Hi,
There must be something wrong with my input file since the test data run successfully.
Attached the error report here.
Running GEMMA
Phenotypes to analyze: urological_ageing
Creating relatedness matrix..
GEMMA 0.98.3 (2020-11-28) by Xiang Zhou and team (C) 2012-2020
Reading Files ...
number of total individuals = 2
number of analyzed individuals = 2
number of covariates = 1
number of phenotypes = 1
number of total SNPs/var = 3798739
number of analyzed SNPs = 828841
Calculating Relatedness Matrix ...
================================================== 100%
**** INFO: Done.
Relatedness matrix created successfully
Starting with urological_ageing analysis..
Output will be saved in output_gwas/Output/Linear_Mixed_Model/urological_ageing/urological_ageing_20240312_213650/
Reading relatedness matrix..
Calculating linear mixed model..
GEMMA 0.98.3 (2020-11-28) by Xiang Zhou and team (C) 2012-2020
Reading Files ...
number of total individuals = 2
number of analyzed individuals = 2
number of covariates = 1
number of phenotypes = 1
number of total SNPs/var = 3798739
number of analyzed SNPs = 828841
Start Eigen-Decomposition...
pve estimate =0.936558
se(pve) =1.24756e+06
GSL ERROR: domain error in beta.c at line 56 errno 1%
Traceback (most recent call last):
File "/home/anaconda3/envs/p39/lib/python3.9/site-packages/vcf2gwas/analysis.py", line 398, in
Post_analysis.check_return_codes(pc_prefix, dir_temp)
File "/home/anaconda3/envs/p39/lib/python3.9/site-packages/vcf2gwas/utils.py", line 1607, in check_return_codes
raise ChildProcessError()
ChildProcessError
Hi, There must be something wrong with my input file since the test data run successfully.
Attached the error report here. Running GEMMA
Phenotypes to analyze: urological_ageing
Creating relatedness matrix.. GEMMA 0.98.3 (2020-11-28) by Xiang Zhou and team (C) 2012-2020 Reading Files ...
number of total individuals = 2
number of analyzed individuals = 2
number of covariates = 1
number of phenotypes = 1
number of total SNPs/var = 3798739
number of analyzed SNPs = 828841
Calculating Relatedness Matrix ... ================================================== 100% **** INFO: Done. Relatedness matrix created successfully Starting with urological_ageing analysis.. Output will be saved in output_gwas/Output/Linear_Mixed_Model/urological_ageing/urological_ageing_20240312_213650/ Reading relatedness matrix.. Calculating linear mixed model.. GEMMA 0.98.3 (2020-11-28) by Xiang Zhou and team (C) 2012-2020 Reading Files ...
number of total individuals = 2
number of analyzed individuals = 2
number of covariates = 1
number of phenotypes = 1
number of total SNPs/var = 3798739
number of analyzed SNPs = 828841
Start Eigen-Decomposition... pve estimate =0.936558 se(pve) =1.24756e+06 GSL ERROR: domain error in beta.c at line 56 errno 1% Traceback (most recent call last): File "/home/anaconda3/envs/p39/lib/python3.9/site-packages/vcf2gwas/analysis.py", line 398, in
Post_analysis.check_return_codes(pc_prefix, dir_temp)
File "/home/anaconda3/envs/p39/lib/python3.9/site-packages/vcf2gwas/utils.py", line 1607, in check_return_codes
raise ChildProcessError()
ChildProcessError