Galaxy Error

Question: Galaxy Error

5.4 years ago by

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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modified 5.4 years ago by Jennifer Hillman Jackson ♦ 25k • written 5.4 years ago by Toni Delorey • 20

5.4 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k 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 -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org

ADD COMMENT • link written 5.4 years ago by Jennifer Hillman Jackson ♦ 25k

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 -- 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

ADD REPLY • link written 5.4 years ago by Toni Delorey • 20

Toni, As a quick work-around until set up natively, you may be able to use the Extract DNA tool with a custom reference genome: http://wiki.galaxyproject.org/Support#Custom_reference_genome See the example in: "Tools on the Main server", should work on any Galaxy set up as a production server In short, you load a fasta version of the genome into your history and use it with tools. UCSC is the source for sacCer2, in the downloads area: http://genome.ucsc.edu Most, but not all, core tools from the Galaxy team have a custom genome support option on the form. When they don't, there is a reason (likely not practical from a indexing/memory usage perspective). Tools developed by the community set their own priority for this support. Best, Jen Galaxy team -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org

ADD REPLY • link written 5.4 years ago by Jennifer Hillman Jackson ♦ 25k

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