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choishingwan / PRSice

A software package for calculating, applying, evaluating and plotting the results of polygenic risk scores
http://prsice.info
GNU General Public License v3.0
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[BUG]Error: No valid variant remaining #271

Closed joannananana closed 3 years ago

joannananana commented 3 years ago

Describe the bug After using the --extract *.valid file that PRSice produces, I got the following error. The valid file is empty.

Error Log 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) 2021-06-18 01:21:42 /home/gsoft/PRSice_linux/PRSice_linux \ --a1 A1 \ --bar-levels 0.001,0.05,0.1,0.2,0.3,0.4,0.5,1 \ --base /home/jgavra/PRS.17.6/base/Resample02_train.txt.assoc.logistic \ --beta \ --binary-target 3F \ --bp BP \ --chr CHR \ --clump-kb 250kb \ --clump-p 1.000000 \ --clump-r2 0.100000 \ --cov /home/jgavra/PRS.17.6/target/covar/Resample02_covar.txt \ --extract /home/jgavra/PRS.17.6/results/2.valid \ --interval 5e-05 \ --lower 5e-08 \ --num-auto 22 \ --out /home/jgavra/PRS.17.6/results/2 \ --pheno /home/jgavra/PRS.17.6/target_phen.pheno \ --pheno-col TGmgdL,SGOTASTUL,SGPTALTUL \ --print-snp \ --pvalue P \ --seed 4054952183 \ --snp SNP \ --stat OR \ --target /home/jgavra/PRS.17.6/target/pca/Resample02 \ --thread 1 \ --upper 0.5

Initializing Genotype file: /home/jgavra/PRS.17.6/target/pca/Resample02 (bed)

Start processing Resample02_train.txt.assoc ==================================================

SNP extraction/exclusion list contains 0 columns, will assume first column contains the SNP ID

Base file: /home/jgavra/PRS.17.6/base/Resample02_train.txt.assoc.logistic Header of file is: CHR SNP BP A1 TEST
NMISS OR STAT P

2839331 variant(s) observed in base file, with: 2839331 variant(s) excluded based on user input 0 total variant(s) included from base file

Error: No valid variant remaining

comments I have already checked issue #189 and the format of the columns is the same accross the files.

choishingwan commented 3 years ago

Think this might be a bug that I've not got time to fix as of yet (printing empty valid file). You can manually remove duplicated SNPs from your GWAS data and see if this issue persists.

Sam

stale[bot] commented 3 years ago

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.