Error: No valid variant remaining

[ryshi06]

Hello,

I am trying to run the program with a publicly available GWAS summary statistics and my PLINK binary file set with the following command:

Rscript $PRSice/PRSice.R --dir . \
    --prsice $PRSice/PRSice_linux \
    --base ${DIR_NAME}/${BASE_NAME}_updated.txt \
    --snp variant_alternate_id2 --chr chromosome --bp base_pair_location --A1 effect_allele --A2 other_allele --stat odds_ratio --pvalue p_value \
    --extract PRSice.valid \
    --target $TARGET_PLINK \
    --pheno $PHENO --pheno-col z_SUVr \
    --clump-kb 250 \
    --clump-r2 0.1 \
    --clump-p 5e-08 \
    --thread 1 \
    --beta \
    --binary-target F

But I received the error message saying:

Reading 100.00%
21101114 variant(s) observed in base file, with: 
21101114 variant(s) excluded based on user input 
0 total variant(s) included from base file 

Error: No valid variant remaining 

I checked the overlap variants of the two file and returns 17,081,910. I also checked the column format as required. The variant_alternate_id2 is in chr:pos:ref:alt format, and the PLINK file also follows this format.

Can you please guide me on how to solve this? Thank you!

Best,
Ruyu