MemoryError Problem: 2a. Computing 1000 genomes LD

[rootze]

Hello

I wonder if anyone has encountered similar MemoryError problems. I tried to supply fewer SNPs for input --locus, but still received the same error.

python CalcLD_1KG_VCF.py \
--locus chr10_GWAS_Meta.hdl \
--reference ALL.chr1.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz \
--map integrated_call_samples_v3.20130502.ALL.panel \
--effect_allele A1 \
--alt_allele A0 \
--population EUR \
--Zhead Zscore \
--out_name ld_out \
--position pos

MemoryError: Unable to allocate 1.60 TiB?

Traceback (most recent call last):
  File "/dfs7/swaruplab/zechuas/tools_software/PAINTOR/PAINTOR_V3.0/PAINTOR_Utilities/CalcLD_1KG_VCF.py", line 266, in <module>
    if __name__ == "__main__": main()
  File "/dfs7/swaruplab/zechuas/tools_software/PAINTOR/PAINTOR_V3.0/PAINTOR_Utilities/CalcLD_1KG_VCF.py", line 262, in main
    ld_mat = np.corrcoef(pop_haps)
  File "<__array_function__ internals>", line 5, in corrcoef
  File "/opt/apps/anaconda/2020.07/lib/python3.8/site-packages/numpy/lib/function_base.py", line 2526, in corrcoef
    c = cov(x, y, rowvar)
  File "<__array_function__ internals>", line 5, in cov
  File "/opt/apps/anaconda/2020.07/lib/python3.8/site-packages/numpy/lib/function_base.py", line 2454, in cov
    c = dot(X, X_T.conj())
  File "<__array_function__ internals>", line 5, in dot
MemoryError: Unable to allocate 1.60 TiB for an array with shape (468549, 468549) and data type float64
/export/spool/slurm/slurmd.spool/job16156293/slurm_script: line 51: : command not found
/export/spool/slurm/slurmd.spool/job16156293/slurm_script: line 52: : command not found

Thank you!