FeatureCounts gives 0 for all genes

For Bulk RNASeq analysis, I aligned paired end reads that came from a reverse stranded library, using the built-in dm6 (Drosophila melanogaster) available in HISAT2 aligner tool on Galaxy. After this I downloaded and tried using various GTF files corresponding to dm6 genome in FeatureCounts tool. However it produced outputs for all .bam files, with counts = 0 for all genes.
I tried the same with the same process with dm3 genome build and the corresponding dm3 GTF file. However I get the same results (outputs with counts = 0 for all genes).
Why is this? and how can I fix it?

Hi @Neha_Kachewar
a similar question was asked recently. Please search the forum for featureCounts.
Kind regards,