I am currently trying to perform GWAS with HAPNEST generated data. However, an error is thrown once I set gwas to true in config.yaml. The console says:
"Error: Line 1 of data/outputs/test/test-1.phe1 has fewer tokens than
expected."
when trying to execute this step:
"failed process: Process(plink2 --bed data/outputs/test/test-1.bed --bim data/outputs/test/test-1.bim --fam data/outputs/test/test-1.phe1 --glm hide-covar --covar data/outputs/test/evaluation/test-1.syn.pca.eigenvec --ci 0.95 --out data/outputs/test/evaluation/test-1.trait1, ProcessExited(6)) [6]"
When having a look into the .phe1 file I see that it contains only 5 columns and no column where a potential phenotype is located. Could this be the reason for the error? If so, is there any way to amend the file properly?
I would greatly appreciate it if you were able to help me!
Hello,
I am currently trying to perform GWAS with HAPNEST generated data. However, an error is thrown once I set gwas to true in config.yaml. The console says: "Error: Line 1 of data/outputs/test/test-1.phe1 has fewer tokens than expected." when trying to execute this step: "failed process: Process(
plink2 --bed data/outputs/test/test-1.bed --bim data/outputs/test/test-1.bim --fam data/outputs/test/test-1.phe1 --glm hide-covar --covar data/outputs/test/evaluation/test-1.syn.pca.eigenvec --ci 0.95 --out data/outputs/test/evaluation/test-1.trait1, ProcessExited(6)) [6]"When having a look into the .phe1 file I see that it contains only 5 columns and no column where a potential phenotype is located. Could this be the reason for the error? If so, is there any way to amend the file properly?
I would greatly appreciate it if you were able to help me!
Kind regards Nils