Gff3, no gene name in ouput - MissingGeneID

[desmodus1984]

Hi,
I am trying to assess mitochondrial gene expression. I downloaded the fasta and the gff3 from NCBI.
(https://www.ncbi.nlm.nih.gov/nuccore/BK063639.1
Since NCBI doesn't have the gtf, I used the gff3 file to make the index
and it didn't prompt any errors:

STAR --runThreadN 8 \
	--runMode genomeGenerate \
	--genomeDir /DataDrive/juaguila/BVos/RNA-fq/mito-gff3/ \
	--genomeFastaFiles /DataDrive/juaguila/BVos/RNA-fq/mito/mitoBvos.fasta \
	--genomeSAindexNbases 6 \
	--sjdbGTFfile /DataDrive/juaguila/BVos/RNA-fq/mito/MitoBVos.gff3 \
	--sjdbOverhang 49

/home/juaguila/miniconda3/envs/STAR/bin/STAR-avx2 --runThreadN 8 --runMode genomeGenerate --genomeDir /DataDrive/juaguila/BVos/RNA-fq/mito-gff3/ --genomeFastaFiles /DataDrive/juaguila/BVos/RNA-fq/mito/mitoBvos.fasta --genomeSAindexNbases 6 --sjdbGTFfile /DataDrive/juaguila/BVos/RNA-fq/mito/MitoBVos.gff3 --sjdbOverhang 49
STAR version: 2.7.11b   compiled: 2024-07-03T14:39:20+0000 :/opt/conda/conda-bld/star_1720017372352/work/source

Sep 06 21:31:33 ..... started STAR run
Sep 06 21:31:33 ... starting to generate Genome files
Sep 06 21:31:33 ..... processing annotations GTF
Sep 06 21:31:33 ... starting to sort Suffix Array. This may take a long time...
Sep 06 21:31:33 ... sorting Suffix Array chunks and saving them to disk...
Sep 06 21:31:33 ... loading chunks from disk, packing SA...
Sep 06 21:31:33 ... finished generating suffix array
Sep 06 21:31:33 ... generating Suffix Array index
Sep 06 21:31:33 ... completed Suffix Array index
Sep 06 21:31:33 ... writing Genome to disk ...
Sep 06 21:31:33 ... writing Suffix Array to disk ...
Sep 06 21:31:33 ... writing SAindex to disk
Sep 06 21:31:33 ..... finished successfully

Now, I tried to map the reads

for i in *_1_val_1.fq
        do
	base=$(basename $i "_1_val_1.fq")

STAR --runThreadN 12 \
        --genomeDir  /DataDrive/juaguila/BVos/RNA-fq/mito-gff3/\
	--readFilesIn ${base}_1_val_1.fq ${base}_2_val_2.fq  \
	--outFileNamePrefix ${base} \
        --outSAMtype BAM SortedByCoordinate \
        --outSAMattributes NH HI NM MD \
        --alignIntronMin 20 \
        --alignIntronMax 100 \
        --quantMode GeneCounts \
	--limitBAMsortRAM 1096479141
done

And, there is no gene in GeneCounts:
N_unmapped 11131325 11131325 11131325
N_multimapping 6011 6011 6011
N_noFeature 674973 7779465 1127893
N_ambiguous 0 0 0
MissingGeneID 7557418 452926 7104498

I then even converted the gff3 to gtf using AGAT, and the gene names are vague/meaningless:
N_unmapped 19624491 19624491 19624491
N_multimapping 1171 1171 1171
N_noFeature 1050 726463 192370
N_ambiguous 5143 433 4279
agat-gene-1 7 13 2
agat-gene-2 6 2 11
agat-gene-3 2 1 1
agat-gene-4 790 120 684
agat-gene-5 1 12 0
agat-gene-6 9 9 0
agat-gene-7 138981 133349 6023
agat-gene-8 15186 499 15078
agat-gene-9 0 0 0
agat-gene-10 9803 2182 7621
agat-gene-11 29 10 19
agat-gene-12 0 0 8
agat-gene-13 0 1 0
agat-gene-14 0 1 0
agat-gene-15 0 0 0
agat-gene-16 10698 1445 9253
agat-gene-17 38905 1874 37031
agat-gene-18 1 1 0
agat-gene-19 46999 10685 36314
agat-gene-20 4061 3537 549
agat-gene-21 0 4 2
agat-gene-22 585645 33359 552299
agat-gene-23 60897 4222 56675
agat-gene-24 15 6 9

Could you tell why the index with the gff3 worked, but then the mapping output is weird?