[biomart-users] Fehler in value[[3L]](cond) :

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[biomart-users] Fehler in value[[3L]](cond) :

'Bernard Thienpont' via biomart-users
Dear all,

I try to get information out of the snp-mart.
But always when I try to do this I get the following error:
Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.

The code I use is:
source("http://bioconductor.org/biocLite.R")
#biocLite()
library(biomaRt)
#snpmart <- useMart("snp", "hsapiens_snp")
snp = useEnsembl(biomart="snp", dataset="hsapiens_snp", host = "www.ensembl.org")
#ensmart = useMart("ensembl", dataset="hsapiens_gene_ensembl")

#snp = useMart("ENSEMBL_MART_SNP",dataset="hsapiens_snp")

list1='1:69511:69511'
list1='1:888639:888639'
list1='1:1887019:1887019'

test <- getBM(attributes=c("refsnp_id","chr_name","chrom_strand", 'chrom_start'),
              filters ="chromosomal_region",
              values ="1:69511:69511,1:888639:888639,1:1887019:1887019",
              mart = snp)

For additional information, following my session info:
> sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.4 LTS

locale:
 [1] LC_CTYPE=de_DE.UTF-8       LC_NUMERIC=C               LC_TIME=de_DE.UTF-8        LC_COLLATE=de_DE.UTF-8   
 [5] LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=de_DE.UTF-8    LC_PAPER=de_DE.UTF-8       LC_NAME=C                
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C      

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base    

other attached packages:
[1] biomaRt_2.26.1       BiocInstaller_1.20.1

loaded via a namespace (and not attached):
 [1] IRanges_2.4.8        parallel_3.2.3       DBI_0.3.1            tools_3.2.3          RCurl_1.95-4.8       Biobase_2.30.0     
 [7] AnnotationDbi_1.32.3 RSQLite_1.0.0        S4Vectors_0.8.11     BiocGenerics_0.16.1  stats4_3.2.3         bitops_1.0-6       
[13] XML_3.98-1.4       

I also try to connect to different host, but allways the same.

Does sombody has an idea what i am duing wrong?
Best thanks in advanced.

Best
Björn

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Re: [biomart-users] Fehler in value[[3L]](cond) :

Thomas Maurel
Dear Björn,

Just to let you know that I am looking into this issue. Even if you are querying 3 small regions, there is quite a lot of data requested in the background which seems to timeout and return this error to you.
I will investigate and see if we can improve anything from our side. In the meantimes please feel free to use a different filter.

Apologies for any inconvenience caused.
Best regards,
Thomas
On 4 Mar 2016, at 08:43, 'Bjoern g' via biomart-users <[hidden email]> wrote:

Dear all,

I try to get information out of the snp-mart.
But always when I try to do this I get the following error:
Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.

The code I use is:
source("http://bioconductor.org/biocLite.R")
#biocLite()
library(biomaRt)
#snpmart <- useMart("snp", "hsapiens_snp")
snp = useEnsembl(biomart="snp", dataset="hsapiens_snp", host = "www.ensembl.org")
#ensmart = useMart("ensembl", dataset="hsapiens_gene_ensembl")

#snp = useMart("ENSEMBL_MART_SNP",dataset="hsapiens_snp")

list1='1:69511:69511'
list1='1:888639:888639'
list1='1:1887019:1887019'

test <- getBM(attributes=c("refsnp_id","chr_name","chrom_strand", 'chrom_start'),
              filters ="chromosomal_region",
              values ="1:69511:69511,1:888639:888639,1:1887019:1887019",
              mart = snp)

For additional information, following my session info:
> sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.4 LTS

locale:
 [1] LC_CTYPE=de_DE.UTF-8       LC_NUMERIC=C               LC_TIME=de_DE.UTF-8        LC_COLLATE=de_DE.UTF-8   
 [5] LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=de_DE.UTF-8    LC_PAPER=de_DE.UTF-8       LC_NAME=C                
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C      

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base    

other attached packages:
[1] biomaRt_2.26.1       BiocInstaller_1.20.1

loaded via a namespace (and not attached):
 [1] IRanges_2.4.8        parallel_3.2.3       DBI_0.3.1            tools_3.2.3          RCurl_1.95-4.8       Biobase_2.30.0     
 [7] AnnotationDbi_1.32.3 RSQLite_1.0.0        S4Vectors_0.8.11     BiocGenerics_0.16.1  stats4_3.2.3         bitops_1.0-6       
[13] XML_3.98-1.4       

I also try to connect to different host, but allways the same.

