Hello David, Cufflinks requires locally cached data to perform the Bias Correction function. Without seeing any sample data, a quick guess is that changing the option "Tool: Cufflinks -> Perform Bias Correction:" from yes to no in that workflow step will probably correct the problem. Another option is to set the dbkey value in the initial input FASTQ file to be a native database (if possible). Hopefully this helps, but if does not correct the problem, please share a history link with data that demonstrates the problem and I can take closer look (emailing link to me directly, to maintain data privacy, would be fine). Jen Galaxy team On 6/8/11 12:07 PM, David Robinson wrote:
Hello,
When I attempt to run cufflinks based on .sam output from bowtie I get an error:
An error occurred running this job: /cufflinks v1.0.1 cufflinks -q --no-update-check -I 300000 -F 0.050000 -j 0.050000 -p 8 -b /galaxy/data/hg19/sam_index/hg19.fa Error running cufflinks. [Errno 2] No such file or directory: 'transcripts.gtf'
/What can I do to get around this problem and run cufflinks?
My workflow is on http://main.g2.bx.psu.edu and can be found here (I ran it using a .fastq file):
http://main.g2.bx.psu.edu/u/dgrtwo/w/cufflinks-workflow-imported-from-upload...
Thanks in advance for your help!
-David
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David Robinson Graduate Student Lewis-Sigler Institute for Integrative Genomics Carl Icahn Laboratory Princeton University 646-620-6630
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