[BioMart Users] Error while using the RefSeq_mRNA filter in biomart

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[BioMart Users] Error while using the RefSeq_mRNA filter in biomart

Vincent Legagneux
Hello,

I was trying to recover Ensembl gene IDs from a list of RefSeq mRNA IDs
using the Biomart web interface (biomart.org). While retrieving the
results, I got this error message:

Serious Error: Error during query execution: Table
'ensembl_mart_64.ox_RefSeq_mRNA__dm' doesn't exist ERROR: caught
BioMart::Exception::Database: Error during query execution: Table
'ensembl_mart_64.ox_RefSeq_mRNA__dm' doesn't exist

A  similar message was returned after having submitted the same query
through the Bioconductor biomaRt package:

library("biomaRt")
ensembl = useMart("ensembl")
ensembl = useDataset("hsapiens_gene_ensembl",mart=ensembl)
listFilters(ensembl)
data_ensg1=getBM(attributes = c("ensembl_gene_id"), filters =
"refseq_mrna", values = data[,4], mart = ensembl)
Error in getBM(attributes = c("ensembl_gene_id"), filters =
"refseq_mrna",  :
   Query ERROR: caught BioMart::Exception::Database: Error during query
execution: Table 'ensembl_mart_64.ox_RefSeq_mRNA__dm' doesn't exist

Does anybody have any clues on the origin of this error ?

Thanks a lot.

All the best,

vincent

Below are summarized the Biomart settings I used in the web interface:
Dataset
Homo sapiens genes (GRCh37.p5)
Homo sapiens genes (GRCh37.p5)
Filters
Refseq mRNA ID(s) [e.g. NM_001195597]: [ID-list specified]
Attributes
Ensembl Gene ID
Gene Start (bp)
Gene End (bp)
Strand
Chromosome Name
Associated Gene Name
Ensembl Gene ID
Ensembl Transcript ID
[2 enabled][2 enabled]
Ensembl Gene ID
Ensembl Transcript ID
[2 enabled][2 enabled]
Ensembl Gene ID
Ensembl Transcript ID
[2 enabled][2 enabled]
Ensembl Gene ID
Ensembl Transcript ID
Reference ID
[3 enabled][3 enabled]
Protein
Ensembl Gene ID
Ensembl Transcript ID
[3 enabled][3 enabled]
Dataset
[None Selected]
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Re: [BioMart Users] Error while using the RefSeq_mRNA filter in biomart

Syed Haider
Seem like the attribute corresponding filter "refseq_mrna" has got a different internal name in the Ensembl gene v64 (Human) configuration. that needs to be set to same name, and configurations made available again. Rhoda would know the time line of this.


Best,
Syed





________________________________________
From: [hidden email] [[hidden email]] On Behalf Of Vincent Legagneux [[hidden email]]
Sent: Wednesday, September 28, 2011 7:22 AM
To: [hidden email]
Subject: [BioMart Users] Error while using the RefSeq_mRNA filter in biomart

Hello,

I was trying to recover Ensembl gene IDs from a list of RefSeq mRNA IDs
using the Biomart web interface (biomart.org). While retrieving the
results, I got this error message:

Serious Error: Error during query execution: Table
'ensembl_mart_64.ox_RefSeq_mRNA__dm' doesn't exist ERROR: caught
BioMart::Exception::Database: Error during query execution: Table
'ensembl_mart_64.ox_RefSeq_mRNA__dm' doesn't exist

A  similar message was returned after having submitted the same query
through the Bioconductor biomaRt package:

library("biomaRt")
ensembl = useMart("ensembl")
ensembl = useDataset("hsapiens_gene_ensembl",mart=ensembl)
listFilters(ensembl)
data_ensg1=getBM(attributes = c("ensembl_gene_id"), filters =
"refseq_mrna", values = data[,4], mart = ensembl)
Error in getBM(attributes = c("ensembl_gene_id"), filters =
"refseq_mrna",  :
   Query ERROR: caught BioMart::Exception::Database: Error during query
execution: Table 'ensembl_mart_64.ox_RefSeq_mRNA__dm' doesn't exist

Does anybody have any clues on the origin of this error ?

Thanks a lot.

