[biomart-users] "Request to BioMart web service failed" but for only specific ENGSxxx

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[biomart-users] "Request to BioMart web service failed" but for only specific ENGSxxx

Derek Beaton
Hi all,

I am trying to retrieve all SNPs (and some other information) associated with specific ensembl gene IDs.


This works for nearly all IDs for 'ensembl_gene' except just a few that I have. For these few, the same error is returned: "Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down."

This happens for the same IDs across 2 different machines, on 2 different networks, and with useEnsembl(...,GRCh=38) or useEnsembl(...,GRCh=37). 

I am not sure why these specific IDs throw an error about a connection issue. I've attached some sample code that shows which ENGSxxx IDs work, and which routinely fail with the "Request to BioMart web service failed. [...]" message.

Could someone help me understand why these particular IDs fail, and why the error message is about a connection issue?


Cheers,
-Derek

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GetGeneIDs_TEST.R (1K) Download Attachment
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Re: [biomart-users] "Request to BioMart web service failed" but for only specific ENGSxxx

Syed Haider-5
Hi Derek,

really something to take to Ensembl SNP mart experts, but having looked at the number of entries in just the first of the two tables (hsapiens_snp__mart_transcript_variation__dm) in the mysql JOIN statement which selects the two offending genes result in 2486409 rows against those two genes. Which then gets further JOINED with the SNP main table. I imagine its the JOIN which is taking longer than the webserver time out. Just a guess.

Best,
Syed

On 5 December 2015 at 17:47, Derek Beaton <[hidden email]> wrote:
Hi all,

I am trying to retrieve all SNPs (and some other information) associated with specific ensembl gene IDs.


This works for nearly all IDs for 'ensembl_gene' except just a few that I have. For these few, the same error is returned: "Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down."

This happens for the same IDs across 2 different machines, on 2 different networks, and with useEnsembl(...,GRCh=38) or useEnsembl(...,GRCh=37). 

I am not sure why these specific IDs throw an error about a connection issue. I've attached some sample code that shows which ENGSxxx IDs work, and which routinely fail with the "Request to BioMart web service failed. [...]" message.

Could someone help me understand why these particular IDs fail, and why the error message is about a connection issue?


Cheers,
-Derek

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Re: [biomart-users] "Request to BioMart web service failed" but for only specific ENGSxxx

Derek Beaton
Thanks that makes sense.
I'm definitely hoping one of the mart experts chimes in and let's us know what is happening.

In the meantime -- is there a way to get an estimate of how long these joins/queries should take, and then also increasing the wait time via biomaRt calls?


On Saturday, December 5, 2015 at 4:52:25 PM UTC-6, Syed Haider wrote:
Hi Derek,

really something to take to Ensembl SNP mart experts, but having looked at the number of entries in just the first of the two tables (hsapiens_snp__mart_transcript_variation__dm) in the mysql JOIN statement which selects the two offending genes result in 2486409 rows against those two genes. Which then gets further JOINED with the SNP main table. I imagine its the JOIN which is taking longer than the webserver time out. Just a guess.

Best,
Syed

On 5 December 2015 at 17:47, Derek Beaton <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="WWtgB1BoCQAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">derek...@...> wrote:
Hi all,

I am trying to retrieve all SNPs (and some other information) associated with specific ensembl gene IDs.


This works for nearly all IDs for 'ensembl_gene' except just a few that I have. For these few, the same error is returned: "Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down."

This happens for the same IDs across 2 different machines, on 2 different networks, and with useEnsembl(...,GRCh=38) or useEnsembl(...,GRCh=37). 

I am not sure why these specific IDs throw an error about a connection issue. I've attached some sample code that shows which ENGSxxx IDs work, and which routinely fail with the "Request to BioMart web service failed. [...]" message.

Could someone help me understand why these particular IDs fail, and why the error message is about a connection issue?


Cheers,
-Derek

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Re: [biomart-users] "Request to BioMart web service failed" but for only specific ENGSxxx

Thomas Maurel
Dear Derek,

 We have Variant and gene information available in the Ensembl gene and variation marts, the difference between the two is the following:
* Ensembl gene mart is gene centric and only contains variants linked to Ensembl Transcripts.
* Ensembl Variation mart is variant centric and contains all the variants available in Ensembl.
I think that the best thing to do in your situation is to use the Ensembl gene mart since you are only interested in variant information associated with ensembl gene IDs. This will reduce the work that BioMart needs to do to retrieve the data that you are interested in.
I’ve attached a new R file with updated biomaRt query to retrieve the same information but using the Ensembl Gene mart.
I will investigate your query on the Variation mart and see if this can be speed up in any way in the future. 

Hope this helps,
Regards,
Thomas
On 8 Dec 2015, at 04:10, Derek Beaton <[hidden email]> wrote:

Thanks that makes sense.
I'm definitely hoping one of the mart experts chimes in and let's us know what is happening.

In the meantime -- is there a way to get an estimate of how long these joins/queries should take, and then also increasing the wait time via biomaRt calls?


On Saturday, December 5, 2015 at 4:52:25 PM UTC-6, Syed Haider wrote:
Hi Derek,

really something to take to Ensembl SNP mart experts, but having looked at the number of entries in just the first of the two tables (hsapiens_snp__mart_transcript_variation__dm) in the mysql JOIN statement which selects the two offending genes result in 2486409 rows against those two genes. Which then gets further JOINED with the SNP main table. I imagine its the JOIN which is taking longer than the webserver time out. Just a guess.

Best,
Syed

On 5 December 2015 at 17:47, Derek Beaton <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="WWtgB1BoCQAJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;" class="">derek...@...> wrote:
Hi all,

I am trying to retrieve all SNPs (and some other information) associated with specific ensembl gene IDs.


This works for nearly all IDs for 'ensembl_gene' except just a few that I have. For these few, the same error is returned: "Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down."

This happens for the same IDs across 2 different machines, on 2 different networks, and with useEnsembl(...,GRCh=38) or useEnsembl(...,GRCh=37). 

I am not sure why these specific IDs throw an error about a connection issue. I've attached some sample code that shows which ENGSxxx IDs work, and which routinely fail with the "Request to BioMart web service failed. [...]" message.

Could someone help me understand why these particular IDs fail, and why the error message is about a connection issue?


Cheers,
-Derek


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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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GetGeneIDs_TEST_ensembl_gene_mart.R (1K) Download Attachment