Protein sequences comparison failed! ERROR: SnpEff Database check failed.

[ewebi]

Describe the issue
I am currently facing an issue while trying to build a SnpEff database for my dataset. Although I have verified that all relevant files (GFF, CDS, and protein sequences) are formatted correctly and the transcript and gene IDs match across all files, I am still encountering an error during the protein check. CDS check passed with 0.0% error rate.

To Reproduce

1. SnpEff version: 5.2
2. Genome version: PiroplasmaDB-68_TparvaMuguga_AnnotatedProteins
3. SnpEff full command line: java -jar snpEff.jar build -gff3 -v TparvaMuguga
4. Output / Error message: Protein check: TparvaMuguga OK: 0 Not found: 4120 Errors: 0 Error percentage: NaN%
   00:00:02 Protein sequences comparison failed!
   ERROR: Database check failed.

Expected behavior
I expect to build a database with error rates below 2%.

Data
Sample data. No need to add the full genomic dataset, but a few input lines enough to reproduce the conditions.
WARNING: Always attach the data files such as VCF lines.

Additional context
Add any other context about the problem here.