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
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[X] If it is a support/install question I have posted it to the mailing list
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[ ] I have made available the data to reproduce the problem (optional)
To find bugs the GEMMA software developers may ask to install a
development version of the software. They may also ask you for your
data and will treat it confidentially. Please always remember that
GEMMA is written and maintained by volunteers with good
intentions. Our time is valuable too. By helping us as much as
possible we can provide this tool for everyone to use.
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:
This is the log file :
The output is: **** INFO: Done. and the assoc file head:
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
Check list:
To find bugs the GEMMA software developers may ask to install a development version of the software. They may also ask you for your data and will treat it confidentially. Please always remember that GEMMA is written and maintained by volunteers with good intentions. Our time is valuable too. By helping us as much as possible we can provide this tool for everyone to use.