I am now making gene model using augustus v3.3.1. I have multiple RNA-seq data, so I tried to make hints using those data.
When I tried to make intron hints according to this page (http://bioinf.uni-greifswald.de/bioinf/wiki/pmwiki.php?n=IncorporatingRNAseq.Tophat), I found bam2hints created an empty gff file at step 11.
but there was no error message. In addition to that, at step 5, bam2hints worked properly and createda normal .gff file.
What is wrong with my procedure?