problem with Blatsearch

[Philippe Monget]

Dear administrator,

We tried several times to use Blatsearch, but we failed. That is is written:

"

• Error in TCP non-blocking connect() 111 - Connection refused
• Operation now in progress
  Sorry, the BLAT/iPCR server seems to be down. Please try again later."

Is there any technical problem? If yes, when will it be resolved?

Many thanks for your response and your help.

Best regards,

Philippe Monget

[Cath Tyner]

Hello Philippe,

Thank you for contacting the UCSC Genome Browser support team. In order to best assist you, can you reply to this forum and provide more information?

* Are you using command-line BLAT, or the web-based BLAT tool?

* If you are using the web-based BLAT tool, which UCSC Genome Browser url are you using?
  

​  ​

1. http://genome.ucsc.edu/cgi-bin/hgBlat (U.S. server)
  2. http://genome-euro.ucsc.edu/cgi-bin/hgBlat (our official European mirror)
  3. http://genome-asia.ucsc.edu/cgi-bin/hgBlat (our official Asia mirror)

* Which assemblies are you using in your BLAT search?

Once we have more information, we'll be able to assist with troubleshooting to resolve the issue.

Thank you for contacting the UCSC Genome Browser support team. 

​Please send new and follow-up questions to one of our UCSC Genome Browser mailing lists below:

  * Post to the Public Help Forum: E

mail 

gen...@soe.ucsc.edu

​ or search the Public Archives

​  * Post to the Mirror Help Forum: Email

 genome...@soe.ucsc.edu 

or search the Mirror Archives​

​  * Confidential/private help: Email

 genom...@soe.ucsc.edu

UCSC Genome Browser Announcements List (email alerts for new data & software):

  * Subscribe: Email genome-announce+subscribe@soe.ucsc.edu 
  * Unsubscribe: Email genome-announce+unsubscribe@soe.ucsc.edu

Join us on Social Media! Facebook, Twitter, Wordpress Blog, YouTube

​Enjoy,​

Cath
. . .

Cath Tyner

UCSC Genome Browser, Software QA & User Support

UC Santa Cruz Genomics Institute

UCSC Genome Browser

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[Philippe Monget]

Hello Cath,

My responses:

Le 02/05/17 à 19:47, Cath Tyner a écrit :

Hello Philippe,

Thank you for contacting the UCSC Genome Browser support team. In order to best assist you, can you reply to this forum and provide more information?

* Are you using command-line BLAT, or the web-based BLAT tool?

web-based tool

* If you are using the web-based BLAT tool, which UCSC Genome Browser url are you using?
  

​  ​

1. http://genome.ucsc.edu/cgi-bin/hgBlat (U.S. server)
  2. http://genome-euro.ucsc.edu/cgi-bin/hgBlat (our official European mirror)
  3. http://genome-asia.ucsc.edu/cgi-bin/hgBlat (our official Asia mirror)

this one: http://rohsdb.cmb.usc.edu/GBshape/cgi-bin/hgBlat

* Which assemblies are you using in your BLAT search?

Human and chicken, nothing...

Many thanks for your help, we need it in my lab.
Best regards,

Philippe

[Cath Tyner]

Thank you for the information and the fast response, Philippe! 

Users are able to create their own mirrors of the UCSC Genome Browser, and they are responsible for their own content. Since the mirror you are using is not an official UCSC Genome Browser, you will need to contact the Rohs Lab directly: 

http://rohsdb.cmb.usc.edu/index.html

http://rohslab.cmb.usc.edu/People.html

If you would instead prefer to use the official UCSC Genome Browser, please follow one of the 3 urls for the U.S., euro, or asia servers listed in my previous response. 

Please respond to this list if you have further questions!

Thank you for contacting the UCSC Genome Browser support team. 

