The -F gff3 output has no header

[tseemann]

This isn't really your problem, as I assume you just copy what NCBI gives you, but the -F gff3 result doesn't have a header which I think is needed to validate?

 ##gff-version 3

[kblin]

Yes, I'm copying what the NCBI API provides, character by character.

[kblin]

That said, I'm not currently trying to validate GFF files, as validation right now is just checking if Biopython will load the file.

[tseemann]

Does biopython auto-detect the GFF version number?
Or are you just getting lucky because GFF3 is standard now?