Pve is .999

[aguilar-gomez]

Describe the bug
Most of the genomic associations I run results in pve .999.I have decent value peaks that are outliers. I have small sample size.

To Reproduce
Steps to reproduce the behavior:

for n in $(seq 1 13)
do
echo $n
nohup gemma -bfile pumilio.v4 -lmm 4 -o n${n}_${pc}_rescaffold -k pum.v4.sXX.txt -n $n 1> n$n}out 2> out.gemma.n$n &  
done

This is the log file :

##
## GEMMA Version    = 0.98.5 (2021-08-25)
## Build profile    = /gnu/store/8rvid272yb53bgascf5c468z0jhsyflj-profile
## GCC version      = 7.5.0
## GSL Version      = 2.6
## OpenBlas         = OpenBLAS 0.3.9  - OpenBLAS 0.3.9 DYNAMIC_ARCH NO_AFFINITY SkylakeX MAX_THREADS=128
##   arch           = SkylakeX
##   threads        = 64
##   parallel type  = threaded
##
## Command Line Input = gemma -bfile pumilio.v4 -lmm 4 -o n1__rescaffold -k pum.v4.sXX.txt -n 1 
##
## Date = Tue Nov 22 16:54:08 2022
##
## Summary Statistics:
## number of total individuals = 347
## number of analyzed individuals = 199
## number of covariates = 1
## number of phenotypes = 1
## number of total SNPs/var = 10788793
## number of analyzed SNPs/var = 6359583
## REMLE log-likelihood in the null model = -322.303
## MLE log-likelihood in the null model = -317.703
## pve estimate in the null model = 0.99999
## se(pve) in the null model = 0.000833612
## vg estimate in the null model = 1.61183
## ve estimate in the null model = 1.61183e-05
## beta estimate in the null model =   2.36683
## se(beta) =   0.000284599
##
## Computation Time:
## total computation time = 63.7511 min 
## computation time break down: 
##      time on eigen-decomposition = 0.460148 min 
##      time on calculating UtX = 5.07513 min 
##      time on optimization = 52.3442 min 
##

The output is:
**** INFO: Done.
and the assoc file head:

chr	rs	ps	n_miss	allele1	allele0	af	beta	se	logl_H1	l_remle	l_mle	p_wald	p_lrp_score
P_RNA_scaffold_2	.	30316	0	T	C	0.018	7.373270e-01	5.112214e-01	-3.166582e+02	1.000000e+05	1.000000e+05	1.508099e-01	1.482381e-01	1.508918e-01
P_RNA_scaffold_2	.	30337	0	A	C	0.447	-1.177313e-01	1.213347e-01	-3.172290e+02	1.000000e+05	1.000000e+05	3.330857e-01	3.300302e-01	3.317995e-01
P_RNA_scaffold_2	.	30360	0	A	T	0.015	9.879762e-01	5.263806e-01	-3.159398e+02	1.000000e+05	1.000000e+05	6.200688e-02	6.037101e-02	6.299756e-02
P_RNA_scaffold_2	.	30515	0	G	A	0.035	-5.207134e-01	3.915204e-01	-3.168139e+02	1.000000e+05	1.000000e+05	1.850633e-01	1.822937e-01	1.848092e-01
P_RNA_scaffold_2	.	30608	0	T	C	0.023	4.795118e-01	4.024873e-01	-3.169890e+02	1.000000e+05	1.000000e+05	2.349412e-01	2.319874e-01	2.342600e-01
P_RNA_scaffold_2	.	30645	0	T	C	0.070	-5.327640e-02	2.423960e-01	-3.176790e+02	1.000000e+05	1.000000e+05	8.262617e-01	8.251780e-01	8.254173e-01
P_RNA_scaffold_2	.	30843	0	A	C	0.183	-6.070896e-02	1.671540e-01	-3.176367e+02	1.000000e+05	1.000000e+05	7.168511e-01	7.151341e-01	7.155711e-01
P_RNA_scaffold_2	.	56591	0	C	T	0.123	1.191875e-01	2.133095e-01	-3.175458e+02	1.000000e+05	1.000000e+05	5.769643e-01	5.745517e-01	5.753409e-01
P_RNA_scaffold_2	.	56801	0	T	C	0.193	-1.983927e-01	1.757588e-01	-3.170619e+02	1.000000e+05	1.000000e+05	2.603642e-01	2.573548e-01	2.594963e-01

Expected behavior
Get values that describe how much of the variance is explained by the genetics

Additional context
I found a similar issue in the google group discussion but it was not solved:
https://groups.google.com/g/gemma-discussion/c/QmIfq3yDFas/m/eBPmLZF_DQAJ

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