Trouble with PLINK's logistic regression analysis and covariatesTrouble with PLINK's logistic regression analysis and covariates
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20 days ago
F110152169 • 0

I am new to PLINK and I am having trouble using one of the commands. I am trying to perform logistic regression analysis on several Ped and map files. Here is the command I put in:

plink --file TWBR10907-07_TWB2_QC --logistic --covar TWB2.0_2.6_3.txt --covar-name SEX,PARKISON --out logistic_results TWB2.0_2.6_3.txt: FID IID SEX PARKISON TV2N_20203805G TV2N_20203805G 1 0 TV23_20182701G TV23_20182701G 1 0 TV29_20181602E TV29_20181602E 1 0 TV23_20182809B TV23_20182809B 2 0 TV23_20180107G TV23_20180107G 2 0 TV2N_20203806G TV2N_20203806G 2 0 TV23_20180108G TV23_20180108G 1 0 TV29_20181603F TV29_20181603F 1 0 TV21_20180301B TV21_20180301B 1 0 TV2A_20190103E TV2A_20190103E 2 0 TV29_20181605E TV29_20181605E 2 0 TV23_20180105C TV23_20180105C 2 0 TV2A_20190103D TV2A_20190103D 2 0 TV2A_20190108G TV2A_20190108G 2 0 TV2A_20190103G TV2A_20190103G 2 0 TV2A_20190104D TV2A_20190104D 1 0 TV2A_20190104A TV2A_20190104A 2 0

I get back the following message and error:

Hostname: DESKTOP-M3A23KU Working directory: D:\plink Start time: Sat May 25 10:35:23 2024

Random number seed: 1716604523 48997 MB RAM detected; reserving 24498 MB for main workspace. Scanning .ped file... Possibly irregular .ped line. Restarting scan, assuming multichar alleles. .ped scan complete (for binary autoconversion). Performing single-pass .bed write (283083 variants, 81236 people). --file: logistic_results-temporary.bed + logistic_results-temporary.bim + logistic_results-temporary.fam written. 283083 variants loaded from .bim file. 81236 people (25584 males, 55652 females) loaded from .fam. 87 phenotype values present after --pheno. Using 1 thread (no multithreaded calculations invoked). Before main variant filters, 81236 founders and 0 nonfounders present. Calculating allele frequencies... done. Warning: 4937472 het. haploid genotypes present (see logistic_results.hh ); many commands treat these as missing. Total genotyping rate is 0.996745. 283083 variants and 81236 people pass filters and QC. Among remaining phenotypes, 0 are cases and 87 are controls. (81149 phenotypes are missing.) Warning: Skipping --linear/--logistic since phenotype is constant.

I've searched online and I can't find anything on this error. Can anyone please help me out?

PLINK GWAS SNP • 193 views
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