Cannot find covar column in a phenotype file

[lc491]

Hi, I am trying to run GEM analysis, but it keeps showing an error about phenotype file. I have attached my code here. Do you know what is my problem here?

singularity exec \

-B /humgen/ManningLab_ChargeGLI/Sleep_Glycemia/UKBB_AFR/Outputs/HbA1c_STST:/outputs
-B /humgen/ManningLab_ChargeGLI/UKBB_phenotypes/UKBB_AFR:/phenotypes
-B /broad/ukbb/imputed_v3:/genotypes
gem-v1.5.2a-workflow.simg
/bin/bash <<EOF
/GEM/GEM
--bgen /genotypes/ukb_imp_chr22_v3.bgen
--pheno-file /phenotypes/UKBB_ChargeGLI_wo_Diabetes_Phenotypes_AFR_fc_dummy.pheno
--sampleid-name Genotype_ID
--pheno-name hba1c
--exposure-names stst
--covar-names age sex age_sq gPC1 agebystst age2bystst sexbystst
--missing-value NA
--out /outputs/chr22_GEM_HbA1c_STST_UKBB_AFR_COMBINED_M1.txt
--output-style meta
--robust 1
--center 0
EOF

---

Welcome to GEM v1.5.2
(C) 2018-2023 Liang Hong, Han Chen, Duy Pham, Cong Pan
GNU General Public License v3

---

The Phenotype File is: /phenotypes/UKBB_ChargeGLI_wo_Diabetes_Phenotypes_AFR_fc_dummy.pheno
The Phenotype is: hba1c
The Genotype File is: /genotypes/ukb_imp_chr22_v3.bgen
Model-based or Robust: Model-based

The Total Number of Exposures is: 1
The Selected Exposures are: stst
No Interaction Covariates Selected
The Total Number of Selected Covariates is: 8
The Selected Covariates are: age sex age_sq gPC1 agebystst age2bystst sexbystst
Centering strategy: centering interaction covariates only.
Categorical Threshold: 20
Minor Allele Frequency Threshold: 0.001
Number of SNPS in batch: 1
Number of Threads: 26
Output File: gem.out

---

ERROR: Cannot find covariate column in phenotype file.

/bin/bash: line 2: --missing-value: command not found

[hanchenphd]

Are you missing a backslash at the end of each line? Bash may not interpret these multiple lines as a single line of code without backslash.