/lib/python3.7/site-packages/metaphlan/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901
Unable to install database. Error running command: bowtie2-inspect /home/shekhar/anaconda3/envs/py377/lib/python3.7/site-packages/metaphlan/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901 > /home/shekhar/biobakery_workflows_databases/strainphlan_db_markers/all_markers.fasta
While we tried to remove the warning, we replaced import imp with ‘import importlib’. However, that caused the whole biobakery_workflows_databases command to fail without achieving any results.
Here is the log:
(py377) shekhar@shekhar-VirtualBox:~$ biobakery_workflows_databases --install wmgx
Installing humann utility mapping database
Download URL: http://huttenhower.sph.harvard.edu/humann2_data/full_mapping_v201901.tar.gz
Downloading file of size: 1.37 GB
CRITICAL ERROR: Unable to download and extract from URL: http://huttenhower.sph.harvard.edu/humann2_data/full_mapping_v201901.tar.gz
Unable to install database. Error running command: humann_databases --download utility_mapping full /home/shekhar/biobakery_workflows_databases/humann
Thanks
Mukil