> Tool execution generated the following error message:
> Error running cuffcompare. Warning: Your version of Cufflinks is not 
> up-to-date. It is recommended that you upgrade to Cufflinks v1.1.0 to benefit 
> from the most recent features and bug fixes (http://cufflinks.cbcb.umd.edu).
> No fasta index found for ./input1. Rebuilding, please wait..
> Error: sequence lines in a FASTA record must have the same length!
Chandu,

Cufflinks/compare/diff requires that your reference genome dataset have the 
following format:

>my_chrom
AGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGT
AGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGT
AGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGT
...

Note that all lines of sequence data have the same length. 

The problem you're seeing is because there are lines in your sequence data that 
are not the same length, e.g.

>my_chrom
AGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGT
AGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTA
AGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCG
...

The FASTA Width tool in Galaxy can help you format your dataset correctly.

Good luck,
J.
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