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adimitromanolakis / sim1000G

Simulation of rare and common variants based on 1000 genomes data
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Error in eigen(sigma, symmetric = TRUE) : 0 x 0 matrix #3

Closed gpsccs closed 4 years ago

gpsccs commented 4 years ago

when I use the function :startSimulation, it occour this error

gpsccs commented 4 years ago

vcf<-readVCF(vcf_file,maxNumberOfVariants = 600 , min_maf = 0.05, max_maf = 1) [#.......] Reading VCF file.. Parsed with column specification: cols( .default = col_character(), POS = col_double(), QUAL = col_double() ) See spec(...) for full column specifications. [##......] Chromosome: chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chr23 chr24 Mbp: 0.000332 Region Size: 49568.59 kb Num of individuals: 200 [##......] Before filtering Num of variants: 105179 Num of individuals: 200 [###.....] After filtering Num of variants: 600 Num of individuals: 200 There were 50 or more warnings (use warnings() to see the first 50) startSimulation(vcf, totalNumberOfIndividuals = 1000) [#####...] Creating SIM object Error in eigen(sigma, symmetric = TRUE) : 0 x 0 matrix

adimitromanolakis commented 4 years ago

Hi, it seems that you are using a multi-chromosome file as input. sim1000G does not support that. Can you try using a file from a single chromosome?

On Mon, 11 Nov 2019 at 10:38, gpsccs notifications@github.com wrote:

vcf<-readVCF(vcf_file,maxNumberOfVariants = 600 , min_maf = 0.05, max_maf = 1) [#.......] Reading VCF file.. Parsed with column specification: cols( .default = col_character(), POS = col_double(), QUAL = col_double() ) See spec(...) for full column specifications. [##......] Chromosome: chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chr23 chr24 Mbp: 0.000332 Region Size: 49568.59 kb Num of individuals: 200 [##......] Before filtering Num of variants: 105179 Num of individuals: 200 [###.....] After filtering Num of variants: 600 Num of individuals: 200 There were 50 or more warnings (use warnings() to see the first 50) startSimulation(vcf, totalNumberOfIndividuals = 1000) [#####...] Creating SIM object Error in eigen(sigma, symmetric = TRUE) : 0 x 0 matrix

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