All the best,

vincent

Below are summarized the Biomart settings I used in the web interface:
Dataset
Homo sapiens genes (GRCh37.p5)
Homo sapiens genes (GRCh37.p5)
Filters
Refseq mRNA ID(s) [e.g. NM_001195597]: [ID-list specified]
Attributes
Ensembl Gene ID
Gene Start (bp)
Gene End (bp)
Strand
Chromosome Name
Associated Gene Name
Ensembl Gene ID
Ensembl Transcript ID
[2 enabled][2 enabled]
Ensembl Gene ID
Ensembl Transcript ID
[2 enabled][2 enabled]
Ensembl Gene ID
Ensembl Transcript ID
[2 enabled][2 enabled]
Ensembl Gene ID
Ensembl Transcript ID
Reference ID
[3 enabled][3 enabled]
Protein
Ensembl Gene ID
Ensembl Transcript ID
[3 enabled][3 enabled]
Dataset
[None Selected]
_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users
_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users
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Re: [BioMart Users] Error while using the RefSeq_mRNA filter in biomart

Rhoda Kinsella
Hi Vincent and Syed
This is a known bug from this release and i'm afraid we will not be  
able to make the fix live until the next release (e65) due out in  
November. The reason for this is that we now have several live servers  
and it is non trivial to copy around the changes to all the servers  
(including the Ensembl mirrors) and reconfigure everything. I have  
fixed the issue on an internal test server and if you send me the list  
of RefSeq IDs then I will generate the result file for you. An  
alternative is to use the "limit to genes" filter for the RefSeq mRNAs  
and then pull out the results you require from the resulting entire  
set. Apologies for any inconvenience caused.
Regards
Rhoda

On 28 Sep 2011, at 12:51, Syed Haider wrote:

> Seem like the attribute corresponding filter "refseq_mrna" has got a  
> different internal name in the Ensembl gene v64 (Human)  
> configuration. that needs to be set to same name, and configurations  
> made available again. Rhoda would know the time line of this.
>
>
> Best,
> Syed
>
>
>
>
>
> ________________________________________
> From: [hidden email] [[hidden email]] On  
> Behalf Of Vincent Legagneux [[hidden email]]
> Sent: Wednesday, September 28, 2011 7:22 AM
> To: [hidden email]
> Subject: [BioMart Users] Error while using the RefSeq_mRNA filter in  
> biomart
>
> Hello,
>
> I was trying to recover Ensembl gene IDs from a list of RefSeq mRNA  
> IDs
> using the Biomart web interface (biomart.org). While retrieving the
> results, I got this error message:
>
> Serious Error: Error during query execution: Table
> 'ensembl_mart_64.ox_RefSeq_mRNA__dm' doesn't exist ERROR: caught
> BioMart::Exception::Database: Error during query execution: Table
> 'ensembl_mart_64.ox_RefSeq_mRNA__dm' doesn't exist
>
> A  similar message was returned after having submitted the same query
> through the Bioconductor biomaRt package:
>
> library("biomaRt")
> ensembl = useMart("ensembl")
> ensembl = useDataset("hsapiens_gene_ensembl",mart=ensembl)
> listFilters(ensembl)
> data_ensg1=getBM(attributes = c("ensembl_gene_id"), filters =
> "refseq_mrna", values = data[,4], mart = ensembl)
> Error in getBM(attributes = c("ensembl_gene_id"), filters =
> "refseq_mrna",  :
>   Query ERROR: caught BioMart::Exception::Database: Error during query
> execution: Table 'ensembl_mart_64.ox_RefSeq_mRNA__dm' doesn't exist
>
> Does anybody have any clues on the origin of this error ?
>
> Thanks a lot.
>
> All the best,
>
> vincent
>
> Below are summarized the Biomart settings I used in the web interface:
> Dataset
> Homo sapiens genes (GRCh37.p5)
> Homo sapiens genes (GRCh37.p5)
> Filters
> Refseq mRNA ID(s) [e.g. NM_001195597]: [ID-list specified]
> Attributes
> Ensembl Gene ID
> Gene Start (bp)
> Gene End (bp)
> Strand
> Chromosome Name
> Associated Gene Name
> Ensembl Gene ID
> Ensembl Transcript ID
> [2 enabled][2 enabled]
> Ensembl Gene ID
> Ensembl Transcript ID
> [2 enabled][2 enabled]
> Ensembl Gene ID
> Ensembl Transcript ID
> [2 enabled][2 enabled]
> Ensembl Gene ID
> Ensembl Transcript ID
> Reference ID
> [3 enabled][3 enabled]
> Protein
> Ensembl Gene ID
> Ensembl Transcript ID
> [3 enabled][3 enabled]
> Dataset
> [None Selected]
> _______________________________________________
> Users mailing list
> [hidden email]
> https://lists.biomart.org/mailman/listinfo/users

Rhoda Kinsella Ph.D.
Ensembl Bioinformatician,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton
Cambridge CB10 1SD,
UK.

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