# Install database erro **URL:** \ **Category:** bioBakery workflows\ **Created:** [June 14, 2021, 2:24pm UTC](https://forum.biobakery.org/t/install-database-erro/2254 "2021-06-14T14:24:42Z")\ **Posts on this page:** 7\ **Page:** 1
**Author:** ![Bernadette\_Connors](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/bernadette_connors/32/856_2.png) [@Bernadette\_Connors](https://forum.biobakery.org/u/Bernadette_Connors)\ **Post date:** [June 14, 2021, 2:24pm UTC](https://forum.biobakery.org/t/install-database-erro/2254/1 "2021-06-14T14:24:43Z")
Hi there. We are installing biobakery\_workflows on our local machine using conda install -c biobakery biobakery\_workflows. When we installed the databases, using biobakery\_workflows\_databases --install wmgx, we received the error below. We tried wmgx\_demo, 16S, and wmgx\_wmgx, and received the same error in all cases. Could you help us to understand what our error is when installing the databases? It would be much appreciated. Have a great day! (base) biolab@FH-BIOLAB-IMAC ~ % conda install -c biobakery biobakery\_workflows (base) biolab@FH-BIOLAB-IMAC ~ % biobakery\_workflows\_databases --install wmgx Traceback (most recent call last): File “/Users/biolab/opt/miniconda3/bin/biobakery\_workflows\_databases”, line 6, in from biobakery\_workflows.biobakery\_workflows\_databases import main File “/Users/biolab/opt/miniconda3/lib/python3.8/site-packages/biobakery\_workflows/biobakery\_workflows\_databases.py”, line 30, in from . import utilities File “/Users/biolab/opt/miniconda3/lib/python3.8/site-packages/biobakery\_workflows/utilities.py”, line 34, in from anadama2.tracked import TrackedDirectory File “/Users/biolab/opt/miniconda3/lib/python3.8/site-packages/anadama2/ **init**.py”, line 83, in from .workflow import Workflow File “/Users/biolab/opt/miniconda3/lib/python3.8/site-packages/anadama2/workflow.py”, line 24, in from . import backends File “/Users/biolab/opt/miniconda3/lib/python3.8/site-packages/anadama2/backends.py”, line 7, in import leveldb ModuleNotFoundError: No module named ‘leveldb’ ---
**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:** [June 14, 2021, 2:38pm UTC](https://forum.biobakery.org/t/install-database-erro/2254/2 "2021-06-14T14:38:32Z")
Hi, Thank you for the detailed post. It looks like you are missing a dependency which is causing the error. If you install leveldb with conda or pypi it should resolve the issue. Thank you, Lauren ---
**Author:** ![Bernadette\_Connors](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/bernadette_connors/32/856_2.png) [@Bernadette\_Connors](https://forum.biobakery.org/u/Bernadette_Connors)\ **Post date:** [June 14, 2021, 4:06pm UTC](https://forum.biobakery.org/t/install-database-erro/2254/3 "2021-06-14T16:06:51Z")
> [@lauren.j.mciver](#): > > leveldb with conda or pypi Lauren- Thank you so much for your quick and perfect response. I installed leveldb and was successful…at first! I downloaded the HUMAnN database but then ran into an error when strainphlan was being generated (please see below). Again, any advice would be really appreciated. HUMAnN configuration file updated: database\_folders : utility\_mapping = /Users/biolab/biobakery\_workflows\_databases/humann/utility\_mapping Generating strainphlan fasta database Could not locate a Bowtie index corresponding to basename “/Users/biolab/opt/miniconda3/lib/python3.8/site-packages/metaphlan/metaphlan\_databases/mpa\_v30\_CHOCOPhlAn\_201901” Error: Encountered internal Bowtie 2 exception (#1) Command: /Users/biolab/opt/miniconda3/bin/bowtie2-inspect-s --wrapper basic-0 /Users/biolab/opt/miniconda3/lib/python3.8/site-packages/metaphlan/metaphlan\_databases/mpa\_v30\_CHOCOPhlAn\_201901 Unable to install database. Error running command: bowtie2-inspect /Users/biolab/opt/miniconda3/lib/python3.8/site-packages/metaphlan/metaphlan\_databases/mpa\_v30\_CHOCOPhlAn\_201901 \> /Users/biolab/biobakery\_workflows\_databases/strainphlan\_db\_markers/all\_markers.fasta ---
**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:** [June 24, 2021, 10:33pm UTC](https://forum.biobakery.org/t/install-database-erro/2254/4 "2021-06-24T22:33:13Z")
Hi @Bernadette_Connors , Can you install the MetaPhlAn database? The workflows use that database to generate the StrainPhlAn database. Thank you, Lauren ---
