Closed orangelc1221 closed 1 year ago
Hi Ic, It looks like you're dataset somehow causes GEMMA to abort. What is the command you are using to start the analysis?
Hi frankvogt, I tried the same command with the example: vcf2gwas -v all.vcf.gz -pf pool.csv -ap -lmm I have binary values (0,1) for the phenotypes.
Did you try with a different dataset? The test files of vcf2gwas for example? If those work there may be some internal problem with your dataset (wrong formatting within the .vcf etc.).
Hi frankvogt, Yes, the example dataset did work. I also tried different models to run my dataset, seems lmm somehow always aborted in my case, but lm and bayesian models could work. I will try to understand it better. Thank you!
Hello! I have been tring to run this pipeline but keep receiving this error:
Starting with health_status analysis.. Output will be saved in XXX/Output/Linear Mixed Model/health_status/health_status_20220725_171352/ Reading relatedness matrix.. Calculating linear mixed model.. Traceback (most recent call last): File "xxx/vcf2gwas/lib/python3.9/site-packages/vcf2gwas/analysis.py", line 395, in
Post_analysis.check_return_codes(pc_prefix)
File "xxx/vcf2gwas/lib/python3.9/site-packages/vcf2gwas/utils.py", line 1562, in check_return_codes
raise ChildProcessError()
ChildProcessError
vcf2gwas v0.8.7
Initialising..
Any suggestions? Thank you!
Best, lc