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/3b3365a391944f848b403412f226ee9e5499c0d5/tools/metag_tools/megablast_wrapper.xml?at=default

(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.ti...@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:
>
> pub...@nlm.nih.gov - for problems with PubMed
> webad...@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]" <mat...@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
>> mat...@ncbi.nlm.nih.gov
>>
>>
>>
>>
>>
>>
>> On 4/28/14 9:56 AM, "Scott W. Tighe" <scott.ti...@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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