Hello Robert,
This guess turned out to be incorrect. The problem for this user was
solved by either sorting the Bowtie output before using CuffLinks or by
using TopHat output instead.
Hopefully one of these will solve your issues as well,
Best,
Jen
Galaxy team
On 6/22/11 1:17 PM, Robert Curtis Hendrickson wrote:
Jen,
We are running into the same problem on our local install of galaxy.
We're running Cufflinks v.1.0.1, on a BAM file (accepted_reads) from TopHat run
on mm9 based RNAseq data (paired-end 25mer), and pulled down the changes made
to galaxy last month to support the 1.0.1 version of Cufflinks.
We (think) we have mm9 indexes locally installed. We can successfully run
get_genomic_sequence on mm9 .BED's....
Turning off bias correction made no difference.
We also tried rolling back to Cufflinks v0.9.1 (including the Galaxy patch),
and got the same error
An error occurred running this job: cufflinks v0.9.1
cufflinks -q --no-update-check -I 500000 -F 0.000100 -j 0.000100 -p 4 -N
Error running cufflinks. [Errno 2] No such file or directory: 'transcripts.gtf'
An error occurred running this job: cufflinks v1.0.1
cufflinks -q --no-update-check -I 500000 -F 0.000100 -j 0.000100 -p 4 -N
Error running cufflinks. [Errno 2] No such file or directory: 'transcripts.gtf'
I can provide a link to the history on our server that you should
(theoretically) be able to access.
Regards,
Curtis
-----Original Message-----
From: galaxy-user-boun...@lists.bx.psu.edu [mailto:galaxy-user-
boun...@lists.bx.psu.edu] On Behalf Of Jennifer Jackson
Sent: Friday, June 10, 2011 3:58 PM
To: David Robinson
Cc: galaxy-user@lists.bx.psu.edu
Subject: Re: [galaxy-user] Error running cufflinks on Galaxy
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
************************************************
___________________________________________________________
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--
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/
--
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/
