[ensembl-dev] Problems with biomaRt

[Anne Lyle]

Hi again Türküler

Just to help me debug things a bit more, could you let me know when you ran your script? I can then check if that time coincides with any known issues at our end.

Thanks

Anne


> On 19 Mar 2020, at 22:42, Türküler Özgümüş <turkulerc at gmail.com> wrote:
> 
> Hi,
> 
> I had a problem with the below code. It is not about the code itself since the first time I ran it I got the results. But then because of a downstream error, unrelated to this one, I had to run it again. I ran it several times and every time there were different error messages until at the end it ran as expected. I got my results but I don't understand the problem here. So, I am reporting :) 
> 
> Best regards,
> Turkuler
> 
> Code:
> library(biomaRt)
> mart <- useEnsembl(biomart = "ENSEMBL_MART_ENSEMBL", version=99, dataset = "hsapiens_gene_ensembl")
> tx2gene <- getBM(attributes = c("ensembl_transcript_id", "transcript_version", "ensembl_gene_id", "external_gene_name","entrezgene_id"), mart = mart)
> 
> Message #1
> Error in listMarts(host = host, path = path, port = port, includeHosts = TRUE,  : 
>   Unexpected format to the list of available marts.
> Please check the following URL manually, and try ?listMarts for advice.
> http://dec2019.archive.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt <http://dec2019.archive.ensembl.org/biomart/martservice?type=registry&requestid=biomaRt>
> