[BUG]Error: No valid variant remaining

[MaleehaMaria]

Describe the bug Error: No valid variant remaining Error: Execution halted

Please always include the log file generated by PRSice.

My final log file is as follows:

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) 2022-06-09 15:36:28 ./PRSice_linux
--a1 effect_allele
--a2 other_allele
--bar-levels 1
--base baseqc_formatted_for_PRSice2.txt
--beta
--binary-target F
--bp chr_position
--chr chr_name
--chr-id chr_name
--extract xxxx.valid
--fastscore
--id-delim "tab"
--ignore-fid
--keep target.valid.sample.txt
--no-clump
--num-auto 22
--out analysis
--pvalue P
--seed 4074344121
--stat stat
--target target.QC
--thread 1

Initializing Genotype file: target.QC (bed)

Start processing baseqc_formatted_for_PRSice2

SNP extraction/exclusion list contains 0 columns, will assume first column contains the SNP ID

Base file: baseqc_formatted_for_PRSice2.txt Header of file is: chr_name chr_position effect_allele other_allele stat P

6626544 variant(s) observed in base file, with: 6626544 variant(s) excluded based on user input 0 total variant(s) included from base file

Error: No valid variant remaining

Additional context I am using PRSice-2 v2.3.3 I am trying to run Known cad PGS that I downloaded from PGS catalogue on my samples. As my target data is on genome build hg38, I did lift over for the target data, converted from hg19 to hg38. I am following you protocol on https://choishingwan.github.io/PRS-Tutorial/prsice/

The error above appeared when tried to correct following error: Error: A total of 88 duplicated SNP ID detected out of 88 input SNPs! Valid SNP ID (post --extract / --exclude, non-duplicated SNPs) stored at ..xxx.valid. You can avoid this error by using --extract xxxx.valid The .valid file has nothing written. so, as expected running with –exclude result in same error. when I run it with –extract, the error mentioned in the beginning of this post appeared.

I followed your discussion on posts #189, #271 (format checked, columns are numeric in the base data, except effect and other allele columns, they are classified as character). I also tried manually removing duplicated snps from base file and there are none. I also tried using --id-delim tab and also --ignore-fid, but no progress.

why is there nothing written in the .valid file when there were 88 duplicated SNP ID detected out of 88? Upon manual check using R, I could not find any duplicates. Can you please guide me?

Thanks, Maleeha

[choishingwan]

Mind checking the latest version?

On Thu, Jun 9, 2022, 9:07 AM MaleehaMaria @.***> wrote:

Assigned #296 https://github.com/choishingwan/PRSice/issues/296 to @choishingwan https://github.com/choishingwan.

— Reply to this email directly, view it on GitHub https://github.com/choishingwan/PRSice/issues/296#event-6777819783, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAJTRYQW4VKAX3ERYITIFNTVOHUC5ANCNFSM5YKASTPA . You are receiving this because you were assigned.Message ID: @.***>

[MaleehaMaria]

Mind checking the latest version? … On Thu, Jun 9, 2022, 9:07 AM MaleehaMaria @.> wrote: Assigned #296 <#296> to @choishingwan https://github.com/choishingwan. — Reply to this email directly, view it on GitHub <#296 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAJTRYQW4VKAX3ERYITIFNTVOHUC5ANCNFSM5YKASTPA . You are receiving this because you were assigned.Message ID: @.>

Many thanks for your reply. Yes, I did solve the issue ages ago by switching to latest version :).

Kind regards, Maleeha