[galaxy-user] rna-seq CDS, splicing and TSS fails

Hi all, So I am using cuffdiff to find significant differences between two samples (no replicates). The transcript and gene differential expression works and I get significant values. However, consistently, the TSS, CDS, and splicing differences return with "1 line" and no data. I have tried multiple different GTF transcriptome reference files - UCSC refflat, ensembl, but still no luck. Maybe I am missing something very basic - can anyone give me advice here? Richard