I have used SCORE to estimate the genetic correlation of many metabolites. It turned out that in some results the gamma_g(0,1)(0) and SE(gamma_g)(0,1)(0) got -nan values. An example is like this:
Source Value
Vg/Vp(0)(0) 0.171996
Vg/Vp(1)(0) -0.063781
rho_g(0,1)(0) -0.014145
rho_e: 0.244022
gamma_g(0,1)(0) -nan
SE(Vg/Vp)(0)(0) 0.112957
SE(Vg/Vp)(1)(0) 0.164523
SE(gamma_g)(0,1)(0) -nan
SE(rho_g)(0,1)(0) 0.096816
I have used SCORE to estimate the genetic correlation of many metabolites. It turned out that in some results the gamma_g(0,1)(0) and SE(gamma_g)(0,1)(0) got -nan values. An example is like this: Source Value Vg/Vp(0)(0) 0.171996 Vg/Vp(1)(0) -0.063781 rho_g(0,1)(0) -0.014145 rho_e: 0.244022 gamma_g(0,1)(0) -nan SE(Vg/Vp)(0)(0) 0.112957 SE(Vg/Vp)(1)(0) 0.164523 SE(gamma_g)(0,1)(0) -nan SE(rho_g)(0,1)(0) 0.096816
The log file is like this: Binary phenotype: 0 Filling phenotype with mean: 0 Compute heritability: 1 Output write to destination output_M4_p_58_ext_residuals-M4_p_35436_ext_residuals.txt Analysing phenotype M4_p_58_ext_residuals, M4_p_35436_ext_residuals Read in 2 phenotypes There are 4960 2699 individuals with no missing phenotypes Total number of annotation groups: 1 num of random vectors: 10 No Covariate File Specified genotype size: 5034 X 1479401 Total number of blocks: 362 Start reading genotype round 1/2... Reading chromosome 0 Reading chromosome 1 Reading chromosome 2 Reading chromosome 3 Reading chromosome 4 Reading chromosome 5 Reading chromosome 6 Reading chromosome 7 Reading chromosome 8 Reading chromosome 9 Reading chromosome 10 Reading chromosome 11 Reading chromosome 12 Reading chromosome 13 Reading chromosome 14 Reading chromosome 15 Reading chromosome 16 Reading chromosome 17 Reading chromosome 18 Reading chromosome 19 Reading chromosome 20 Reading chromosome 21 A: 5089.16 4855.05 4855.05 4960 b: 4912.21 4959 A: 2697.51 2650.69 2650.69 2699 b: 2643.71 2698 total comman samples: 2699 A: 2772.68 2647.67 2647.67 2699 b: 606.872 621.165 Start reading genotype round 2/2... reading chromosome 0 reading chromosome 1 reading chromosome 2 reading chromosome 3 reading chromosome 4 reading chromosome 5 reading chromosome 6 reading chromosome 7 reading chromosome 8 reading chromosome 9 reading chromosome 10 reading chromosome 11 reading chromosome 12 reading chromosome 13 reading chromosome 14 reading chromosome 15 reading chromosome 16 reading chromosome 17 reading chromosome 18 reading chromosome 19 reading chromosome 20 reading chromosome 21 score_cmd_test_30.sh: line 2: 4161 Segmentation fault /data/programs/bin/gwas/SCORE/build/SCORE -g MyPlinkGenotype -p MyPheno.txt -mpheno M4_p_58_ext_residuals,M4_p_35436_ext_residuals -b 10 -o output_M4_p_58_ext_residuals-M4_p_35436_ext_residuals.txt
It looks like in such cases either the Vg/Vp(0)(0) or Vg/Vp(1)(0) has negative values. Is this as expected?
The other problem is I saw Segmentation fault in every run, and I don’t see it when I did the test run.
Thanks in advance for help!