Chandu,

Are you running your analysis on our public server ( main.g2.bx.psu.edu )? If 
so, can you share your history me please (Options-->Share/Publish-->Share with 
a User-->my email address).

Thanks,
J.

On Oct 11, 2011, at 4:26 PM, Chandu Galaxy wrote:

> 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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