Lattesnow
commented
5 months ago Is there a way to run step by step?
Open Lattesnow opened 5 months ago
Lattesnow
commented
5 months ago Is there a way to run step by step?
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