cuffmerge not work for all samples

[dawn1313]

Hi,

I am doing cuffmerge to merge the six assemblies. It worked well for the three samples together, but it has the following error when the total six assemblies in the assembly_list.txt.

---------------------------------------
> cuffmerge -p 4 -g ../ref_annotation.gff3 -s CMV_ref.fa assembly_list.txt

[Tue Sep 8 10:19:15 2015] Beginning transcriptome assembly merge
-------------------------------------------

[Tue Sep 8 10:19:15 2015] Preparing output location ./merged_asm/
[Tue Sep 8 10:19:15 2015] Converting GTF files to SAM
[10:19:15] Loading reference annotation.
[10:19:15] Loading reference annotation.
[10:19:15] Loading reference annotation.
GFF Error: duplicate/invalid 'transcript' feature ID=UL122
[FAILED]
Error: could not execute gtf_to_sam

----------------------------------------
Is there some help? Thanks a lot!
Dawn