Error: No valid entries in --score file. [PLINK]

Question

[beginner123]

Hi everyone,

I am following the PRS PLINK tutorial (https://choishingwan.github.io/PRS-Tutorial/plink/) and performing it on my GWAS data and base dataset. However, I am encountering some problems. I am stuck at the part where we calculate the PRS (look at the tutorial).

this is what I get: an error saying there are no valid entries in my IBD_basefile_hg38_PRS.txt But I'm not so sure why this error is present.

this is the command in the tutorial that I'm having trouble with.

plink \
    --bfile EUR.QC \
    --score Height.QC.Transformed 3 4 12 header \
    --q-score-range range_list SNP.pvalue \
    --extract EUR.valid.snp \
    --out EUR

This is my script.

plink \\
    --bfile final_IBP \\
    --score IBD_basefile_hg38_PRS.txt 1 7 9 header \\
    --q-score-range range_list SNP.pvalue \\
    --extract final_IBP.valid.snp \\
    --out final_IBP

In my file: the 1,7 and 9 are the SNP_IDs, the effective allele, and the effect size estimate (beta) respectively. I added --allow-no-sex because there was a warning saying I had to put it there if I want them included as well.

193099 MB RAM detected; reserving 96549 MB for main workspace.
29070215 variants loaded from .bim file.
3864 people (0 males, 0 females, 3864 ambiguous) loaded from .fam.
Ambiguous sex IDs written to final_IBP.nosex .
3864 phenotype values loaded from .fam.
--extract: 728614 variants remaining.
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 3864 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is exactly 1.
728614 variants and 3864 people pass filters and QC.
Among remaining phenotypes, 3060 are cases and 804 are controls.
Error: No valid entries in --score file.

If you need any specifications, do ask me!

[Sam]

Can you show the first 2-3 lines of your IBD_basefile_hg38_PRS.txt and SNP.pvalue file? And are you sure the ID in the score file match those in your final_IBP.valid.snp file?

Answer 1

[beginner123]

I got it eventually. In my case it was the fact that the alleles were in lowercase. They should be in uppercase in order for the clumping to work.