Hello, Thanks for your response. I can almost never get anything done on the public instance of Galaxy. It can take an entire day to even load a.bed file. When I was encountering the error I was on the Broad Instance. Marco, I tried following the instructions above to ensure that genome was available but got lost. Is there a way to link this with the Broad Instance so I can use this tool? Thanks, Toni On Tue, Jul 23, 2013 at 7:48 PM, Jennifer Jackson <jen@bx.psu.edu> wrote:
Hi Toni,
Bjoern is correct - if you are using a local Galaxy that does not have this reference genome available, it needs to be added. The "Extract DNA" tool requires a .2bit version of the genome available and the alignseq.loc file configured. More is here, section " LASTZ and EXTRACT Genomic DNA": http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup
The builds.txt file would need to be intact and the genome assigned for this specific error to come up, but in general when adding new reference genomes, that file also needs to be adjusted. Instructions are on this wiki page, along with rsync instructions if you would like to get/model your data after ours: http://wiki.galaxyproject.org/Admin/Data%20Integration
The public Main server and the cloud AMI both have this build available. So, if you are using the public server, and this error came up, the issue is likely related to a temporary, earlier issue with job dispatching. Processing load at this time is extremely high as this resolves - so a re-run may not be successful immediately, but do try again in a few hours or even tomorrow morning.
Our apologies for any confusion this may have caused,
Jen Galaxy team
On 7/23/13 9:24 AM, Toni Delorey wrote:
Hello,
I'm trying to convert a .bed file to a FASTA file. I get the following error when I do.
"An error occurred with this dataset: *No sequences are available for 'sacCer2', request them by reporting this error.*"
I'm not sure what the issue is?
Thanks, Toni -- Toni Marie Delorey Regev Lab, 6175-OO The Broad Institute of MIT and Harvard 7 Cambridge Center Cambridge, MA 02141 Email: delorey@broadinstitute.org Phone: 617-714-8225
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-- Toni Marie Delorey Regev Lab, 6175-OO The Broad Institute of MIT and Harvard 7 Cambridge Center Cambridge, MA 02141 Email: delorey@broadinstitute.org Phone: 617-714-8225