Gtool missing output .sample file

Question

[m98]

I am using Gtool to exclude some SNPs from a .imputed file. My command is as follows:

/apps/gtool/0.7.5/gtool -S \
--g ../../../Imputation/chr10.11.imputed \
--s gwas_pheno.sample \
--og chr10.11.imputed.after_exclusion.imputed \
--os chr10.11.imputed.after_exclusion.sample \
--exclusion ../../../Imputation/chr10.11.imputed.exclude.txt \
--log chr10.11.imputed.exclude.log

This command is working but I have a problem: I get the chr10.11.imputed.after_exclusion.imputed in my folder, but not the chr10.11.imputed.after_exclusion.sample. I am absolutely sure that all my directories are correct, and that all files are where I am telling Gtool they are.

My question is: is it possible that I don't get an output .sample file because I am not actually excluding samples? (I am only excluding SNPs here). I have only ever used GTOOL to exclude samples before so I am unsure. Has anyone every experienced this?