choishingwan
commented
2 years ago 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.
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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