All the data conversions (SNP file and metadata file) have been done correctly. The impute command is also executed correctly. Both the "frequency" and "neighbour" commands were tried, but all the missing data simply gets replaced by "NA" and does not allocate an imputed value. Can someone tell what is going wrong?

Note: My species is an oprhan tree species, which does not have any population sequencing data to use as a reference panel, although the genome has been sequenced for a standalone tree. I want to use de novo imputation using the existing data.