I am trying to run rmats (alternative splicing tool) using fastq files as input files using the following command:

rmats.py --s1 /files/s1.txt --s2 /files/s2.txt --gtf /files/rmats_analysis/gencode.v39.annotation.gtf --bi /files/STAR/hg38/ -t paired --readLength 50 --nthread 4 --od /files --tmp /files/

the gtf file I am using for the analysis is:

gencode.v39.annotation.gtf  

and the genome (fasta file) I used is:

 gencode.v39.transcripts.fa

so I used exactly the same version of genome and gtf file for this analysis. but I am getting this error:

Jan 06 00:40:19 ..... started STAR run
Jan 06 00:40:19 ..... loading genome
Jan 06 00:42:02 ..... processing annotations GTF

Fatal INPUT FILE error, no valid exon lines in the GTF file: /files/gencode.v39.annotation.gtf
Solution: check the formatting of the GTF file. One likely cause is the difference in chromosome naming between GTF and FASTA file.

Jan 06 00:42:18 ...... FATAL ERROR, exiting
Traceback (most recent call last):
  File "/usr/local/bin/rmats.py", line 595, in <module>
    main()
  File "/usr/local/bin/rmats.py", line 558, in main
    args = get_args()
  File "/usr/local/bin/rmats.py", line 203, in get_args
    args.b1, args.b2 = doSTARMapping(args)
  File "/usr/local/bin/rmats.py", line 81, in doSTARMapping
    raise Exception()
Exception

since I used the same version of genome and gtf file and both from GENCODE, would you please let me know how to fix this issue? I checked both of them and in both chromosomes name start with chr.