Thank you for the response.
I can't check my reference genome dataset because I'm using reference
provided by Galaxy (*Mosquito (Anopheles gambiae): AgamP3*). Is there any
solution? Thank you.

--
Chandu



On Mon, Oct 10, 2011 at 7:15 AM, Jeremy Goecks <jeremy.goe...@emory.edu>wrote:

>
> 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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