All individuals have missing/invalid values for all traits
Closed this issue · 3 comments
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
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.
Thank you very much! It worked for me too.