Cufflink running error: Processed 0 loci

[NGS2009]

I used both old and the most recent cufflinks version (v1.3.0), I got the following error:

[17:14:20] Loading reference annotation.
[17:14:36] Inspecting reads and determining fragment length distribution.
> Processed 0 loci. [*************************] 100%
> Map Properties:
> Total Map Mass: 11202207.00
> Fragment Length Distribution: Truncated Gaussian (default)
> Default Mean: 200
> Default Std Dev: 80
[17:14:55] Estimating transcript abundances.
> Processed 0 loci. [*************************] 100%


Any suggestions?

Thanks!!