John,

My best guess is that you are using bias correction but do not have the needed 
reference genome(s) for the builds that you want to use. See this page for 
instructions about setting up HTS tools; in particular, you'll need to set up 
the sam_fa_indices.loc file:

https://bitbucket.org/galaxy/galaxy-central/wiki/NGSLocalSetup

Best,
J. 

On Jun 9, 2011, at 4:44 AM, 吳正華 wrote:

> Hi galaxy dev team:
>  
> I just installed galaxy on my ubuntu box and tried to do RNA-seq analysis 
> according to Jeremy's excellent tutorial
>  
> http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise
>  
> however, I encountered following error messages when I was trying to execute 
> Cufflinks in galaxy..
>  
> Dataset generation errors
> Dataset 121: Cufflinks on data 92: gene expression
> Tool execution generated the following error message:
> Error running cufflinks. [Errno 2] No such file or directory: 
> 'transcripts.gtf'
> The tool produced the following additional output:
> cufflinks v1.0.3
> cufflinks -q --no-update-check -I 300000 -F 0.050000 -j 0.050000 -p 4 -b
>  
> how should I solve this problem?
>  
> Thanks in advance.
>  
>  
> Best Regards,
>  
> John Wu
>  
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