cuffmerge problems

[ccstaats]

Hello
I'm founding some problems with cuffmerge
I've a fasta file of 27 supercontigs from broad institute, which I edited to this format
>Supercontig_1.1

I've downloaded also the gtf file from Broad
As an example, the first lane is
Supercontig_1.1 CNB1_FINAL_CALLGENES_3 start_codon 5909 5911 . - 0 gene_id "CNBG_0001"; transcript_id "CNBG_0001T0";

I ran bowtie-build, tophat and cufflinks on my fastq files and everything is fine
However, when I run cuffmerge, I got the message:
You are using Cufflinks v1.3.0, which is the most recent release.
Warning: couldn't find fasta record for '>Supercontig_1.1'!
Warning: couldn't find fasta record for '>Supercontig_1.10'!
Warning: couldn't find fasta record for '>Supercontig_1.11'!

Moreover, I got a merged gtf file with 2 entries for the same sequence. For example:

>Supercontig_1.1 Cufflinks exon 13250 13293 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "1"; gene_name "CNBG_0004"; oId "CNBG_0004T0"; nearest_ref "CNBG_0004T0"; class_code "="; tss_id "TSS1";

Supercontig_1.1 Cufflinks exon 13233 13293 . + . gene_id "XLOC_006239" transcript_id "TCONS_00006365" exon_number "1" oId "CUFF.148.1" class_code "u" tss_id "TSS6299"

I noted that in the first case, a ">" commes before the Supercontig. So I replace every entry in gtf adding or reoving the ">" before the "Supercontig"
Nothing worked.
Any clues?
Thanks
Charley