could you post the complete output of plink 1.07 on this command?

Thank you very much for your response. Here it is:

Options in effect:

--file chr15

--pheno pheno.txt

--all-pheno

--linear

--covar CovSex.txt

--ci 0.95

--hide-covar

--missing-phenotype -9

--out chr15

19389 (of 19389) markers to be included from [ chr15.map ]

3152 individuals read from [ chr15.ped ]

0 individuals with nonmissing phenotypes

Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)

Missing phenotype value is also -9

0 cases, 0 controls and 3152 missing

1446 males, 1706 females, and 0 of unspecified sex

Reading alternate phenotype from [ pheno.txt ]

0 individuals with non-missing alternate phenotype

Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)

Missing phenotype value is also -9

0 cases, 0 controls and 3152 missing

Reading 9 covariates from [ CovSex.txt ] with nonmissing values for 0 individuals

Before frequency and genotyping pruning, there are 19389 SNPs

3152 founders and 0 non-founders found

Total genotyping rate in remaining individuals is 0.978897

0 SNPs failed missingness test ( GENO > 1 )

0 SNPs failed frequency test ( MAF < 0 )

After frequency and genotyping pruning, there are 19389 SNPs

After filtering, 0 cases, 0 controls and 3152 missing

After filtering, 1446 males, 1706 females, and 0 of unspecified sex

Converting data to Individual-major format

Writing logistic model association results to [ chr15.P1.assoc.logistic ]

Reading alternate phenotype from [ pheno.txt ]

0 individuals with non-missing alternate phenotype

Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)

Missing phenotype value is also -9

0 cases, 0 controls and 3152 missing

And the output from plink 1.9 is as follows:

19389 variants loaded from .bim file.

3152 people (1446 males, 1706 females) loaded from .fam.

0 phenotype values present after --pheno.

Using 1 thread (no multithreaded calculations invoked).

Error: No --covar values loaded.

Seems that plink doesn't find the phenotypes and covariate values to each of your individuals in the genotype file. Please make sure, that coding of IDs is consistent across ped and alternate phenotype as well as covariate files (lower/upper case is important here) and consider that any individual is denoted by two ID values: (i) family or pedigree id and (ii) individual id within family (exactly in this order). In addition make sure to use exactly one whitespace (blank or tab) as column delimiter in the phenotype and covariate files and remove quotation marks your software possibly intrudoces when saving the tables as text.

Dear Josef, 

Thank you very much for your suggestion. I will try this and hopefully it will make a difference.

Kind regards,

Maja