[galaxy-user] When will megablast be working again

Discussion:

Scott W. Tighe

2014-04-28 13:56:19 UTC

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)

Scott W. Tighe

2014-04-28 16:25:09 UTC

Permalink

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 at nlm.nih.gov - for problems with PubMed
webadmin at 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)

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 at ncbi.nlm.nih.gov

Post by Scott W. Tighe
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)

Peter Cock

2014-04-28 16:39:38 UTC

Permalink

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

Post by Scott W. Tighe
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
pubmed at nlm.nih.gov - for problems with PubMed
webadmin at 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.
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)

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Jennifer Jackson

2014-04-28 17:23:02 UTC

Permalink

Hi Peter,

Thanks for clarifying all of this!

Main (usegalaxy.org) was restarted, perhaps why you encountered an
intermittent access delay. Let us know if are still unable to reach.

For the megablast issue over the weekend, we are updating the databases.
I replied to Scott's first galaxy-user at bx.psu.edu post and also to a
similar question posted to Galaxy Biostar:
https://biostar.usegalaxy.org/p/7335/#7340

Take care,

Jen
Galaxy team

Post by Peter Cock
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
galaxy-central/tools/metag_tools/megablast_wrapper.xml
<tool id="megablast_wrapper" name="Megablast" version="1.2.0">
...
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
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

--
Jennifer Hillman-Jackson
http://galaxyproject.org

Scott Tighe

2014-04-28 20:01:31 UTC

Permalink

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)

Peter Cock

2014-04-28 20:28:49 UTC

Permalink

Post by Scott Tighe
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

Hi Scott,

Galaxy is back for me now, and yes, the Galaxy tool you are
talking about is called Megablast (version 1.2.0), and only
offers these target databases:

htgs 13-Apr-2014
nt 17-Apr-2014
wgs 20-Apr-2014
phiX174

This Galaxy tool does *not* connect to the NCBI BLAST
service over the internet.

It sounds like the problem was due to the Galaxy team
updating these databases - as Jennifer mentioned?

I don't understand how you got an NCBI web server
error message (in your email to Wayne), but perhaps
you were separately testing the NCBI BLAST service
outside of Galaxy?

Regards,

Peter

Scott Tighe

2014-04-28 20:56:37 UTC

Permalink

Peter

Actually I was running blast separately and got error messages from them as well and I assumed it was a connection problem But in fact it was two separate problems unrelated. Good catch And thanks again

Scott
Vermont Cancer Center
Advanced Genome Techology Lab

Post by Peter Cock

Post by Scott Tighe
Peter
Thank you for your detailed response and I should have noted that I

was

Post by Scott Tighe
using the Main Public Galaxy. Thank you for confirming that it is

down!

Post by Scott Tighe
I appreciate your input!
Scott

Hi Scott,
Galaxy is back for me now, and yes, the Galaxy tool you are
talking about is called Megablast (version 1.2.0), and only
htgs 13-Apr-2014
nt 17-Apr-2014
wgs 20-Apr-2014
phiX174
This Galaxy tool does *not* connect to the NCBI BLAST
service over the internet.
It sounds like the problem was due to the Galaxy team
updating these databases - as Jennifer mentioned?
I don't understand how you got an NCBI web server
error message (in your email to Wayne), but perhaps
you were separately testing the NCBI BLAST service
outside of Galaxy?
Regards,
Peter

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Matten, Wayne (NIH/NLM) [C]

2014-04-28 16:11:48 UTC

Permalink

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 at ncbi.nlm.nih.gov