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Error in seqVCF2GDS(vcf.fn, "chr1.gds", storage.option = "LZMA_RA", parallel = FALSE) : std::bad_alloc #92

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LiuYuMeng987654 opened this issue May 23, 2024 · 1 comment
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@LiuYuMeng987654
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Hello, I am trying to use seqVCF2GDS to change vcf to GDS files, and am getting the following error:
Error in seqVCF2GDS(vcf.fn, "chr1.gds", storage.option = "LZMA_RA", parallel = FALSE) :
std::bad_alloc
FILE: /data/results/liuyumeng/550H.disease.vcf/550H.chr1.vcf.gz
LINE: 293, COLUMN: 5, A
Execution halted

this is my code:
seqVCF2GDS(vcf.fn, "chr1.gds", storage.option="LZMA_RA",parallel=FALSE)
联想截图_20240523232024
联想截图_20240523232137

I'm not sure what's wrong with my vcf file format

@zhengxwen zhengxwen self-assigned this May 24, 2024
@zhengxwen
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zhengxwen commented May 24, 2024

Show me the session information:

sessionInfo()

It shows "std::bad_alloc", so increasing the memory limit might help if you submitted a job to the cluster.
Or try gz instead of lzma comression:

seqVCF2GDS(vcf.fn, "chr1.gds", storage.option="ZIP_RA")

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