Error when converting vcf to gds

zhengxwen / SNPRelate

R package: parallel computing toolset for relatedness and principal component analysis of SNP data (Development version only)

http://www.bioconductor.org/packages/SNPRelate

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Error when converting vcf to gds #96

Open AmanahLW opened 2 years ago

AmanahLW commented 2 years ago

I'm starting to get an error when running seqVCF2GDS function to covert BCFTools, Strelka2 and GATK uncompressed VCF to GDS. The code i'm using: gatkgds<-seqVCF2GDS(gatk.fn, "samples50_gatk_WT.gds", parallel = 17 , storage.option="LZMA_RA")

Error in seqOpen(fn, allow.duplicate = TRUE) : The number of compression blocks should be defined.

AmanahLW commented 2 years ago

Sorry, this issue should have been posted on seqarray repo.

zhengxwen commented 2 years ago

Please use a single core: parallel = 1