Error: No valid variant remaining

[Shrishtee-kandoi]

Dear Author,

I am trying to run PRS but keep getting this error:
Error: No valid variant remaining

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)
2024-02-27 18:36:56
./PRSice_linux
--a1 ref
--a2 alt
--bar-levels 0.001,0.05,0.1,0.2,0.3,0.4,0.5,1
--base GWAS_file.gz
--base-maf MAF:0.01
--binary-target F
--bp pos
--chr chrom
--clump-kb 250kb
--clump-p 1.000000
--clump-r2 0.100000
--interval 5e-05
--lower 5e-08
--num-auto 22
--or
--out Output_file
--pheno phenofile
--print-snp
--pvalue p_value
--seed 2360945017
--snp rsid
--stat beta
--target target_file
--thread 1
--upper 0.5

Warning: MAF field not found in base file. Will not perform
MAF filtering on the base file

Initializing Genotype file:
target_file
(bed)

Start processing GWAS_file

Base file:
GWAS_file.gz
GZ file detected. Header of file is:

rsid chrom pos ref alt neg_log_pvalue beta stderr_beta alt_allele_freq p_value

7227799 variant(s) observed in base file, with:
7227799 NA stat/p-value observed
0 total variant(s) included from base file

Error: No valid variant remaining

Would you please be able to help? Is there something that I'm missing?

[choishingwan]

P values are NA or invalid. Sam

…

On Tue, Feb 27, 2024 at 6:47 PM Shrishtee kandoi ***@***.***> wrote: Assigned #352 <#352> to @choishingwan <https://github.com/choishingwan>. — Reply to this email directly, view it on GitHub <#352 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAJTRYQJU6ORTQNEISBBYDLYVZWBDAVCNFSM6AAAAABD5AVSVOVHI2DSMVQWIX3LMV45UABCJFZXG5LFIV3GK3TUJZXXI2LGNFRWC5DJN5XDWMJRHE2DINBSGAYDOOI> . You are receiving this because you were assigned.Message ID: ***@***.***>

[Shrishtee-kandoi]

I just checked and did not find any NA values. Could you tell what the criteria for invalid p-values is?

The range of p-values is:
[1] 1.937e-110 1.000e+00

[choishingwan]

7227799 variant(s) observed in base file, with: 7227799 NA stat/p-value observed Try and see if 2.3.5 handle this better. I vaguely remember old versions have problem with scientific values. As long as the p value is more than 1e-231 then 2.3.5 should in theory handle that Sam

…

On Tue, Feb 27, 2024 at 6:53 PM Shrishtee kandoi ***@***.***> wrote: I just checked and did not find any NA values. Could you tell what the criteria for invalid p-values is? The range of p-values is: [1] 1.937e-110 1.000e+00 — Reply to this email directly, view it on GitHub <#352 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAJTRYQLCH2CW5BFIEBZCETYVZWXJAVCNFSM6AAAAABD5AVSVOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNRXHEZDSMRVGU> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[Shrishtee-kandoi]

Is there a different way to upgrade to 2.3.5?
I cloned the repository from Github only a few weeks and also did it again right now but it gives me the same error.

I also had another question (may not be relevant to this): Is it possible to run a PRS without stats and/or A1,A2 values? Because a lot of GWASes don't give out those information..

[choishingwan]

We were at 2.3.5 since I left academic in 2022. Maybe you can try and download the binaries? You meant running a PRS? You can’t run PRS without effect sizes or the effective allele Sam

…

On Tue, Feb 27, 2024 at 7:07 PM Shrishtee kandoi ***@***.***> wrote: Is there a different way to upgrade to 2.3.5? I cloned the repository from Github only a few weeks and also did it again right now but it gives me the same error. I also had another question (may not to relevant to this): Is it possible to run a GWAS without stats and/or A1,A2 values? Because a lot of GWASes don't give out those information.. — Reply to this email directly, view it on GitHub <#352 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAJTRYRMCKKVAYPOCEQ4LA3YVZYMHAVCNFSM6AAAAABD5AVSVOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNRXHE2DEOJRG4> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[Shrishtee-kandoi]

Yes, I meant PRS sorry! Thanks.
I will try downloading that.