I was doing a RNA analyse and I wished to compare the transcription and 
expression of two samples using a reference annotation, however this is the 
error message I got:

Error running cuffmerge. 
[Thu Jul  4 07:32:59 2013] Beginning transcriptome assembly merge

[Thu Jul  4 07:32:59 2013] Preparing output location cm_output/
[Thu Jul  4 07:34:07 2013] Converting GTF files to SAM
[07:34:07] Loading reference annotation.
[07:34:07] Loading reference annotation.
[Thu Jul  4 07:34:08 2013] Quantitating transcripts
You are using Cufflinks v2.1.1, which is the most recent release.
Command line:
cufflinks -o cm_output/ -F 0.05 -g 
/galaxy/main_pool/pool7/files/006/446/dataset_6446730.dat -q 
--overhang-tolerance 200 --library-type=transfrags -A 0.0 
--min-frags-per-transfrag 0 --no-5-extend -p 4 
[bam_header_read] EOF marker is absent.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
File cm_output/tmp/mergeSam_fileIO17rb doesn't appear to be a valid BAM file, 
trying SAM...
[07:34:08] Loading reference annotation.
[07:35:53] Inspecting reads and determining fragment length distribution.
Processed 33854 loci.                       
> Map Properties:
>       Normalized Map Mass: 8719.00
>       Raw Map Mass: 8719.00
>       Fragment Length Distribution: Truncated Gaussian (default)
>                     Default Mean: 200
>                  Default Std Dev: 80
[07:35:53] Assembling transcripts and estimating abundances.
Processed 33854 loci.                       
[Thu Jul  4 07:39:29 2013] Comparing against reference file 
You are using Cufflinks v2.1.1, which is the most recent release.
Error: duplicate GFF ID 'ENST00000361547.2' encountered!
Error: could not execute cuffcompare

======End quote======

The job goes well without the annotation reference. 
The annotation file I used can be downloaded here:

Can anyone help me please?

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