Burden test error in ukb23158_500k_OQFE.sets.txt.gz

I got the same error that was reported earlier here

• Hi everyone, I am running Regenie form the RAP Command line. I got tis error "set file : [ukb23158_500k_OQFE.sets.txt.gz] ERROR: unknown chromosome code in set list file". I am using the files already available on UKBiobank RAP.

I did the following

for chr in {1..21}; do

run_regenie_burden="regenie --step 2 --pred ap38_results_pred.list --out assoc.c${chr} \

--bed ${data_field}_c${chr}_b0_v1 --ref-first \

--phenoFile Ex1.phe --covarFile Ex1.covar \

--phenoCol Exercise_cc --covarCol age --covarCol sex \

--covarCol genotyping --covarCol PCA{1:10} \

--covarCol Centre --covarCol Month \

--set-list ukb23158_500k_OQFE.sets.txt.gz --anno-file ukb23158_500k_OQFE.annotations.txt.gz --mask-def ldl_custom_masks.txt

--aaf-bins 0.01,0.001 --nauto 23 --bsize 200 --extract-sets extract_gene_names.txt --check-burden-files --threads 16 --gz\

--write-mask-snplist --vc-tests skato,acato-full --out Exercise_skato_acato_chr${i}"

dx run swiss-army-knife -iin="${exome_file_dir}/${data_field}_c${chr}_b0_v1.bed" \

-iin="${exome_file_dir}/${data_field}_c${chr}_b0_v1.bim" \

-iin="${exome_file_dir}/${data_field}_c${chr}_b0_v1.fam" \

-iin="${txt_file_dir}/ldl_custom_masks.txt" \

-iin="${txt_file_dir}/Ex1.phe" \

-iin="${txt_file_dir}/Ex1.covar" \

-iin="${txt_file_dir}/extract_gene_names.txt" \

-iin="${data_file_dir}/ap38_results_pred.list" \

-iin="${data_file_dir}/ap38_results_1.loco.gz" \

-iin="${txt_file_dir}/ukb23158_500k_OQFE.sets.txt.gz" \

-iin="${txt_file_dir}/ukb23158_500k_OQFE.annotations.txt.gz" \

-icmd="${run_regenie_burden}" --tag="burden_EX" --instance-type "mem2_ssd1_v2_x96" \

--destination="${project}:/Data/ap_wes_gwas/" --brief --yes

done

and I got this error 

* set file         : [ukb23158_500k_OQFE.sets.txt.gz] ERROR: unknown chromosome code in set list file.

I tried to modify the sets file but it's read only file and I can't modify it or make it tab delimited

I even tried to run the same script as bash script on Jupyter notebook 

./regenie_v2.2.4.gz_x86_64_Linux_mkl \
   --step 2 \
   --pred "Exercise_cc /mnt/project/Data/ap_wes_gwas/ap38_results_1.loco" \
   --ref-first \
   --bed "/mnt/project/Bulk/Exome sequences/Population level exome OQFE variants, PLINK format - final release/ukb23158_c21_b0_v1" \
   --phenoFile "/mnt/project/gwas_cohort_textfiles/Ex1.phe" \
   --covarFile "/mnt/project/gwas_cohort_textfiles/Ex1.covar" \
   --phenoCol Exercise_cc --covarCol age --covarCol sex \
   --covarCol genotyping --covarCol PCA{1:10} \
   --covarCol Centre --covarCol Month \
   --set-list "/mnt/project/gwas_cohort_textfiles/ukb23158_500k_OQFE.sets.txt.gz" \
   --anno-file "/mnt/project/gwas_cohort_textfiles/ukb23158_500k_OQFE.annotations.txt.gz" \
   --mask-def "/mnt/project/gwas_cohort_textfiles/ukb23158_500k_OQFE.masks" \
   --nauto 23 \
   --aaf-bins 0.01,0.001 \
   --bsize 200 \
   --extract-sets "/mnt/project/gwas_cohort_textfiles/extract_gene_names.txt" \
   --out ldl_pcsk9 \
   --gz

and I got the following error * phenotypes       : [/mnt/project/gwas_cohort_textfiles/Ex1.phe] ERROR: cannot read file : Exercise_cc /mnt/project/Data/ap_wes_gwas/ap38_results_1.loco though the file is present in the same directory.