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, trygit 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
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, trygit 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`