gffread error

hello

I am currently trying to do RNA-seq using public data in brassica juncea.

To use htseq-count for making count table, I have to convert gff file which downloaded in brassica database to gtf file.

So I used gffread for converting gff file with below command

gffread Bju.genome.gff -T -o Bju.genome.gtf

But when I type above command, I got a lot of error message like below

Error: discarding overlapping duplicate mRNA feature (24650-31472) with ID=BjuO004617
Error: discarding overlapping duplicate mRNA feature (39979-40535) with ID=BjuO004618
Error: discarding overlapping duplicate mRNA feature (30824-34680) with ID=BjuO001651
Error: discarding overlapping duplicate mRNA feature (56651-57957) with ID=BjuO001652
Error: discarding overlapping duplicate mRNA feature (78160-80198) with ID=BjuO001654
Error: discarding overlapping duplicate mRNA feature (74204-77329) with ID=BjuO001653
Error: discarding overlapping duplicate mRNA feature (4453-4737) with ID=BjuO006559
Error: discarding overlapping duplicate mRNA feature (10094-10618) with ID=BjuO009958
Error: discarding overlapping duplicate mRNA feature (15520-17470) with ID=BjuO010812
Error: discarding overlapping duplicate mRNA feature (22118-22816) with ID=BjuO010813
Error: discarding overlapping duplicate mRNA feature (5722-6432) with ID=BjuO010811
Error: discarding overlapping duplicate mRNA feature (3944-4429) with ID=BjuO007439
Error: discarding overlapping duplicate mRNA feature (790-2307) with ID=BjuO007438
Error: discarding overlapping duplicate mRNA feature (6457-6978) with ID=BjuO005411

To check if the file was created properly, I checked file size.
And it looks like ok.

40M Bju.genome.gff
56M Bju.genome.gtf

and I also used ‘head’ command, and there seems to be no problem

A01     GeneWise        gene    3352    5985    1195.88 +       .       ID=BjuA000594;
A01     GeneWise        mRNA    3352    5985    1195.88 +       .       ID=BjuA000594;Parent=BjuA000594;
A01     GeneWise        CDS     3352    3675    1195.88 +       0       ID=BjuA000594.cds;Parent=BjuA000594;
A01     GeneWise        CDS     4225    4447    1195.88 +       0       ID=BjuA000594.cds;Parent=BjuA000594;
A01     GeneWise        CDS     4579    4949    1195.88 +       2       ID=BjuA000594.cds;Parent=BjuA000594;
A01     GeneWise        CDS     5091    5326    1195.88 +       0       ID=BjuA000594.cds;Parent=BjuA000594;
A01     GeneWise        CDS     5421    5691    1195.88 +       1       ID=BjuA000594.cds;Parent=BjuA000594;
A01     GeneWise        CDS     5785    5985    1195.88 +       0       ID=BjuA000594.cds;Parent=BjuA000594;
A01     GeneWise        gene    8012    14242   1731.69 +       .       ID=BjuA002557;
A01     GeneWise        mRNA    8012    14242   1731.69 +       .       ID=BjuA002557;Parent=BjuA002557;

So, I wonder why the error message appeared and whether it is okay to use the created file.
I would be really grateful if someone reply.