PRSice clumping was not processed for almost 9 hours with a stopped progress rate of 3.33%

Question

[runye]

Hi, I wish to do PRS on imputed chromosome files. However, the clumping process stopped at 3.33% and never move forward for almost 10hrs. That's weird and I wish to know why.

I have tried with --no-clump and it works, but I'm wondering whether the association found using this PRS calculation is not reliable enough or just say distorted.

I also tried with --allow-inter for clumping but the process stopped at 3.33% either.

PRSice 2.3.3 (2020-08-05) https://github.com/choishingwan/PRSice (C) 2016-2020 Shing Wan (Sam) Choi and Paul F. O'Reilly GNU General Public License v3 If you use PRSice in any published work, please cite: Choi SW, O'Reilly PF. PRSice-2: Polygenic Risk Score Software for Biobank-Scale Data. GigaScience 8, no. 7 (July 1, 2019) 2022-04-06 23:59:43 ../PRS/PRSice_linux \ --a1 A1 \ --allow-inter \ --bar-levels 0.00040005,1 \ --base logistic_results.assoc_2.logistic \ --binary-target T \ --chr CHR \ --clump-kb 250kb \ --clump-p 1.000000 \ --clump-r2 0.100000 \ --cov pca.eigenvec \ --extract PRSice.valid \ --fastscore \ --no-regress \ --num-auto 22 \ --or \ --out PRSice \ --pvalue P \ --seed 3365717295 \ --snp SNP \ --stat OR \ --target ukb_imp_chr#_v3 \ --thread 20

?[1;33mWarning: B not found in base file ?[0m ?[1;33mWarning: Intermediate not required. Will not generate intermediate file ?[0m

Initializing Genotype file: ukb_imp_chr#_v3 (bed)

Start processing logistic_results.assoc_2

==================================================

SNP extraction/exclusion list contains 5 columns, will assume first column contains the SNP ID

Base file: logistic_results.assoc_2.logistic Header of file is: CHR SNP BP A1 TEST NMISS
OR STAT P

Reading 100.00%

4244228 variant(s) observed in base file, with: 940502 variant(s) excluded based on user input 3303726 total variant(s) included from base file

Loading Genotype info from target

==================================================

487409 people (223025 male(s), 264353 female(s)) observed 487409 founder(s) included

89788042 variant(s) not found in previous data 1563 variant(s) with mismatch information 2292 ambiguous variant(s) excluded 3303726 variant(s) included

Start performing clumping

Clumping Progress: 3.33%

Can anyone help me with the progress stopped issue? Thanks a lot!!

Answer 1

[Sam]

Likely it is just too much for PRSice. You can try to run the clumping with plink instead.

I was previously working on a new version of PRSice that should kinda solve that, but due to recent change of circumstances, I was not able to complete the update. Will see when will I have time to pick that up again and hopefully these kind of problem can be solved.

[runye]

Thanks Sam. I'm really new to genetic analysis. I'll try plink.