When running Genotypeharmonizer, I come across an odd error:

GenotypeHarmonizer.sh --input file --o file2 -r reference.file -R VCF

Input data loaded

Reference data loaded

Beginning alignment

Iteration 1 - 10,000 variants processed

Iteration 1 - Completed, non A/T and non G/C SNPs are aligned 8,723 found and 4,372 swapped

Iteration 2 - Skipped, non A/T and non G/C SNPs are not LD checked

Iteration 3 - Completed, non A/T and non G/C SNPs are aligned. Extra LD check skipped

Swapped 0 A/T or G/C variants based on LD patterns

Alignment complete

Excluded in total 3,723 variants during alignment phase

Writing results

Error writing output data: Trying to write alleles [G] for G\A SNP

I've looked online, but the documentation especially for this type of error seems to be sparse. Any suggestions on how to correct or learn more about the issue? I added in the "--debug" variable too, but there wasn't a difference in output.