Hi there! I hope you are well, and hope you might be able to help me with some errors. I am trying to install and run biobakery_workflows, but there are two problems that I’m facing.
Context (How I installed biobakery_workflows):
This is how I installed the biobakery workflow:
conda create -n biobakerywf -c biobakery biobakery_workflows
Problem 1: Trouble downloading and installing databases with biobakery_workflows_databases
When I first tried to install the databases with biobakery_workflows_databases, I received a tbb error:
error while loading shared libraries: libtbb.so.2: cannot open shared object file: No such file or directory (ERR): Description of arguments failed!
This was not too big of a deal, because it’s a known issue with bowtie2. I resolved this by downgrading tbb.:
conda install tbb=2020.2
After these changes, I again tried to install databases with:
biobakery_workflows_databases --install wmgx --location /home/bsingh/bin/biobakery_databases
I received the following error:
Installing humann utility mapping database Download URL: http://huttenhower.sph.harvard.edu/humann2_data/full_mapping_v201901.tar.gz Downloading file of size: 2.55 GB 2.55 GB 100.00 % 10.70 MB/sec 0 min -0 sec Extracting: /home/bsingh/bin/biobakery_databases/humann/full_mapping_v201901.tar.gz Database installed: /home/bsingh/bin/biobakery_databases/humann/utility_mapping HUMAnN configuration file updated: database_folders : utility_mapping = /home/bsingh/bin/biobakery_databases/humann/utility_mapping Generating strainphlan fasta database Could not locate a Bowtie index corresponding to basename "/home/bsingh/miniconda3/envs/biobakerywf/lib/python3.7/site-packages/metaphlan/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901" Error: Encountered internal Bowtie 2 exception (#1) Command: /home/bsingh/miniconda3/envs/biobakerywf/bin/bowtie2-inspect-s --wrapper basic-0 /home/bsingh/miniconda3/envs/biobakerywf/lib/python3.7/site-packages/metaphlan/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901 Unable to install database. Error running command: bowtie2-inspect /home/bsingh/miniconda3/envs/biobakerywf/lib/python3.7/site-packages/metaphlan/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901 > /home/bsingh/bin/biobakery_databases/strainphlan_db_markers/all_markers.fasta
Any help would be appreciated!
Problem 2: "Unpickling Error"
When I try to even do
biobakery_workflows wmgx --help, I get the following error:
File "/home/bsingh/miniconda3/envs/biobakerywf/bin/wmgx.py", line 41, in <module> workflow = Workflow(version="0.1", description="A workflow for whole metagenome shotgun sequences") File "/home/bsingh/miniconda3/envs/biobakerywf/lib/python3.7/site-packages/anadama2/workflow.py", line 120, in __init__ self.document=PweaveDocument() File "/home/bsingh/miniconda3/envs/biobakerywf/lib/python3.7/site-packages/anadama2/document.py", line 96, in __init__ self.vars=self.get_vars() File "/home/bsingh/miniconda3/envs/biobakerywf/lib/python3.7/site-packages/anadama2/document.py", line 325, in get_vars vars = pickle.load(open(pickle_file,"rb")) _pickle.UnpicklingError: pickle data was truncated
I think this error is separate from the database download errors. For this one, I’m truly lost. Once again, any help would be appreciated!