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
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[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 <#353> to @choishingwan <https://github.com/choishingwan>. — Reply to this email directly, view it on GitHub <#353 (comment)>, 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 <#353 (comment)>, 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.