biomaRt error while querying homo sapien structural variants
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iyerl • 0
@iyerl-11626
Last seen 8.2 years ago
enotype_or_Disease   1   R
Error in getBM(attributessnp[, 1], filters = c("chr_name", "start", "end"),  : 
  The query to the BioMart webservice returned an invalid result: the number of columns in the result table does not equal the number of attributes in the query. Please report this to the mailing list.

 

> sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server release 6.7 (Santiago)

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

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

other attached packages:
[1] biomaRt_2.26.1 reshape_0.8.5  ggplot2_2.1.0 

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.4          IRanges_2.4.8        XML_3.98-1.4         digest_0.6.9         bitops_1.0-6         grid_3.2.3           plyr_1.8.3           DBI_0.3.1           
 [9] gtable_0.2.0         stats4_3.2.3         RSQLite_1.0.0        scales_0.4.0         S4Vectors_0.8.11     tools_3.2.3          Biobase_2.30.0       munsell_0.4.3       
[17] RCurl_1.95-4.8       parallel_3.2.3       yaml_2.1.13          BiocGenerics_0.16.1  AnnotationDbi_1.32.3 colorspace_1.2-6     knitr_1.12.3        
 
 
biomaRt • 889 views
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> installed.packages ()["biomaRt",]
                           Package                            LibPath                            Version                           Priority 
                         "biomaRt"             "/usr/lib64/R/library"                           "2.26.1"                                 NA 
                           Depends                            Imports                          LinkingTo                           Suggests 
                         "methods" "utils, XML, RCurl, AnnotationDbi"                                 NA                         "annotate" 
                          Enhances                            License                    License_is_FOSS              License_restricts_use 
                                NA                     "Artistic-2.0"                                 NA                                 NA 
                           OS_type                             MD5sum                   NeedsCompilation                              Built 
                                NA                                 NA                               "no"                            "3.2.3" 

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Thomas Maurel ▴ 800
@thomas-maurel-5295
Last seen 22 months ago
United Kingdom

I am afraid that we have a bug affecting the multiple datasets selection in the release 86 gene mart. This is causing the BiomaRt getLDS function to fail over.

We have a working fix that we will push live early next week, I will let you know as soon as the release 86 gene mart is working again.

In the meantime, please feel free to use our previous release e!85 marts:

human <- useMart("ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl", host = "e85.ensembl.org")

Apologies for any inconvenience caused,
Best Regards,
Thomas

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Thomas Maurel ▴ 800
@thomas-maurel-5295
Last seen 22 months ago
United Kingdom

Dear all,

Just to let you know that we have now pushed a fix to our main website www.ensembl.org, you can access it by running:

human <- useMart("ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl", host = "www.ensembl.org")
or
human = useMart("ensembl", dataset = "hsapiens_gene_ensembl") 

We will fix the US West, US East and Asian mirrors next week.

Thank you for your patience.
Best Regards,
Thomas

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Thomas Maurel ▴ 800
@thomas-maurel-5295
Last seen 22 months ago
United Kingdom

Dear all,

Just to let you know that the US West, US East and Asian mirrors have now been fixed too.

Thank you for your patience.
Best Regards,
Thomas

 

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