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ImportError related to allel, libpmix.so #53

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QingData opened this issue Dec 9, 2024 · 0 comments
Open

ImportError related to allel, libpmix.so #53

QingData opened this issue Dec 9, 2024 · 0 comments

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@QingData
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QingData commented Dec 9, 2024

Hi.
I am trying to run the script for the Demo, but encounter an error about importing a package.
"ImportError: libpmix.so.2: cannot open shared object file: No such file or directory". It seem coming from the package "allel".
Would you please tell me how to install the package correctly?
Below is my command:

python3 gnomix.py demo/data/small_query_chr22.vcf.gz demo_output 22 True pretrained_gnomix_models/chr22/model_chm_22.pkl > out_gnomix_demo.log

Below is the error message:

Traceback (most recent call last):
File "gnomix.py", line 9, in
from src.utils import run_shell_cmd, join_paths, read_vcf, vcf_to_npy, npy_to_vcf, update_vcf
File "/MYSCRIPT_DIR/gnomix/src/utils.py", line 1, in
import allel
File "/MY_PACKAGE_DIR/lib/python3.8/site-packages/allel/init.py", line 4, in
from .model.ndarray import *
File "/MY_PACKAGE_DIR/lib/python3.8/site-packages/allel/model/ndarray.py", line 18, in
from allel.opt.model import genotype_array_pack_diploid, genotype_array_unpack_diploid,
ImportError: libpmix.so.2: cannot open shared object file: No such file or directory

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