search

zhengxwen / SeqArray

Data management of large-scale whole-genome sequence variant calls (Development version only)
http://www.bioconductor.org/packages/SeqArray
43 stars 12 forks source link

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

Open LiuYuMeng987654 opened 1 month ago

LiuYuMeng987654 commented 1 month ago

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 commented 1 month ago

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")