I was trying to get the longest isoform from ensemble genomesbut the function is exiting with an error

Error: Gene_ID or Peptide_IDs between the gtf file and the headers of the fasta file did not match! Please make sure that the 'transcript_id' column in the gtf file matches the IDs given in the headers of the fasta file.

I have a feeling that the function only works for features from refseq.
Is there an easy way to fix this?