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Trouble doing GWAS #31

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SpasskYoY opened this issue May 8, 2024 · 0 comments
Open

Trouble doing GWAS #31

SpasskYoY opened this issue May 8, 2024 · 0 comments

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@SpasskYoY
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SpasskYoY commented May 8, 2024

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

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