bcftools csq cannot parse bacterial gff3 files

Use the attached bcftools_csq.zip and reproduce the three commands and stderr output first. Inspect csq.c around gff_parse_id, especially the reported lines 692 and 699, and compare the accepted attribute formats with the supplied GFF3 and GTF files. Done means the bacterial inputs are parsed appropriately or the diagnostics clearly identify the unsupported format.

I have tried the bcftools csq command with the attached fasta, and three different gff files (one from ncbi, one ncbi modified to add transcripts, and one from ensembl bacteria). In all cases the gff cannot be parsed, and I haven't found the error message informative as to why.

Files to replicate this are attached here:
bcftools_csq.zip

The commands I tried with their stderr are in bcftools_csq.stderr

Parsing Streptococcus_pneumoniae_atcc_700669.ASM2666v1.32.chromosome.Chromosome.gff3.gz ...
[csq.c:699 gff_parse_id] Could not parse the line: Chromosome	ena	gene	186	1547	.	+	.	ID=gene:SPN23F00010;Name=dnaA;biotype=protein_coding;description=chromosomal replication initiator protein;gene_id=SPN23F00010;logic_name=ena

bcftools csq -f Streptococcus_pneumoniae_ATCC_700669_v1.fa -g transcripts.gtf dhh.vcf.gz 2>> bcftools_csq.stderr
Parsing transcripts.gtf ...
[csq.c:692 gff_parse_id] Could not parse the line, "Parent=transcript:" not present: FM211187	protein_coding	exon	186	1547	.	+	0	gene_id ""FM211187.2.1""; transcript_id ""dnaA""; exon_number "1"; 

bcftools csq -f Streptococcus_pneumoniae_ATCC_700669_v1.fa -g Streptococcus_pneumoniae_ATCC_700669_v1.gff dhh.vcf.gz 2>> bcftools_csq.stderr
Parsing Streptococcus_pneumoniae_ATCC_700669_v1.gff ...
ignore: FM211187	EMBL	databank_entry	1	2221315	0.000	+	.	ID="FM211187.1";organism="Streptococcus pneumoniae ATCC 700669";strain="ATCC 700669";mol_type="genomic DNA";db_xref="taxon:561276"
[csq.c:692 gff_parse_id] Could not parse the line, "Parent=transcript:" not present: FM211187	EMBL	CDS	186	1547	0.000	+	0	ID="FM211187.2";transl_table=11;gene="dnaA";locus_tag="SPN23F00010";product="chromosomal replication initiator protein";db_xref="GOA:B8ZJH9";db_xref="InterPro:IPR001957";db_xref="InterPro:IPR003593";db_xref="InterPro:IPR010921";db_xref="InterPro:IPR013159";db_xref="InterPro:IPR013317";db_xref="InterPro:IPR018312";db_xref="InterPro:IPR020591";db_xref="UniProtKB/Swiss-Prot:B8ZJH9";protein_id="CAR67867.1";translation="MKEKQFWNRILEFAQERLTRSMYDFYAIQAELIKVEENVATIFLPRSEMEMVWEKQLKDIIVVAGFEIYDAEITPHYIFTKPQDTTSSQVEEATNLTLYDYSPKLVSIPYSDTGLKEKYTFDNFIQGDGNVWAVSAALAVSEDLALTYNPLFIYGGPGLGKTHLLNAIGNEILKNIPNARVKYIPAESFINDFLDHLRLGEMEKFKKTYRSLDLLLIDDIQSLSGKKVATQEEFFNTFNALHDKQKQIVLTSDRSPKHLEGLEERLVTRFSWGLTQTITPPDFETRIAILQSKTEHLGYNFQSDTLEYLAGQFDSNVRDLEGAINDITLIARVKKIKDITIDIAAEAIRARKQDVSQMLVIPIDKIQTEVGNFYGVSIKEMKGSRRLQNIVLARQVAMYLSRELTDNSLPKIGKEFGGKDHTTVIHAHAKIKSLIDQDDNLRLEIESIKKKIK"```