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.