Kivanc Corut

Hi @ctb, Sorry for my late reply. I was away the last couple of weeks and finally had time to go through the issues and test `snakemake-minimal`. First of all,...

Hi @VanOverbeeke, Sorry for my late response. Unfortunately, it is not possible to run kGWASflow with k-mer sizes bigger than 31. This is due to the underlying method used during...

Hi @Ax3man, Thank you for reporting this issue. You are right about the `plot_manhattan` setting. I originally planned manhattan plot generation to be optional, but later I decided to keep...

Hi @DavideGue, This error seems to be related to the phenotype file. Do you mind sharing your `.pheno` file with me so I can have a look? Best, Kivanc

Okay, it looks like there is one missing phenotype information for your accession `WB-359`. If you remove the row with the missing pheno (WB-359) and run the pipeline again, it...

Hi @DavideGue, Can you share the content of `results/kmers_gwas/Flowering_Time/kmers/`. You can just name the files that exist in that directory. This is most likely an issue with kmersGWAS and GEMMA,...

Hi @DavideGue, Is the `output/` folder empty?