[biomart-users] Biomart down again?

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smh
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[biomart-users] Biomart down again?

smh
Hi all,
As  a new Biomart user, I have downloaded the SNP annotations using the GrCh37 since I needed the older rsID to map to compare with previous data.
The R package worked a few days ago and I downloaded chromosomes 9-22, however when I try downloading the other larger chromosomes it gives me the error message "Error in value[[3L]](cond) : 
  Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.". Funnily enough the same works still for chromosome 22 so am wondering if there is some kind of server time out.
I have tried everything - changing the host, etc and nothing works. Really need to get this done this week for some analysis.
Any help would be greatly appreciated.
Kind regards
SMH

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Re: [biomart-users] Biomart down again?

Thomas Maurel
Dear SMH,

I am afraid that the BioMart software is not designed to handle genome wide query so it’s recommended to split your query in smaller chucks, for example downloading only one chromosome at a time. 
The server is timing out because the amount of data requested is so huge that the server can’t cope with it.

Hope this helps,
Regards,
Thomas
On 24 Oct 2016, at 11:51, smh <[hidden email]> wrote:

Hi all,
As  a new Biomart user, I have downloaded the SNP annotations using the GrCh37 since I needed the older rsID to map to compare with previous data.
The R package worked a few days ago and I downloaded chromosomes 9-22, however when I try downloading the other larger chromosomes it gives me the error message "Error in value[[3L]](cond) : 
  Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.". Funnily enough the same works still for chromosome 22 so am wondering if there is some kind of server time out.
I have tried everything - changing the host, etc and nothing works. Really need to get this done this week for some analysis.
Any help would be greatly appreciated.
Kind regards
SMH

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Thomas Maurel
Bioinformatician - Ensembl Production Team
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom

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smh
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[biomart-users] Re: Biomart down again?

smh
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Dear Thomas,
Thank-you for your reply. 
I am downloading only one chromosome at a time and it is still killing the job/timing out so not sure what to do.
Kind regards
SMH

On Monday, October 24, 2016 at 8:54:49 PM UTC+10, smh wrote:
Hi all,
As  a new Biomart user, I have downloaded the SNP annotations using the GrCh37 since I needed the older rsID to map to compare with previous data.
The R package worked a few days ago and I downloaded chromosomes 9-22, however when I try downloading the other larger chromosomes it gives me the error message "Error in value[[3L]](cond) : 
  Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.". Funnily enough the same works still for chromosome 22 so am wondering if there is some kind of server time out.
I have tried everything - changing the host, etc and nothing works. Really need to get this done this week for some analysis.
Any help would be greatly appreciated.
Kind regards
SMH

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Re: [biomart-users] Re: Biomart down again?

Thomas Maurel
Dear SMH,

Could you please let me know which chromosomes are timing out? 

Thank you,
Thomas
On 24 Oct 2016, at 20:31, smh <[hidden email]> wrote:

Dear Thomas,
Thank-you for your reply. 
I am downloading only one chromosome at a time and it is still killing the job/timing out so not sure what to do.
Kind regards
SMH

On Monday, October 24, 2016 at 8:54:49 PM UTC+10, smh wrote:
Hi all,
As  a new Biomart user, I have downloaded the SNP annotations using the GrCh37 since I needed the older rsID to map to compare with previous data.
The R package worked a few days ago and I downloaded chromosomes 9-22, however when I try downloading the other larger chromosomes it gives me the error message "Error in value[[3L]](cond) : 
  Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.". Funnily enough the same works still for chromosome 22 so am wondering if there is some kind of server time out.
I have tried everything - changing the host, etc and nothing works. Really need to get this done this week for some analysis.
Any help would be greatly appreciated.
Kind regards
SMH

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--
Thomas Maurel
Bioinformatician - Ensembl Production Team
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom

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