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xihaoli / STAARpipeline-Tutorial

The tutorial for performing single-/multi-trait association analysis of whole-genome/whole-exome sequencing (WGS/WES) studies using FAVORannotator, STAARpipeline and STAARpipelineSummary
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FATAL ERROR - Too many first alleles as the major allele (~21.5%). #61

Closed jingydz closed 1 month ago

jingydz commented 3 months ago

Start time is 2024/06/12--12:53 KING 2.2 - (c) 2010-2019 Wei-Min Chen

The following parameters are in effect: Binary File : /xxx/rare_variant/GRM/chrall.2082.mac1.filt.mind.geno.maf.bed (-bname)

Additional Options Close Relative Inference : --related, --duplicate Pairwise Relatedness Inference : --kinship, --ibdseg [ON], --ibs, --homog Inference Parameter : --degree [4] Relationship Application : --unrelated, --cluster, --build QC Report : --bysample, --bySNP, --roh, --autoQC QC Parameter : --callrateN, --callrateM Population Structure : --pca, --mds Structure Parameter : --projection Disease Association : --tdt Quantitative Trait Association : --mtscore Association Model : --trait [], --covariate [] Association Parameter : --invnorm, --maxP Genetic Risk Score : --risk, --model [], --prevalence, --noflip Computing Parameter : --cpus [10] Optional Input : --fam [], --bim [], --sexchr [23] Output : --prefix [/xxx/rare_variant/GRM/KING.PCa], --rplot

KING starts at Wed Jun 12 12:53:24 2024 Loading genotype data in PLINK binary format... Read in PLINK fam file /xxx/rare_variant/GRM/chrall.2082.mac1.filt.mind.geno.maf.fam... PLINK pedigrees loaded: 2071 samples Read in PLINK bim file /xxx/rare_variant/GRM/chrall.2082.mac1.filt.mind.geno.maf.bim... Genotype data consist of 5593621 autosome SNPs PLINK maps loaded: 5593621 SNPs Read in PLINK bed file /xxx/rare_variant/GRM/chrall.2082.mac1.filt.mind.geno.maf.bed... 0%^M6%^M13%^M19%^M25%^M31%^M38%^M44%^M50%^M56%^M63%^M69%^M75%^M81%^M88%^M PLINK binary genotypes loaded. 94%^M KING format genotype data successfully converted.

Options in effect: --ibdseg --degree 4 --cpus 10 --prefix /xxx/rare_variant/GRM/KING.PCa

FATAL ERROR -

Too many first alleles as the major allele (~21.5%). Please use plink1.9 --make-bed to regenerate the genotype data again.

Finish time is 2024/06/12--12:54

In the FastSparseGRM pipeline, I met this error.

But I indeed used the plink1.9 (PLINK v1.90b6.9 64-bit (4 Mar 2019)) to generate the genotype, why it run unsuccessfully?

xihaoli commented 3 months ago

Hi @jingydz,

Thanks for letting me know. This issue could be more related to KING or FastSparseGRM. Please create an issue here and redirect this issue.