Does sombody has an idea what i am duing wrong?
Best thanks in advanced.

Best
Björn

--
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For more options, visit https://groups.google.com/d/optout.

--
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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Re: [biomart-users] Fehler in value[[3L]](cond) :

'Bernard Thienpont' via biomart-users
Dear Thomas,

thanks for your reply.
Here a short explanation what I want/have to do.

I get my data out of a vcf-file. From this a try to get information about the variations.
As I can see there is no other way to query the biomart, right?

Or can I split up my query somehow, for time improvements?

Best
Björn


On Tuesday, March 8, 2016 at 1:31:54 PM UTC+1, Thomas Maurel wrote:
Dear Björn,

Just to let you know that I am looking into this issue. Even if you are querying 3 small regions, there is quite a lot of data requested in the background which seems to timeout and return this error to you.
I will investigate and see if we can improve anything from our side. In the meantimes please feel free to use a different filter.

Apologies for any inconvenience caused.
Best regards,
Thomas
On 4 Mar 2016, at 08:43, 'Bjoern g' via biomart-users <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="tyV8mK_CJgAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">biomar...@googlegroups.com> wrote:

Dear all,

I try to get information out of the snp-mart.
But always when I try to do this I get the following error:
Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.

The code I use is:
source("<a href="http://bioconductor.org/biocLite.R" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fbioconductor.org%2FbiocLite.R\46sa\75D\46sntz\0751\46usg\75AFQjCNEQ5YwoteD6c8DYB_lNDMnHysiRPg&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fbioconductor.org%2FbiocLite.R\46sa\75D\46sntz\0751\46usg\75AFQjCNEQ5YwoteD6c8DYB_lNDMnHysiRPg&#39;;return true;">http://bioconductor.org/biocLite.R")
#biocLite()
library(biomaRt)
#snpmart <- useMart("snp", "hsapiens_snp")
snp = useEnsembl(biomart="snp", dataset="hsapiens_snp", host = "<a href="http://www.ensembl.org" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fwww.ensembl.org\46sa\75D\46sntz\0751\46usg\75AFQjCNEhRkMjGzJ0Ux5vBUiT-NWHb0ycIg&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fwww.ensembl.org\46sa\75D\46sntz\0751\46usg\75AFQjCNEhRkMjGzJ0Ux5vBUiT-NWHb0ycIg&#39;;return true;">www.ensembl.org")
#ensmart = useMart("ensembl", dataset="hsapiens_gene_ensembl")

#snp = useMart("ENSEMBL_MART_SNP",dataset="hsapiens_snp")

list1='1:69511:69511'
list1='1:888639:888639'
list1='1:1887019:1887019'

test <- getBM(attributes=c("refsnp_id","chr_name","chrom_strand", 'chrom_start'),
              filters ="chromosomal_region",
              values ="1:69511:69511,1:888639:888639,1:1887019:1887019",
              mart = snp)

For additional information, following my session info:
> sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.4 LTS

locale:
 [1] LC_CTYPE=de_DE.UTF-8       LC_NUMERIC=C               LC_TIME=de_DE.UTF-8        LC_COLLATE=de_DE.UTF-8   
 [5] LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=de_DE.UTF-8    LC_PAPER=de_DE.UTF-8       LC_NAME=C                
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C      

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base    

other attached packages:
[1] biomaRt_2.26.1       BiocInstaller_1.20.1

loaded via a namespace (and not attached):
 [1] IRanges_2.4.8        parallel_3.2.3       DBI_0.3.1            tools_3.2.3          RCurl_1.95-4.8       Biobase_2.30.0     
 [7] AnnotationDbi_1.32.3 RSQLite_1.0.0        S4Vectors_0.8.11     BiocGenerics_0.16.1  stats4_3.2.3         bitops_1.0-6       
[13] XML_3.98-1.4       

I also try to connect to different host, but allways the same.

Does sombody has an idea what i am duing wrong?
Best thanks in advanced.

