Phenotype file issue

[ZhiyiZhu0226]

Hello, I encountered a problem with phenotype files while running step one. while running it gives the error "ERROR: all individuals have missing/invalid values for all traits."

The full command and output is as below: '/cellar/users/zhzhu/software/regenie/regenie --step 1 --bgen /nrnb/ukb-genetic/imputation/ukb_imp_chr16_v3.bgen --extract qc_pass.prune.in --sample /nrnb/ukb-genetic/imputation/ukb_imp_chr16_v3.sample --keep qc_pass.id --phenoFile ../tg_hdl.cleaned.HDLonly.pheno --covarFile ../tg_hdl.cleaned.cov --apply-rint --bsize 1000 --lowmem --lowmem-prefix tmpdir/regenie_tmp_preds --phenoColList HDL --out ukb_step1 Start time: Wed Feb 2 22:38:24 2022

          |============================|
          |        REGENIE v2.2.4      |
          |============================|

Copyright (c) 2020-2021 Joelle Mbatchou, Andrey Ziyatdinov and Jonathan Marchini. Distributed under the MIT License.

Log of output saved in file : ukb_step1.log

Options in effect: --step 1 \ --bgen /nrnb/ukb-genetic/imputation/ukb_imp_chr16_v3.bgen \ --extract qc_pass.prune.in \ --sample /nrnb/ukb-genetic/imputation/ukb_imp_chr16_v3.sample \ --keep qc_pass.id \ --phenoFile ../tg_hdl.cleaned.HDLonly.pheno \ --covarFile ../tg_hdl.cleaned.cov \ --apply-rint \ --bsize 1000 \ --lowmem \ --lowmem-prefix tmpdir/regenie_tmp_preds \ --phenoColList HDL \ --out ukb_step1

Fitting null model

• bgen : [/nrnb/ukb-genetic/imputation/ukb_imp_chr16_v3.bgen] -summary : bgen file (v1.2 layout, zlib compressed) with 487409 anonymous samples and 3089612 variants with 8-bit encoding. -index bgi file [/nrnb/ukb-genetic/imputation/ukb_imp_chr16_v3.bgen.bgi] -keeping variants specified by --extract -number of variants remaining in the analysis = 83752 -sample file: /nrnb/ukb-genetic/imputation/ukb_imp_chr16_v3.sample -keeping only individuals specified by --keep
• phenotypes : [../tg_hdl.cleaned.HDLonly.pheno] n_pheno = 1 -dropping observations with missing values at any of the phenotypes ERROR: all individuals have missing/invalid values for all traits.

(base) [zhzhu@nrnb-login-01 chr16]$ cat -A ../tg_hdl.cleaned.HDLonly.pheno | head -n 3 FID IID HDL$ 2014295 2014295 2.2039999961853027$ 2764517 2764517 1.5479999780654907$'

I have another phenotype file that looks exactly like the tg_hdl.cleaned.HDLonly.pheno file, and it passed step one with no problem. That file looks like this: '(base) [zhzhu@nrnb-login-01 chr16]$ cat -A ../tg_hdl.cleaned.TGonly.pheno | head -n 3 FID IID TG$ 3598999 3598999 83.9000015258789$ 3124338 3124338 87.5$'

Is there any way to solve this issue? Best regards, Zhiyi Zhu BS Bioinformatics Student

[joellembatchou]

Hi Zhiyi,

Have you checked that the IDs in the phenotype file match with those in the sample file (ie ukb_imp_chr16_v3.sample)?

If you do

grep -wFf <(tail -n +2 ../tg_hdl.cleaned.TGonly.pheno | awk '{print $1,$2}') ukb_imp_chr16_v3.sample | wc -l

what do you get? (it will print out the number of individuals in the phenotype file who are also in the sample file)

[ZhiyiZhu0226]

Ah yeah turns out I applied the wrong filter there's not common samples in those files, causing that step to fail. Thanks for your help!