MemoryError: When running LDSCORE analysis

[chirrie]

I am getting memory error when generating LDscores;

./ldsc.py --bfile "/dataE/AWIGenGWAS/shared/imputed_data_plink/all_imputed_map_qc" --chunk-size 500000 --l2 --ld-wind-cm 1 --out Awi-gen-LDscores

Reading genotypes from /dataE/AWIGenGWAS/shared/imputed_data_plink/all_imputed
After filtering, 13976041 SNPs remain
Estimating LD Score.
Traceback (most recent call last):
File "./ldsc.py", line 620, in
ldscore(args, log)
File "./ldsc.py", line 316, in ldscore
lN = geno_array.ldScoreVarBlocks(block_left, args.chunk_size, annot=annot_$
File "/home/chebii/Awi-gen/FG_raw/boltlmm/ldsc/ldscore/ldscore.py", line 125$
return self.corSumVarBlocks(block_left, c, func, snp_getter, annot)
File "/home/chebii/Awi-gen/FG_raw/boltlmm/ldsc/ldscore/ldscore.py", line 189$
A = snp_getter(b)
File "/home/chebii/Awi-gen/FG_raw/boltlmm/ldsc/ldscore/ldscore.py", line 397$
X = np.array(slice.decode(self._bedcode), dtype="float64").reshape((b, nru$
MemoryError

Analysis finished at Thu Mar 21 09:06:42 2024

[aikedan]

hello. how do you handle this problem in your research ? ? since I have this issue now. looking forward your reply.

[aksarkar]

@chirrie @aikedan Run ldsc on a machine with more memory available.

[chirrie]

I am running it on HPC with massive memory. I am not sure if it us an issue with mem

…

On Sun, 5 May 2024, 23:18 Abhishek Sarkar, ***@***.***> wrote: @chirrie <https://github.com/chirrie> @aikedan <https://github.com/aikedan> Run ldsc on a machine with more memory available. — Reply to this email directly, view it on GitHub <#426 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAZTQ2VGSEBHHIWRM3747N3ZA2HXXAVCNFSM6AAAAABFA4ERUSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOJUHEZTKNJVGM> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[aksarkar]

@chirrie Confirm with your HPC administrator that you are correctly requesting and receiving the requested amount of memory.

Also note that you should not change --chunk-size from the default value.