Best
Björn

--
You received this message because you are subscribed to the Google Groups "biomart-users" group.
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Visit this group at <a href="https://groups.google.com/group/biomart-users" target="_blank" rel="nofollow" onmousedown="this.href=&#39;https://groups.google.com/group/biomart-users&#39;;return true;" onclick="this.href=&#39;https://groups.google.com/group/biomart-users&#39;;return true;">https://groups.google.com/group/biomart-users.
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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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Re: [biomart-users] Fehler in value[[3L]](cond) :

Thomas Maurel
Dear Björn,

If you have variant IDs in your vcf file (e.g: rs196358560), you can use the “Filter by Variant Name (e.g. rs123, CM000001)” filter in the “GENERAL VARIANT FILTERS” section.
You can also split up your query in smaller chunks and request mart to send you the result file by email (mart will run the query on our server and send you an email with the result file attached), please see more information on the following page: http://www.ensembl.org/info/data/biomart/how_to_use_biomart.html#resultselection.
Alternatively, you can try our VEP tool (Variant effect predictor) by uploading your VCF file on the following page: http://www.ensembl.org/common/Tools/VEP?db=core.
You can find more information regarding the VEP on the following page: http://www.ensembl.org/info/docs/tools/vep/index.html

Hope this helps,
Best Regards,
Thomas
On 8 Mar 2016, at 13:38, Bjoern g <[hidden email]> wrote:

Dear Thomas,

thanks for your reply.
Here a short explanation what I want/have to do.

I get my data out of a vcf-file. From this a try to get information about the variations.
As I can see there is no other way to query the biomart, right?

Or can I split up my query somehow, for time improvements?

Best
Björn


On Tuesday, March 8, 2016 at 1:31:54 PM UTC+1, Thomas Maurel wrote:
Dear Björn,

Just to let you know that I am looking into this issue. Even if you are querying 3 small regions, there is quite a lot of data requested in the background which seems to timeout and return this error to you.
I will investigate and see if we can improve anything from our side. In the meantimes please feel free to use a different filter.

Apologies for any inconvenience caused.
Best regards,
Thomas
On 4 Mar 2016, at 08:43, 'Bjoern g' via biomart-users <[hidden email]> wrote:

Dear all,

I try to get information out of the snp-mart.
But always when I try to do this I get the following error:
Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.

The code I use is:
source("http://bioconductor.org/biocLite.R")
#biocLite()
library(biomaRt)
#snpmart <- useMart("snp", "hsapiens_snp")
snp = useEnsembl(biomart="snp", dataset="hsapiens_snp", host = "www.ensembl.org")
#ensmart = useMart("ensembl", dataset="hsapiens_gene_ensembl")

#snp = useMart("ENSEMBL_MART_SNP",dataset="hsapiens_snp")

list1='1:69511:69511'
list1='1:888639:888639'
list1='1:1887019:1887019'

test <- getBM(attributes=c("refsnp_id","chr_name","chrom_strand", 'chrom_start'), 
              filters ="chromosomal_region", 
              values ="1:69511:69511,1:888639:888639,1:1887019:1887019", 
              mart = snp)

For additional information, following my session info:
> sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.4 LTS

locale:
 [1] LC_CTYPE=de_DE.UTF-8       LC_NUMERIC=C               LC_TIME=de_DE.UTF-8        LC_COLLATE=de_DE.UTF-8    
 [5] LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=de_DE.UTF-8    LC_PAPER=de_DE.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] biomaRt_2.26.1       BiocInstaller_1.20.1

loaded via a namespace (and not attached):
 [1] IRanges_2.4.8        parallel_3.2.3       DBI_0.3.1            tools_3.2.3          RCurl_1.95-4.8       Biobase_2.30.0      
 [7] AnnotationDbi_1.32.3 RSQLite_1.0.0        S4Vectors_0.8.11     BiocGenerics_0.16.1  stats4_3.2.3         bitops_1.0-6        
[13] XML_3.98-1.4        

I also try to connect to different host, but allways the same.

Does sombody has an idea what i am duing wrong?
Best thanks in advanced.

Best
Björn

-- 
You received this message because you are subscribed to the Google Groups "biomart-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
Visit this group at https://groups.google.com/group/biomart-users.
For more options, visit https://groups.google.com/d/optout.

