openSNPDataProcessing/king.stdout at master · chenlab-uva/openSNPDataProcessing · GitHub

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KING  - (c) 2010-2019 Wei-Min Chen

The following parameters are in effect:
                   Binary File :   merge3301.bed (-bname)

Additional Options
         Close Relative Inference : --related [ON], --duplicate
   Pairwise Relatedness Inference : --kinship, --ibdseg, --ibs, --homog
              Inference Parameter : --degree
         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
                   Optional Input : --fam [], --bim [], --sexchr [23]
                           Output : --prefix [king], --rplot

KING starts at Wed Jul 17 10:17:59 2019
Loading genotype data in PLINK binary format...
Read in PLINK fam file merge3301.fam...
  PLINK pedigrees loaded: 2406 samples
Read in PLINK bim file merge3301.bim...
  Genotype data consist of 1483968 autosome SNPs, 43777 X-chromosome SNPs, 6400 Y-chromosome SNPs, 6827 mitochondrial SNPs
  PLINK maps loaded: 1540972 SNPs
Read in PLINK bed file merge3301.bed...
0%6%13%19%25%31%38%44%50%56%63%69%75%81%88%  PLINK binary genotypes loaded.
94%  KING format genotype data successfully converted.
Autosome genotypes stored in 23187 words for each of 2406 individuals.

Options in effect:
	--related

Sorting autosomes...
Total length of 39 chromosomal segments usable for IBD segment analysis is 2694.6 MB.
  In addition to autosomes, 2 segments of length 152.0 MB on X-chr can be further used.
  Information of these chromosomal segments can be found in file kingallsegs.txt

Each family consists of one individual.
A subset of informative SNPs will be used to screen close relatives.
Relationship inference across families starts at Wed Jul 17 10:18:04 2019
96 CPU cores are used...
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%  Stages 1&2 (with 32768 SNPs): 145 pairs of relatives are detected (with kinship > 0.1250)
                               Screening ends at Wed Jul 17 10:18:04 2019
  Final Stage (with 1483968 SNPs): 142 pairs of relatives (up to 1st-degree) are confirmed
                               Inference ends at Wed Jul 17 10:18:04 2019

Relationship summary (total relatives: 0 by pedigree, 142 by inference)
        	MZ	PO	FS	2nd
  =====================================================
  Inference	111	24	7	0


Between-family relatives (kinship >= 0.17678) saved in file king.kin0
  X-Chr IBD-sharing inference saved in file kingX.kin0

Note only duplicates and 1st-degree relatives are included in the inference.
  Specifying '--degree 2' if a higher degree relationship inference is needed.

KING ends at Wed Jul 17 10:18:04 2019