cufflinks GTF files incompatible with cuffmerge?

Question

[sahilbioinf0]

Hello all..

I was trying to merge cufflink generated GTF file using Cuffmerge into single merged.gtf file but didn't succeeded. Running the script gave following error:

(base) [ska112@login002 cufflinks-2.2.1.Linux_x86_64]$ cuffmerge -o cuffmerge_new -g Bombyx.gtf -s bombyx.fa assmeblies.txt 

[Wed Jun 24 17:34:43 2020] Beginning transcriptome assembly merge
-------------------------------------------

[Wed Jun 24 17:34:43 2020] Preparing output location cuffmerge_new/
[Wed Jun 24 17:34:45 2020] Converting GTF files to SAM
[17:34:45] Loading reference annotation.
GFF Error: duplicate/invalid 'transcript' feature ID=BGIBMGA005056-RA
        [FAILED]
Error: could not execute gtf_to_sam