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

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

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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

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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.