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frankvogt / vcf2gwas

Python API for comprehensive GWAS analysis using GEMMA
GNU General Public License v3.0
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ChildProcessError #14

Closed orangelc1221 closed 1 year ago

orangelc1221 commented 2 years ago

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

frankvogt commented 2 years 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?

orangelc1221 commented 2 years ago

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.

frankvogt commented 1 year ago

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.).

orangelc1221 commented 1 year ago

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!