All individuals have missing/invalid values for all traits

[som-soremekun]

I am getting the error below for step 1 regenie.
I have used this script for other datasets and had no issues.

How can i resolve thhis issue?

Options in effect:
--force-step1
--step 1
--bed /home/././imputation/ugr500k
--extract ugrqc_pass.snplist
--keep ugrqc_pass.id
--phenoFile /home/././imputation/ugrid_64042
--phenoCol t2d
--covarFile /home/././imputation/ugrid_64042
--covarCol sex,age,age2,bmi
--bsize 1000
--bt
--loocv
--threads 4
--lowmem
--out /home/././imputation/step1_t2d

Fitting null model

• bim : [/home/././imputation/ugr500k.bim] n_snps = 500000
  -keeping variants specified by --extract
  -number of variants remaining in the analysis = 131058
• fam : [/home/././imputation/ugr500k.fam] n_samples = 6412
  -keeping only individuals specified by --keep
• bed : [/home/././imputation/ugr500k.bed]
• phenotypes : [/home/././imputation/ugrid_64042] n_pheno = 1
  -dropping observations with missing values at any of the phenotypes
  ERROR: all individuals have missing/invalid values for all traits.

I have checked previous issues and most of the solutions were for the sample files to be passed to the bgen file. But I am using bed files here, which needs no sample file.

I have also confirmed that the some individual IDs in the phenotype file (ugrid_64042) are also in the plink .fam file
grep 197814_B03_APP5117345_197814_B03_APP5117345 ugrid_64042
197814_B03_APP5117345_197814_B03_APP5117345 197814_B03_APP5117345_197814_B03_APP5117345 APP5117345 0 0 48.531139 2355.2715 20.4

other files include:
head ugrqc_pass.snplist
1_764648
1_785301

head ugrqc_pass.id
0 197814_A03_APP5117343_197814_A03_APP5117343
0 197814_A04_APP5117354_197814_A04_APP5117354

Thank you

[PreciousEunice]

Hi! Did you resolve this issue? I also encounter this error and I checked the Phenofile to be in the right format.

--step 1
--bed output_prefix
--phenoFile phenotype_ts.txt
--phenoCol Y1
--bsize 1000
--bt
--out fit_bin_out

n_pheno = 1
-dropping observations with missing values at any of the phenotypes
ERROR: all individuals have missing/invalid values for all traits.

[som-soremekun]

Yes I did My FID was not the same within the genotyped file.

…

On Wed 24. Apr 2024 at 4:06 PM, PreciousEunice ***@***.***> wrote: Hi! Did you resolve this issue? I also encounter this error and I checked the Phenofile to be in the right format. --step 1 --bed output_prefix --phenoFile phenotype_ts.txt --phenoCol Y1 --bsize 1000 --bt --out fit_bin_out n_pheno = 1 -dropping observations with missing values at any of the phenotypes ERROR: all individuals have missing/invalid values for all traits. — Reply to this email directly, view it on GitHub <#510 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AP2PRFVA63CRSJPFY2TOG4LY6636DAVCNFSM6AAAAABFYA4E4WVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANZVGAZTMNRXGE> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[PreciousEunice]

Thank you very much! It worked for me too.