Error running bgen file: ImportError: libbgen.so.3

[onebeingmay]

Hi MetaXcan team,
I am trying to run MetaXcan/software/Predict.py on UKB imputed genotypes (bgen files) but got an error. This error also happened to the example data you provided. Specifically, when I ran:

#setup environment
git clone https://github.com/hakyimlab/MetaXcan.git
conda env create -f MetaXcan/software/conda_env.yaml
conda activate imlabtools

#unpack the sample data
tar -xvpf models/predixcan_sample_data.tar --no-same-owner 
cd /home/dnanexus/data
METAXCAN=/home/dnanexus/MetaXcan/software

#bgen input
python3 $METAXCAN/Predict.py \
--model_db_path models/gtex_v8_en/en_Whole_Blood.db \
--bgen_genotypes 1000G_hg37_bgen/chr22.bgen \
--bgen_use_rsid \
--prediction_output test_outputs/bgen_1000G_hg37_en/Whole_Blood__predict.txt \
--prediction_summary_output test_outputs/bgen_1000G_hg37_en/Whole_Blood__summary.txt \
--verbosity 8 \
--throw

The output was:

INFO - Loading samples
Traceback (most recent call last):
File "/home/dnanexus/MetaXcan/software/Predict.py", line 272, in
run(args)
File "/home/dnanexus/MetaXcan/software/Predict.py", line 160, in run
samples = load_samples(args)
File "/home/dnanexus/MetaXcan/software/Predict.py", line 90, in load_samples
from metax.genotype import BGENGenotype
File "/home/dnanexus/MetaXcan/software/metax/genotype/BGENGenotype.py", line 1, in
import bgen_reader
File "/home/dnanexus/miniconda3/envs/imlabtools/lib/python3.7/site-packages/bgen_reader/init.py", line 26, in
from ._metadata import create_metafile
File "/home/dnanexus/miniconda3/envs/imlabtools/lib/python3.7/site-packages/bgen_reader/_metadata.py", line 4, in
from ._bgen import bgen_file
File "/home/dnanexus/miniconda3/envs/imlabtools/lib/python3.7/site-packages/bgen_reader/_bgen.py", line 3, in
from ._ffi import ffi, lib
ImportError: libbgen.so.3: cannot open shared object file: No such file or directory

I can run the vcf sample data without problem. Any idea?
Thank you!

[Fnyasimi]

Kindly ensure the bgen reader is installed properly with the correct version as defined here.

[onebeingmay]

Kindly ensure the bgen reader is installed properly with the correct version as defined here.

Hi Fnyasimi,
Are you referring to

conda env create -f /path/to/this/repo/software/conda_env.yaml
conda activate imlabtools

I can confirm I ran this to set up a new environment.
Thanks

[Fnyasimi]

Then you need to ensure this library libbgen.so.3: is available within your path