How to resolve "Error: All remaining samples for --glm phenotype 'pheno' are cases" in Plink?

Question

[anamaria]

Hello,

I was running GWAS via:

plink2 --threads 24 --pfile temporary17 --recover-var-ids NVCFchr17.vcf.gz 'force' --pheno  pheno_hes_nephropathy_hba1c.txt --pheno-name pheno --covar pheno_hes_nephropathy_hba1c.txt --covar-name sex,age,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10,TD,array,HBA1C --glm genotypic cols=+beta,+err hide-covar --out nephropathy_chr17

I got this error:

PLINK v2.00a3LM 64-bit Intel (9 Apr 2020)
Options in effect:
  --covar pheno_hes_nephropathy_hba1c.txt
  --covar-name sex,age,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10,TD,array,HBA1C
  --glm genotypic cols=+beta,+err hide-covar
  --out nephropathy_chr17
  --pfile temporary17
  --pheno pheno_hes_nephropathy_hba1c.txt
  --pheno-name pheno
  --recover-var-ids NVCFchr17.vcf.gz force
  --threads 24


Random number seed: 1591280761
128656 MiB RAM detected; reserving 64328 MiB for main workspace.
Using up to 24 threads (change this with --threads).
487409 samples (0 females, 0 males, 487409 ambiguous; 487409 founders) loaded
from temporary17.psam.
134908 variants loaded from temporary17.pvar.
1 binary phenotype loaded (286 cases, 21313 controls).
--recover-var-ids: 154080 lines scanned.
--recover-var-ids: 134908/134908 IDs updated.
15 covariates loaded from pheno_hes_nephropathy_hba1c.txt.
Calculating allele frequencies... done.
Error: All remaining samples for --glm phenotype 'pheno' are cases.

My pheno file looks like this:

FID IID pheno sex age PC1 PC2 PC3 PC4 PC5 PC6 PC7 PC8 PC9 PC10 TD HBA1C array
1000017 1000017 -9 Female 69 -10.208 4.89464 -1.69068 -1.29238 -5.91204 -0.209965 -0.527499 -0.454909 2.62045 -1.25741 -9 39.9 Biobank

In addition I am able to run with a different pheno file (pheno_question_hba1c_all.txt) I am able to run without issues... but when I use pheno_hes_nephropathy_hba1c.txt I got that error