Hi, I have just tried to convert the synchronized file into a gene-based synchronized file, and the command runs, but the output file is empty. Any ideas? The input sync file works fine with other commands. Perhaps it is the gtf file,

I have converted the mikado.gff3 file into gtf file using the "gffread" tool.

here is the heading of gftf file

Chr1    Mikado_loci     transcript      32398   36487   19.0    +       .       transcript_id "mikado.Chr1G1.1"; gene_id "mikado.Chr1G1"

Chr1    Mikado_loci     exon    32398   32919   .       +       .       transcript_id "mikado.Chr1G1.1"; gene_id "mikado.Chr1G1";

Chr1    Mikado_loci     exon    33696   33859   .       +       .       transcript_id "mikado.Chr1G1.1"; gene_id "mikado.Chr1G1";

any idea is highly appreciated. thank you