Error: Invalid .bed file size for .bed

[zfchen1]

Describe the bug I got the problem"Error: Invalid .bed file size for xxxx.bed". And I have no idea to deal with it.

Error Log 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) 2024-02-29 15:05:12 D:\PRSice\PRSice_win64 ABCDv\ABCD\test\PRSice_win64.exe \ --a1 A1 \ --a2 A2 \ --bar-levels 0.001,0.05,0.1,0.2,0.3,0.4,0.5,1 \ --base GWAS.assoc \ --beta \ --binary-target F \ --bp BP \ --chr CHR \ --clump-kb 250kb \ --clump-p 1.000000 \ --clump-r2 0.100000 \ --interval 5e-05 \ --lower 5e-08 \ --num-auto 22 \ --out PRSice \ --pvalue P \ --seed 1959031011 \ --snp SNP \ --stat BETA \ --target ABCD \ --thread 1 \ --upper 0.5

Initializing Genotype file: ABCD (bed)

Start processing GWAS ==================================================

Base file: GWAS.assoc Header of file is: SNP CHR BP A1 A2 EAF BETA SE P

1047456 variant(s) observed in base file, with: 156922 ambiguous variant(s) excluded 890534 total variant(s) included from base file

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

3016 people (0 male(s), 0 female(s)) observed 3016 founder(s) included

Error: Invalid .bed file size for ABCD.bed

To Reproduce If possible, provide a minimum working example for me to reproduce the problem. This can usually speed up the debugging process.

Additional context Add any other context about the problem here.

[choishingwan]

Your file is invalid, check and see if it works with plink

Sam

On Thu, Feb 29, 2024 at 2:52 AM zfchen1 @.***> wrote:

Assigned #353 https://github.com/choishingwan/PRSice/issues/353 to @choishingwan https://github.com/choishingwan.

— Reply to this email directly, view it on GitHub https://github.com/choishingwan/PRSice/issues/353#event-11962039812, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAJTRYWRTS25VQI3RP7JJEDYV3O3PAVCNFSM6AAAAABD7NYIN2VHI2DSMVQWIX3LMV45UABCJFZXG5LFIV3GK3TUJZXXI2LGNFRWC5DJN5XDWMJRHE3DEMBTHE4DCMQ . You are receiving this because you were assigned.Message ID: @.***>

[zfchen1]

Thanks for your reply! But my teacher used this .bed file and worked successfully. I'm sure the .bed file is right. Is there any possibility of this problem? Thanks!

[choishingwan]

Nope

Unless you are running this on your teacher’s computer, there’d still be chances for this to go wrong, e.g. corrupted download etc

Sam

On Thu, Feb 29, 2024 at 9:34 PM zfchen1 @.***> wrote:

Thanks for your reply! But my teacher used this .bed file and worked successfully. I'm sure the .bed file is right. Is there any possibility of this problem? Thanks!

— Reply to this email directly, view it on GitHub https://github.com/choishingwan/PRSice/issues/353#issuecomment-1972350411, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAJTRYQO4Y5S234CSVSJPULYV7SMLAVCNFSM6AAAAABD7NYIN2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNZSGM2TANBRGE . You are receiving this because you were mentioned.Message ID: @.***>

[zfchen1]

I got it. Thanks for your reply.