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-uploaded-file

Thanks in advance for your help!

-David


************************************************

David Robinson
Graduate Student
Lewis-Sigler Institute for Integrative Genomics
Carl Icahn Laboratory
Princeton University
646-620-6630

************************************************



___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

   http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

   http://lists.bx.psu.edu/

--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

 http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

 http://lists.bx.psu.edu/

Reply via email to