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chrchang / plink-ng

A comprehensive update to the PLINK association analysis toolset. Beta testing of the first new version (1.90), focused on speed and memory efficiency improvements, is finishing up. Development is now focused on building out support for multiallelic, phased, and dosage data in PLINK 2.0.
https://www.cog-genomics.org/plink/2.0/
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Logistic regression returns NAs output---FIRTH_CONVERGE_FAIL #263

Closed shenlan17 closed 6 months ago

shenlan17 commented 6 months ago

Hello!

I'm trying to run logistic regression using PLINK2, but the most of output are 'NA'(not all SNPs), the ERRCODE is "FIRTH_CONVERGE_FAIL".

The phenotype(Y) is balanced with case-control ratio closed to 1:1.5

The .log file and results is as follows

PLINK v2.00a3.6LM 64-bit Intel (14 Aug 2022) www.cog-genomics.org/plink/2.0/ (C) 2005-2022 Shaun Purcell, Christopher Chang GNU General Public License v3 Logging to /gpfs/lab/groupYU/members/liumengge/UKBB/onesample/chr9.log. Options in effect: --allow-no-sex --bfile ukb500k_info0.3_maf0.001_chr9 --covar cov.txt --covar-name sex_22001-PC10 --covar-variance-standardize --glm firth-fallback hide-covar --out chr9 --pheno env_binomial.txt --pheno-name f.6138 --threads 16 --vif 1000000000 Start time: Thu Mar 14 12:58:51 2024 Note: --allow-no-sex no longer has any effect. (Missing-sex samples are automatically excluded from association analysis when sex is a covariate, and treated normally otherwise.) 257587 MiB RAM detected; reserving 128793 MiB for main workspace. Using up to 16 threads (change this with --threads). 442716 samples (238133 females, 204583 males; 442716 founders) loaded from ukb500k_info0.3_maf0.001_chr9.fam. 651057 variants loaded from ukb500k_info0.3_maf0.001_chr9.bim. 1 binary phenotype loaded (116117 cases, 184228 controls). 15 covariates loaded from cov.txt. --covar-variance-standardize: 15 covariates transformed. Calculating allele frequencies... 100% done. --glm logistic-Firth hybrid regression on phenotype 'f.6138'

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Could you give me some hints to solve this issue, thank you!

chrchang commented 6 months ago

Please ask usage questions like this in the plink2-users Google group.