Sample quality control was performed using ukb_sqc_v2.txt

[lzy-59]

I am calculating a polygenic risk score based on the content in this link and the sample data provided (Betas.csv). Sample quality control is one of the steps.https://2cjenn.github.io/PRS_Pipeline/#Sample_QC

The link gives the following example code:
plink2 --pfile raw
--memory 15000
--extract snpQC.snplist
--keep-fam usedinpca.txt
--write-samples
--out sampleQC

However, in the UK Biobank database, USedinPc.txt has been renamed ukb_sqc_v2.txt. When I tried to change usedinpca.txt from the command line to ukb-sqc-v2.txt and run the sample code, I failed.

I use a Swiss Army knife to execute the order.Here are my input files and command line and output error messages.

Input files (in):
[ukb_sqc_v2.txt]
[snpQC.snplist]
[raw.pvar]
[raw.pgen]
[raw.psam]
[raw.afreq]

Command line:
plink2 --pfile raw --memory 15000 --extract snpQC.snplist --keep-fam ukb_sqc_v2.txt --write-samples --out sampleQC

Output:
Error: No samples remaining after main filters.
(C) 2005-2022 Shaun Purcell, Christopher Chang GNU General Public License v3
Logging to sampleQC.log.
Options in effect:
--extract snpQC.snplist
--keep-fam ukb_sqc_v2.txt
--memory 15000
--out sampleQC
--pfile raw
--write-samples
Start time: Mon Oct 7 15:02:59 2024
7677 MiB RAM detected; reserving 15000 MiB for main workspace.
Allocated 6327 MiB successfully, after larger attempt(s) failed.
Using up to 4 compute threads.
487409 samples (264092 females, 222857 males, 460 ambiguous; 487409 founders)
loaded from raw.psam.
223 variants loaded from raw.pvar.
Note: No phenotype data present.
--extract: 214 variants remaining.
--keep-fam: 0 samples remaining.

So I have a question, using the sample data provided in the link, it is not possible to filter without sample file output? Does anyone know how to solve this problem?