Warning: No significant --clump results. Skipping.

[Liaoyi Xu]

Hi Chris,

I am trying to clump my GWAS summary statistics, but I received the error: “Warning: No significant –clump results. Skipping.” I am sure that my summary statistics contain p-values less than 1.

It seems that the issue is related to this particular GWAS summary statistics file, as --clump works correctly for other GWAS summary statistics. However, I haven’t been able to identify the source of the problem. I have attached the log and the summary statistics for your reference.

Thanks in advance for your help!

Luis

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PLINK v2.0.0-a.7LM AVX2 Intel (1 Sep 2025) cog-genomics.org/plink/2.0/ (C) 2005-2025 Shaun Purcell, Christopher Chang GNU General Public License v3 Logging to ../../ukb/PLINK_CLUMP_OUTPUT/20250828_all_13_traits/20250828_female_dom.HbA1c.log. Options in effect: --clump ../../ukb/PLINK_LM_OUTPUT/all_13_traits/DOMDEV_flt/test.tsv --clump-id-field ID --clump-kb 500 --clump-p-field P --clump-p1 1 --clump-p2 1 --clump-r2 0.1 --clump-range ../../ukb/GWAS_INPUT/glist-hg19 --keep-females --out ../../ukb/PLINK_CLUMP_OUTPUT/20250828_all_13_traits/20250828_female_dom.HbA1c --pfile ../../ukb_pfile/wb_qced_maf0.001 --threads 1 Start time: Sat Sep 13 16:09:46 2025 31952 MiB RAM detected, ~24200 available; reserving 15976 MiB for main workspace. Allocated 5054 MiB successfully, after larger attempt(s) failed. Using 1 compute thread. 402040 samples (217326 females, 184714 males; 402040 founders) loaded from ../../ukb_pfile/wb_qced_maf0.001.psam. 13868376 variants loaded from ../../ukb_pfile/wb_qced_maf0.001.pvar. Note: No phenotype data present. 184714 samples removed due to sex filter(s). 217326 samples (217326 females, 0 males; 217326 founders) remaining after main filters. End time: Sat Sep 13 16:09:48 2025

Warning: No significant --clump results. Skipping.

[Chris Chang]

From the --clump documentation:

"By default, if there is a 'TEST' column, only lines where the test value is 'ADD' are considered. (This is a change from PLINK 1.x.) These default values can be changed with --clump-test-field and --clump-test, respectively."

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[Luis]

Ah thanks! I appologize for not reading the document carefully.