Stringetie merge problem


I have mapped my reads with bowtie2, assembled transcripts with stringtie and now I would like to use StringTie Merge to merge my transcripts with a reference transcript list from Arabidopsis. I found several TAIR10.gff files, however I always get an error message: “WARNING: no reference transcripts were found for the genomic sequences where reads were mapped! Please make sure the -G annotation file uses the same naming convention for the genome sequences”. Can someone tell me what I’m doing wrong or which is the correct TAIR10 file to use here?
I also tried to run stringtie with the same reference file as above and get the same error message. I tried to tun stringtie with the built-in reference genomes (as I used them for bowtie), however the selection list is empty.