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.

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

Good luck,

J.