KneadData workfolw Installation problem

Infrastructure and utilities KneadData
1

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

2

I am bumping this because I am having the same issue.

conda create -n metagenome 
conda activate metagenome
conda install -c biobakery biobakery_workflows
conda install -c biobakery biobakery_workflows

biobakery_workflows_databases --install wmgx_demo

Error message:

Installing humann2 utility mapping database
Download URL: http://huttenhower.sph.harvard.edu/humann2_data/full_mapping_1_1.tar.gz
Downloading file of size: 0.58 GB

0.58 GB 100.00 %   8.18 MB/sec  0 min -0 sec
Extracting: /home/emilyw/biobakery_workflows_databases/humann2/full_mapping_1_1.tar.gz

Database installed: /home/emilyw/biobakery_workflows_databases/humann2/utility_mapping

HUMAnN2 configuration file updated: database_folders : utility_mapping = /home/emilyw/biobakery_workflows_databases/humann2/utility_mapping
Generating strainphlan fasta database
Could not locate a Bowtie index corresponding to basename "/home/emilyw/.conda/envs/metagenome/bin/metaphlan_databases/mpa_v20_m200"
Error: Encountered internal Bowtie 2 exception (#1)
Command: /home/emilyw/.conda/envs/metagenome/bin/bowtie2-inspect-s --wrapper basic-0 /home/emilyw/.conda/envs/metagenome/bin/metaphlan_databases/mpa_v20_m200
Unable to install database. Error running command: b o w t i e 2 - i n s p e c t   / h o m e / e m i l y w / . c o n d a / e n v s / m e t a g e n o m e / b i n / m e t a p h l a n _ d a t a b a s e s / m p a _ v 2 0 _ m 2 0 0   >   / h o m e / e m i l y w / b i o b a k e r y _ w o r k f l o w s _ d a t a b a s e s / s t r a i n p h l a n _ d b _ m a r k e r s / a l l _ m a r k e r s . f a s t a