Error when using --keep-ambig

[Xinpeng He]

Hi,

I ran the PRS analyses with the option --keep-ambig. But there was no output file and only log file said BgenError occurred. Could you please help me with the issue?

Here follows the log file:

PRSice 2.3.5 (2021-09-20)
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)
2024-06-18 19:55:52
./PRSice_linux \
    --a1 A1 \
    --a2 A2 \
    --bar-levels 0.001,0.05,0.1,0.2,0.3,0.4,0.5 \
    --base effect_size2.txt \
    --beta  \
    --binary-target F \
    --bp BP \
    --chr CHR \
    --interval 5e-05 \
    --keep-ambig  \
    --lower 5e-08 \
    --no-clump  \
    --no-full  \
    --no-regress  \
    --num-auto 22 \
    --out ALC_PRS_withambig \
    --pheno /data/ukb/bulk-data/22828/v3/ukb_imp_chr1-chr22_v3.sample \
    --pvalue Pvalue \
    --seed 3400407428 \
    --snp SNP \
    --stat Beta \
    --target /data/ukb/bulk-data/22828/v3/ukb_imp_chr#_v3 \
    --thread 1 \
    --type bgen \
    --upper 0.5

Warning: By selecting --keep-ambig, PRSice assume the base
         and target are reporting alleles on the same
         strand and will therefore only perform dosage flip
         for the ambiguous SNPs. If you are unsure of what
         the strand is, then you should not select the
         --keep-ambig option

Initializing Genotype file:
/data/ukb/bulk-data/22828/v3/ukb_imp_chr#_v3 (bgen)

Start processing effect_size2
==================================================

Base file: effect_size2.txt
Header of file is:
SNP CHR BP A1 A2 EAF Beta SE Pvalue
 

99 variant(s) observed in base file, with:
14 ambiguous variant(s)
99 total variant(s) included from base file

Loading Genotype info from target
==================================================

487409 people (222980 male(s), 264277 female(s)) observed
487409 founder(s) included

BGenError

Thanks in advance!

Xinpeng