Hi, I have generated my own annotation file for feature count, However I do not get any error in running but I get zero number which means none of the reads are aligned to my selected regions (created in annotation file). In IGV, I can see that reads are aligned to the selected regions. The annotation file is like this: 

GeneID   Chr   Start    End    Strand

>HLA:HLA00627   chr6  1   786  +

>HLA:HLA00629   chr6   1  769  + 

.....