I am using Shapeit to phase my genetic data. I keep getting this error. Is there anyone facing the same problem, or does anyone have experience on it? I am looking forward to hearing from you. Thanks!
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MODE -phase : PHASING GENOTYPE DATA * Autosome (chr1 ... chr22) * Window-based model (SHAPEIT v2) * Reference panel of haplotypes used * MCMC iteration
Parameters : * Seed : 1473702489 * Parallelisation: 1 threads * Ref allele is NOT aligned on the reference genome * MCMC: 35 iterations [7 B + 1 runs of 8 P + 20 M] * Model: 100 states per window [100 H + 0 PM + 0 R + 0 COV ] / Windows of ~2.0 Mb / Ne = 15000
Reading SNPs to exclude from input file in [/home/yxwang6/CHS_GWAS/chr22test/20160909/chr22_37.aligments.snp.strand.exclude] * 799 snps found in the exclude list
Reading site list in [/home/yxwang6/CHS_GWAS/chr22test/20160909/c1_gru-22_37_afterFlip.bim] * 4815 sites included * 793 sites excluded
Reading sample list in [/home/yxwang6/CHS_GWAS/chr22test/20160909/c1_gru-22_37_afterFlip.fam] * 3802 samples included * 3802 unrelateds / 0 duos / 0 trios in 3802 different families
Reading genotypes in [/home/yxwang6/CHS_GWAS/chr22test/20160909/c1_gru-22_37_afterFlip.bed] * Plink binary file SNP-major mode
Reading sample list [/home/yxwang6/CHS_imputation/test/1000GP_Phase3.sample.gz] * 5008 reference haplotypes included
Reading SNPs in [/home/yxwang6/CHS_imputation/test/1000GP_Phase3_chr22.legend.gz] * 4815 reference panel sites included
- 1105402 reference panel sites excluded
Reading reference haplotypes in [/home/yxwang6/CHS_imputation/test/1000GP_Phase3_chr22.hap.gz]
Reading genetic map in [/home/yxwang6/CHS_GWAS/chr22test/20160909/c1_gru-22_37_afterFlip_3col.gz] * 5607 genetic positions found * #set=0 / #interpolated=4815 * Physical map [16.95 Mb -> 51.18 Mb] / Genetic map [inf cM -> inf cM]
Checking missingness and MAF... * 37 individuals with high rates of missing data (>5%) * 33 SNPs with high rates of missing data (>5%)
Building graphs [3802/3802] * 3802 graphs / 2165791 segments / ~8 SNPs per segment / 75047288 transitions * 0 haploids / 3802 unrelateds / 0 duos / 0 trios * 7604 founder haplotypes * 5008 reference haplotypes
Sampling haplotypes [3802/3802]
ERROR: Nan in expectationUNR / i=45701199 s=0 b=1 sp=nan
