I am trying to generate a correlation.matrix file using the PLINK --r command using the instructions outlined at https://zzz.bwh.harvard.edu/plink/ld.shtml

However, the only files generated are plink.ld, plink.log, and .pversion.

It had been working previously (producing files called 'correlation.matrix'), but for analysis purposes I renamed the file XYZ.matrix (I was analysing five different datasets and didn't want the files to be overwritten as I went through them). It has not worked since.

I have tried each of the following and then re-run the commands: (1) deleted the .matrix file I had re-named, (2) deleted the plink.exe from the folder I was working in and saved a new one into the folder, (3) generated new .map and .ped files, (4) moved all the files including the plink.exe into a new folder, and (5) downloaded a fresh install of plink. None of these have rectified the problem.

The plink.log shows that I am running the command:

Options in effect: --file all --r --matrix

15 (of 15) markers to be included from [ all.map ] 151 individuals read from [ all.ped ] 151 individuals with nonmissing phenotypes Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) Missing phenotype value is also -9 32 cases, 119 controls and 0 missing 115 males, 36 females, and 0 of unspecified sex Before frequency and genotyping pruning, there are 15 SNPs 151 founders and 0 non-founders found Total genotyping rate in remaining individuals is 0.987196 0 SNPs failed missingness test ( GENO > 1 ) 0 SNPs failed frequency test ( MAF < 0 ) After frequency and genotyping pruning, there are 15 SNPs After filtering, 32 cases, 119 controls and 0 missing After filtering, 115 males, 36 females, and 0 of unspecified sex Writing LD statistics to [ plink.ld ]

Any guidance would be appreciated!