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)

---

The Galaxy User List is being replaced by the Galaxy Biostar User Support Forum at https://biostar.usegalaxy.org/

Posts to this list will be disabled in May 2014. In the meantime, you are encouraged to post all new questions to Galaxy Biostar.

For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:

http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists, please use the interface at:

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To search Galaxy mailing lists use the unified search at:

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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)

---

The Galaxy User List is being replaced by the Galaxy Biostar User Support Forum at https://biostar.usegalaxy.org/

Posts to this list will be disabled in May 2014. In the meantime, you are encouraged to post all new questions to Galaxy Biostar.

For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:

http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists, please use the interface at:

http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

http://galaxyproject.org/search/mailinglists/

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

On April 28, 2014 4:28:49 PM EDT, Peter Cock p.j.a.cock@googlemail.com wrote:

On Mon, Apr 28, 2014 at 9:01 PM, Scott Tighe scott.tighe@uvm.edu wrote:

...

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