Gene count file was empty after Stringtie

I am new to galaxy and have little knowledge on coding. I was running differentially expressed genes using three replicates of RNAseq data from controls and samples. My workflow was from FASTQC >> Trimmomatic >> HISAT2 >> Stringtie >> Stringtie merge >> Stringtie (using Stringtie merge as a reference genome) >> DESeq2. However, the results from Stringtie giving out gene count file which had no information in it. The assembled transcript file showed mapped transcripts. So when I performed DESeq2, the error showed up. Can anyone help me out with this issue? Thanks in advance!