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 https://github.com/choishingwan/PRSice/issues/352 to @choishingwan https://github.com/choishingwan.

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[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 https://github.com/choishingwan/PRSice/issues/352#issuecomment-1967929255, 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 https://github.com/choishingwan/PRSice/issues/352#issuecomment-1967942917, 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.