Peter Thank you for your detailed response and I should have noted that I was using the Main Public Galaxy. Thank you for confirming that it is down! I appreciate your input! Scott Scott Tighe Senior Core Laboratory Research Staff Advanced Genome Technologies Core NextGen Sequencing/Flow Cytometry University of Vermont and Vermont Cancer Center 149 Beaumont ave Health Science Research Facility 303/305 Burlington Vermont 05405 802-656-2482 (AGTC) On 4/28/2014 12:39 PM, Peter Cock wrote:
Hi Scott,
Could you clarify *which* Galaxy server you are using, and *which* megablast tool within Galaxy? Most BLAST options within Galaxy do NOT send the queries to the NCBI servers.
(1) Main Public Galaxy
I would guess you are using the main Galaxy Server, which only has this megablast wrapper using BLAST+ blastn internally for a limited set of databases (I would check but https://usegalaxy.org/ is down right now for me):
galaxy-central/tools/metag_tools/megablast_wrapper.xml
<tool id="megablast_wrapper" name="Megablast" version="1.2.0"> ...
Current Galaxy stable source link: https://bitbucket.org/galaxy/galaxy-dist/src/3b3365a391944f848b403412f226ee9...
(2) A local Galaxy with the BLAST+ wrappers
The BLAST+ wrappers that I manage all run BLAST on the local server/cluster, although we are looking at an option to run this via the NCBI using the -remote switch: https://github.com/peterjc/galaxy_blast/issues/39
(3) A local Galaxy with custom BLAST tools
Are you perhaps using JJ's experimental BLAST+ wrappers with -remote support developed as part of the Galaxy-P project? See links on https://github.com/peterjc/galaxy_blast/issues/39
Thanks,
Peter
On Mon, Apr 28, 2014 at 5:25 PM, Scott W. Tighe <Scott.Tighe@uvm.edu> wrote:
Dear Wayne
Here is the error message I get back.
Server Error
Your request could not be processed due to a problem on our Web server. This could be a transient problem, please try the query again. If it doesn't clear up within a reasonable period of time, e-mail a short description of your query and the diagnostic information shown below to:
pubmed@nlm.nih.gov - for problems with PubMed webadmin@ncbi.nlm.nih.gov - for problems with other services
Thank you for your assistance. We will try to fix the problem as soon as possible.
Diagnostic Information: Error: 500 URL: h t t p : / / b l a s t . n c b i . n l m . n i h . g o v / b l a s t / B l a s t . c g i ? Client: 130.14.26.12 Server: blast339 Time: Mon Apr 28 12:23:50 EDT 2014
NOTE: The above is an internal URL which may differ from the one you used to address the page.
Rev. 01/04/08
-- Core Laboratory Research Staff Advanced Genome Technologies Core Deep Sequencing (MPS) Facility Vermont Cancer Center 149 Beaumont Ave University of Vermont HSRF 303 Burlington Vermont USA 05045 802-656-AGTC 802-999-6666 (cell)
Quoting "Matten, Wayne (NIH/NLM) [C]" <matten@ncbi.nlm.nih.gov>:
Hello, Scott,
The web blast service, including megablast, is functioning normally. I don't know how Galaxy submits searches to us, but my guess is via our blast URLAPI, which is also functioning well at the moment.
If your searches using our web page directly are also not working, please send me an RID from a search today, or describe a search in enough detail that I can reproduce it.
Best regards, Wayne
<<><<<><<<<<<>>>>>>> Wayne Matten, PhD NCBI Public Services matten@ncbi.nlm.nih.gov
On 4/28/14 9:56 AM, "Scott W. Tighe" <Scott.Tighe@uvm.edu> wrote:
Dear NCBI and Galaxy Team
I have sent a note to determine when the Megablast option will be active again. Whether you use Galaxy or NCBI directly, it is inoperative.
Scott
-- Core Laboratory Research Staff Advanced Genome Technologies Core Deep Sequencing (MPS) Facility Vermont Cancer Center 149 Beaumont Ave University of Vermont HSRF 303 Burlington Vermont USA 05045 802-656-AGTC 802-999-6666 (cell)
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