--
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


--
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

--
You received this message because you are subscribed to the Google Groups "biomart-users" group.
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Re: [biomart-users] Fehler in value[[3L]](cond) :

Thomas Maurel
Dear Björn,

Just to let you know that we have identified a problem with the region filter performance. We have incorporated a fix for it in the latest release of Ensembl 85 (July 19th 2016) on www.ensembl.org and our mirrors which should help to resolve the problems you are experiencing. 
Furthermore, we have identified how the filter performance can be improved further and plan to incorporate more improvements in future releases.

Thank you for your patience.
Regards,
Thomas
On 8 Mar 2016, at 14:12, Thomas Maurel <[hidden email]> wrote:

Dear Björn,

If you have variant IDs in your vcf file (e.g: rs196358560), you can use the “Filter by Variant Name (e.g. rs123, CM000001)” filter in the “GENERAL VARIANT FILTERS” section.
You can also split up your query in smaller chunks and request mart to send you the result file by email (mart will run the query on our server and send you an email with the result file attached), please see more information on the following page: http://www.ensembl.org/info/data/biomart/how_to_use_biomart.html#resultselection.
Alternatively, you can try our VEP tool (Variant effect predictor) by uploading your VCF file on the following page: http://www.ensembl.org/common/Tools/VEP?db=core.
You can find more information regarding the VEP on the following page: http://www.ensembl.org/info/docs/tools/vep/index.html

Hope this helps,
Best Regards,
Thomas
On 8 Mar 2016, at 13:38, Bjoern g <[hidden email]> wrote:

Dear Thomas,

thanks for your reply.
Here a short explanation what I want/have to do.

I get my data out of a vcf-file. From this a try to get information about the variations.
As I can see there is no other way to query the biomart, right?

Or can I split up my query somehow, for time improvements?

Best
Björn


On Tuesday, March 8, 2016 at 1:31:54 PM UTC+1, Thomas Maurel wrote:
Dear Björn,

Just to let you know that I am looking into this issue. Even if you are querying 3 small regions, there is quite a lot of data requested in the background which seems to timeout and return this error to you.
I will investigate and see if we can improve anything from our side. In the meantimes please feel free to use a different filter.

Apologies for any inconvenience caused.
Best regards,
Thomas
On 4 Mar 2016, at 08:43, 'Bjoern g' via biomart-users <biomar...@googlegroups.com> wrote:

Dear all,

I try to get information out of the snp-mart.
But always when I try to do this I get the following error:
Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.

The code I use is:
source("http://bioconductor.org/biocLite.R")
#biocLite()
library(biomaRt)
#snpmart <- useMart("snp", "hsapiens_snp")
snp = useEnsembl(biomart="snp", dataset="hsapiens_snp", host = "www.ensembl.org")
#ensmart = useMart("ensembl", dataset="hsapiens_gene_ensembl")

#snp = useMart("ENSEMBL_MART_SNP",dataset="hsapiens_snp")

list1='1:69511:69511'
list1='1:888639:888639'
list1='1:1887019:1887019'

test <- getBM(attributes=c("refsnp_id","chr_name","chrom_strand", 'chrom_start'), 
              filters ="chromosomal_region", 
              values ="1:69511:69511,1:888639:888639,1:1887019:1887019", 
              mart = snp)

For additional information, following my session info:
> sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.4 LTS

locale:
 [1] LC_CTYPE=de_DE.UTF-8       LC_NUMERIC=C               LC_TIME=de_DE.UTF-8        LC_COLLATE=de_DE.UTF-8    
 [5] LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=de_DE.UTF-8    LC_PAPER=de_DE.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] biomaRt_2.26.1       BiocInstaller_1.20.1

loaded via a namespace (and not attached):
 [1] IRanges_2.4.8        parallel_3.2.3       DBI_0.3.1            tools_3.2.3          RCurl_1.95-4.8       Biobase_2.30.0      
 [7] AnnotationDbi_1.32.3 RSQLite_1.0.0        S4Vectors_0.8.11     BiocGenerics_0.16.1  stats4_3.2.3         bitops_1.0-6        
[13] XML_3.98-1.4        

I also try to connect to different host, but allways the same.

Does sombody has an idea what i am duing wrong?
Best thanks in advanced.

Best
Björn

-- 
You received this message because you are subscribed to the Google Groups "biomart-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to biomart-user...@googlegroups.com.
Visit this group at https://groups.google.com/group/biomart-users.
For more options, visit https://groups.google.com/d/optout.

--
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


--
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


--
You received this message because you are subscribed to the Google Groups "biomart-users" group.
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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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