TopHat v2.1.1- Warning: TopHat did not find any junctions in GTF file

[Munmun]

I'm running TopHat v2.1.1 on Mycobacterium tuberculosis genome using the gtf file download from the EnsemblBacteria FTP. When trying map to genome I get a warning:

[2018-07-17 11:55:54] Beginning TopHat run (v2.1.1)
[2018-07-17 11:55:54] Checking for Bowtie
Bowtie version: 2.3.4.1
[2018-07-17 11:55:54] Checking for Bowtie index files (genome)..
[2018-07-17 11:55:54] Checking for reference FASTA file
[2018-07-17 11:55:54] Generating SAM header for /exthome/users/rna_seq/bowtie2/ref
[2018-07-17 11:55:54] Reading known junctions from GTF file
Warning: TopHat did not find any junctions in GTF file
[2018-07-17 11:55:54] Preparing reads

I want to know what might be the reason for this warning. And what should be done to avoid this. Any idea please let me know..