​Please send new and follow-up questions to one of our UCSC Genome Browser mailing lists below:

  * Post to the Public Help Forum: E

mail 

gen...@soe.ucsc.edu

​ or search the Public Archives

​  * Post to the Mirror Help Forum: Email

 genome...@soe.ucsc.edu 

or search the Mirror Archives​

​  * Confidential/private help: Email

 genom...@soe.ucsc.edu

UCSC Genome Browser Announcements List (email alerts for new data & software):

  * Subscribe: Email genome-announce+subscribe@soe.ucsc.edu 
  * Unsubscribe: Email genome-announce+unsubscribe@soe.ucsc.edu

Join us on Social Media! Facebook, Twitter, Wordpress Blog, YouTube

​Enjoy,​

Cath
. . .

Cath Tyner

UCSC Genome Browser, Software QA & User Support

UC Santa Cruz Genomics Institute

UCSC Genome Browser

  * Subscribe: Email genome-announce+subs...@soe.ucsc.edu 
  * Unsubscribe: Email genome-announce+unsub...@soe.ucsc.edu

[Philippe Monget]

What should we do? Do you advise us to create our own mirror site? Do you think that it will work?...

Le 02/05/17 à 20:18, Cath Tyner a écrit :

[Cath Tyner]

Hi Philippe,

You were using a mirror of our site - this can be seen by looking at the url you were using, which is different from the 3 official sites that I mentioned. If there is a reason that you are using that particular Rohs Lab mirror instead of the official UCSC Genome Browser, you will need to contact them for assistance with their BLAT tool.

However, if you just want to use the official UCSC Genome Browser, you can reach our site at any of the 3 urls below:

1. http://genome.ucsc.edu/cgi-bin/hgBlat (U.S. server)
2. http://genome-euro.ucsc.edu/cgi-bin/hgBlat (our official European mirror)
3. http://genome-asia.ucsc.edu/cgi-bin/hgBlat (our official Asia mirror)

You should be able to perform your BLAT search on one of the three sites listed above, selecting the site that is closest to your location. If you have any issues with your blat search on the official UCSC Genome Browser, please feel free to respond to this forum!

For future reference, if you are ever interested in creating your own mirror, you can start by taking a look at our documentation:
http://genome.ucsc.edu/goldenPath/help/mirror.html

Cath
. . .

Cath Tyner

UCSC Genome Browser, Software QA & User Support

UC Santa Cruz Genomics Institute

UCSC Genome Browser

On Tue, May 2, 2017 at 11:24 AM, Philippe Monget <Philipp...@inra.fr> wrote:

What should we do? Do you advise us to create our own mirror site? Do you think that it will work?...

Le 02/05/17 à 20:18, Cath Tyner a écrit :

Thank you for the information and the fast response, Philippe! 

Users are able to create their own mirrors of the UCSC Genome Browser, and they are responsible for their own content. Since the mirror you are using is not an official UCSC Genome Browser, you will need to contact the Rohs Lab directly: 

http://rohsdb.cmb.usc.edu/index.html

http://rohslab.cmb.usc.edu/People.html

If you would instead prefer to use the official UCSC Genome Browser, please follow one of the 3 urls for the U.S., euro, or asia servers listed in my previous response. 

Please respond to this list if you have further questions!

Thank you for contacting the UCSC Genome Browser support team. 

​Please send new and follow-up questions to one of our UCSC Genome Browser mailing lists below:

  * Post to the Public Help Forum: E

mail 

gen...@soe.ucsc.edu

​ or search the Public Archives

​  * Post to the Mirror Help Forum: Email

 genome...@soe.ucsc.edu 

or search the Mirror Archives​

​  * Confidential/private help: Email

 genom...@soe.ucsc.edu

UCSC Genome Browser Announcements List (email alerts for new data & software):

  * Subscribe: Email genome-announce+subscribe...@soe.ucsc.edu 
  * Unsubscribe: Email genome-announce+unsubscri...@soe.ucsc.edu

[Philippe Monget]

Many thanks Cath, we will do that tomorrow.

You are wonderfull...

Best regards,

Philippe

Megane, please, try one of the url below.

Le 02/05/17 à 20:41, Cath Tyner a écrit :