KING relatedness inference hanging

Question

[marcus.tutert]

Hi, I am trying to run KING relatedness inference on two GWAS datasets. In total there are roughly 12k samples and 500k SNPs that are aligned across these datasets. My command is as followed:

(base) mt27@hm-05:/lustre/scratch123/hgi/mdt2/projects/ibdgwas_bioresource/mt27/CSI/Scratch$ /software/team152/king  -b KING_Plink_Cohorts/GWAS1.bed,KING_Plink_Cohorts/GWAS2.bed --related --degree 1 --prefix KING_Cohort_Results/GWAS1_GWAS2
KING 2.2.4 - (c) 2010-2019 Wei-Min Chen

The following parameters are in effect:
                   Binary File : KING_Plink_Cohorts/GWAS1.bed,KING_Plink_Cohorts/GWAS2.bed (-bname)

Additional Options
         Close Relative Inference : --related [ON], --duplicate
   Pairwise Relatedness Inference : --kinship, --ibdseg, --ibs, --homog
              Inference Parameter : --degree [1]
         Relationship Application : --unrelated, --cluster, --build
                        QC Report : --bysample, --bySNP, --roh, --autoQC
                     QC Parameter : --callrateN, --callrateM
             Population Structure : --pca, --mds
              Structure Parameter : --projection, --pcs
              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_Cohort_Results/GWAS1_GWAS2],
                                    --rpath [], --rplot

KING starts at Thu Feb 24 12:28:37 2022
Read in PLINK fam files
    KING_Plink_Cohorts/GWAS1.fam...
    KING_Plink_Cohorts/GWAS2.fam...
  PLINK pedigrees loaded: 12431 samples
Read in PLINK bim files
    KING_Plink_Cohorts/GWAS1.bim...
    KING_Plink_Cohorts/GWAS2.bim...
  Genotype data consist of 325381 autosome SNPs, 6959 X-chromosome SNPs
  PLINK maps loaded: 332340 SNPs
Read in PLINK bed files
    KING_Plink_Cohorts/GWAS1.bed...
    KING_Plink_Cohorts/GWAS2.bed...
  PLINK binary genotypes loaded: 12431 samples
  KING format genotype data successfully converted
Autosome genotypes stored in 5085 words for each of 12431 individuals.

Options in effect:
    --related
    --degree 1
    --prefix KING_Cohort_Results/GWAS1_GWAS2

Sorting autosomes...
Total length of 40 chromosomal segments usable for IBD segment analysis is 2630.8 MB.
  In addition to autosomes, 2 segments of length 147.4 MB on X-chr can be further used.
  Information of these chromosomal segments can be found in file KING_Cohort_Results/GWAS1_GWAS2allsegs.txt

However, at this stage here, my code seems to hang and I don't receive any output. I've asked for a very high amount of memory (1 TB) to ensure I am not constrained by the RAM but I am unsure why else this might not be working?

Would appreciate any tips! Thanks.

[Sam]

if you check top, do you see the program running? KING can take a long time to run when sample size is high.