rule compute LD scores: numpy issue when running on a singularity image

[ElizabethWallace97]

I am running CELLECT on a singularity image by necessity (large files that need to be run on a remote data cluster). I am running into this error when the ldsc reaches the compute_LD_scores step and cannot figure out how to solve it:
Error in rule compute_LD_scores_all_genes: jobid: 128 input: /data/CELLECT_ATAC/CELLECT-LDSC/precomputation/control.all_genes_in_dataset/all_genes_in_data.18.annot.gz output: /project/stefanoberto/musc/ASD_Multiome/CELLECT_ATAC/CELLECT-LDSC/precomputation/control.all_genes_in_dataset/all_genes_in_data.18.l2.ldscore.gz, /data/CELLECT_ATAC/CELLECT-LDSC/precomputation/control.all_genes_in_dataset/all_genes_in_data.18.l2.M, /data/CELLECT_ATAC/CELLECT-LDSC/precomputation/control.all_genes_in_dataset/all_genes_in_data.18.l2.M_5_50, /data/CELLECT_ATAC/CELLECT-LDSC/precomputation/control.all_genes_in_dataset/all_genes_in_data.18.log log: /data/CELLECT_ATAC/CELLECT-LDSC/logs/log.compute_LD_scores.all_genes_in_dataset.data.18.txt (check log file(s) for error details) conda-env: /home/elizabethwallace/f9098b7cb53074bc8a6e22639fba8910_ shell: /home/elizabethwallace/Documents/CELLECT/ldsc/ldsc.py --l2 --bfile /home/elizabethwallace/Documents/CELLECT/data/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.18 --ld-wind-cm 1 --annot /data/CELLECT_ATAC/CELLECT-LDSC/precomputation/control.all_genes_in_dataset/all_genes_in_ASD_Multiome.18.annot.gz --thin-annot --out /data/CELLECT_ATAC/CELLECT-LDSC/precomputation/control.all_genes_in_dataset/all_genes_in_data.18 --print-snps /home/elizabethwallace/Documents/CELLECT/data/ldsc/print_snps.txt &> /data/CELLECT_ATAC/CELLECT-LDSC/logs/log.compute_LD_scores.all_genes_in_dataset.data.18.txt (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Log file:
Traceback (most recent call last): File "/home/elizabethwallace/Documents/CELLECT/ldsc/ldsc.py", line 12, in <module> import ldscore.ldscore as ld File "/home/elizabethwallace/Documents/CELLECT/ldsc/ldscore/ldscore.py", line 2, in <module> import numpy as np File "/home/elizabethwallace/f9098b7cb53074bc8a6e22639fba8910_/lib/python2.7/site-packages/numpy/__init__.py", line 142, in <module> from . import add_newdocs File "/home/elizabethwallace/f9098b7cb53074bc8a6e22639fba8910_/lib/python2.7/site-packages/numpy/add_newdocs.py", line 13, in <module> from numpy.lib import add_newdoc File "/home/elizabethwallace/f9098b7cb53074bc8a6e22639fba8910_/lib/python2.7/site-packages/numpy/lib/__init__.py", line 8, in <module> from .type_check import * File "/home/elizabethwallace/f9098b7cb53074bc8a6e22639fba8910_/lib/python2.7/site-packages/numpy/lib/type_check.py", line 11, in <module> import numpy.core.numeric as _nx File "/home/elizabethwallace/f9098b7cb53074bc8a6e22639fba8910_/lib/python2.7/site-packages/numpy/core/__init__.py", line 24, in <module> raise ImportError(msg) ImportError: Importing the multiarray numpy extension module failed. Most likely you are trying to import a failed build of numpy. If you're working with a numpy git repo, try git clean -xdf (removes all files not under version control). Otherwise reinstall numpy.

The singularity def file is as follows:
`Bootstrap: docker
From: continuumio/miniconda3:latest

%post
apt-get update && apt-get install -y nano wget git build-essential git-lfs libz-dev
git clone --recurse-submodules https://github.com/perslab/CELLECT.git
conda install python=3.8
conda install -c bioconda -c conda-forge snakemake mamba
pip install pybedtools numpy==1.16 pandas`

[HansLambda]

I think I had this issue once, it's caused by the numpy package in the conda environment that is set up to run python2.7. The error message should point you to the offending conda env conda-env: /home/elizabethwallace/f9098b7cb53074bc8a6e22639fba8910_
If you manually activate this environment and run python, try >>>import numpy. If that gives the same error ImportError: Importing the multiarray numpy extension module failed. then exit python and reinstall numpy in this specific conda environment.