Identical P-Values at end of run

[jeremysutherland]

The gwas produces identical p-values at the end of my run(s).

GEMMA 0.98.3 (2020-11-28) by Xiang Zhou and team (C) 2012-2020

mdtr_1 = Plink binary ped file format host_selectivity.fam = mean traits for replicated genotypes sorted to match genotype file. "-gk 2" for standardized matrix, “-km 2” to accompany PLINK binary ped format "-miss 0.1" adjusts missingness threshold "-o" output k matrix

LOG KMAT

GEMMA Version = 0.98.3 (2020-11-28) Build profile = GCC version = 7.5.0 GSL Version = 1.16 OpenBlas = OpenBLAS 0.3.12 - OpenBLAS 0.3.23 DYNAMIC_ARCH NO_AFFINITY SkylakeX MAX_THREADS=128 arch = SkylakeX threads = 8 parallel type = threaded

Command Line Input = gemma -bfile mdtr_1 -p host_selectivity.fam -km 2 -gk 2 -miss 0.1 -o medtr_1_ksmat

Date = Wed Mar 20 11:04:12 2024

Summary Statistics: number of total individuals = 206 number of analyzed individuals = 206 number of covariates = 1 number of phenotypes = 1 number of total SNPs/var = 1029052 number of analyzed SNPs/var = 1029052

Computation Time: total computation time = 1.09729 min computation time break down: time on calculating relatedness matrix = 0.997235 min

LOG GWAS

GEMMA Version = 0.98.3 (2020-11-28) Build profile = GCC version = 7.5.0 GSL Version = 1.16 OpenBlas = OpenBLAS 0.3.12 - OpenBLAS 0.3.23 DYNAMIC_ARCH NO_AFFINITY SkylakeX MAX_THREADS=128 arch = SkylakeX threads = 8 parallel type = threaded

Command Line Input = gemma -bfile mdtr_1 -p host_selectivity.fam -k ./output/medtr_1_ksmat.sXX.txt -lmm 4 -o medtr_1_ulmm_host_selectivity

Date = Wed Mar 20 11:22:56 2024

Summary Statistics: number of total individuals = 206 number of analyzed individuals = 206 number of covariates = 1 number of phenotypes = 1 number of total SNPs/var = 1029052 number of analyzed SNPs/var = 1029052 REMLE log-likelihood in the null model = 89.519 MLE log-likelihood in the null model = 90.4807 pve estimate in the null model = 0.0408771 se(pve) in the null model = 0.150637 vg estimate in the null model = 0.000999738 ve estimate in the null model = 0.0234575 beta estimate in the null model = 0.171998 se(beta) = 0.010671

Computation Time: total computation time = 9.36723 min computation time break down: time on eigen-decomposition = 0.00977162 min time on calculating UtX = 0.669829 min time on optimization = 8.37971 min

Screenshots P-value tails occur regardless of whether I run the analysis on the whole genome or on chroms individually. This was run on all 8 chromosomes.

Thinking it might have been an memory issue, this was run on each chromosome individually:

[renhamm]

I have the exact some problem. At first I thought there was some sort of error with my covariate file, but regardless of inclusion, all the outputs are identical.