**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:** [December 25, 2021, 7:54pm UTC](https://forum.biobakery.org/t/install-database-erro/2254/5 "2021-12-25T19:54:44Z")
Hello, I tried this but if did not works for me (metaphlan) microviable@DESKTOP-39BJL73:~$ biobakery\_workflows\_databases --install wmgx\_demo Traceback (most recent call last): File “/home/microviable/anaconda3/envs/metaphlan/bin/biobakery\_workflows\_databases”, line 6, in from biobakery\_workflows.biobakery\_workflows\_databases import main File “/home/microviable/anaconda3/envs/metaphlan/lib/python3.7/site-packages/biobakery\_workflows/biobakery\_workflows\_databases.py”, line 30, in from . import utilities File “/home/microviable/anaconda3/envs/metaphlan/lib/python3.7/site-packages/biobakery\_workflows/utilities.py”, line 34, in from anadama2.tracked import TrackedDirectory File “/home/microviable/anaconda3/envs/metaphlan/lib/python3.7/site-packages/anadama2/ **init**.py”, line 83, in from .workflow import Workflow File “/home/microviable/anaconda3/envs/metaphlan/lib/python3.7/site-packages/anadama2/workflow.py”, line 24, in from . import backends File “/home/microviable/anaconda3/envs/metaphlan/lib/python3.7/site-packages/anadama2/backends.py”, line 7, in import leveldb ModuleNotFoundError: No module named ‘leveldb’ (metaphlan) microviable@DESKTOP-39BJL73:~$ pip install leveldb Requirement already satisfied: leveldb in ./anaconda3/envs/metaphlan/lib/python3.7/site-packages (0.201) (metaphlan) microviable@DESKTOP-39BJL73:~$ conda install leveldb Collecting package metadata (current\_repodata.json): done Solving environment: done # All requested packages already installed. (metaphlan) microviable@DESKTOP-39BJL73:~$ biobakery\_workflows\_databases --install wmgx\_demo Traceback (most recent call last): File “/home/microviable/anaconda3/envs/metaphlan/bin/biobakery\_workflows\_databases”, line 6, in from biobakery\_workflows.biobakery\_workflows\_databases import main File “/home/microviable/anaconda3/envs/metaphlan/lib/python3.7/site-packages/biobakery\_workflows/biobakery\_workflows\_databases.py”, line 30, in from . import utilities File “/home/microviable/anaconda3/envs/metaphlan/lib/python3.7/site-packages/biobakery\_workflows/utilities.py”, line 34, in from anadama2.tracked import TrackedDirectory File “/home/microviable/anaconda3/envs/metaphlan/lib/python3.7/site-packages/anadama2/ **init**.py”, line 83, in from .workflow import Workflow File “/home/microviable/anaconda3/envs/metaphlan/lib/python3.7/site-packages/anadama2/workflow.py”, line 24, in from . import backends File “/home/microviable/anaconda3/envs/metaphlan/lib/python3.7/site-packages/anadama2/backends.py”, line 7, in import leveldb ModuleNotFoundError: No module named ‘leveldb’ ---
**Author:** ![adler-sudo](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/adler-sudo/32/1146_2.png) [@adler-sudo](https://forum.biobakery.org/u/adler-sudo)\ **Post date:** [February 2, 2022, 6:18am UTC](https://forum.biobakery.org/t/install-database-erro/2254/6 "2022-02-02T06:18:57Z")
This worked for me to solve the error message that @Bernadette_Connors got above. I shifted to my conda environment where I already had installed metaphlan. I was then able to successfully run the following command: ```auto biobakery_workflows_databases --install wmgx ``` Additionally, it should be noted that the commands I had run to install metphlan on this conda environment initially were ```auto conda install tbb=2020.2 conda install -c bioconda metaphlan metphalan --install --nproc 8 ``` It should be noted that there is information about this in the github page [GitHub - biobakery/biobakery\_workflows: bioBakery workflows is a collection of workflows and tasks for executing common microbial community analyses using standardized, validated tools and parameters.](https://github.com/biobakery/biobakery_workflows). HOWEVER, the location of these instructions coming after the necessary command caused me confusion. It might be better to move those instructions regarding prerequisite packages to up above the command. ---
**Author:** ![DSPINTO21](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/dspinto21/32/1401_2.png) [@DSPINTO21](https://forum.biobakery.org/u/DSPINTO21)\ **Post date:** [April 22, 2022, 7:03am UTC](https://forum.biobakery.org/t/install-database-erro/2254/8 "2022-04-22T07:03:01Z")
Hello, I’ve also been having the same issue. I installed leveldb using conda. And leveldb shows up in the conda list, but I keep getting this error. Please let me know if you were able to find a solution for this. Thank You UPDATE: Managed to find the solution thanks to @BITsmyoon install levelDB using the command below: conda install -c conda-forge python-leveldb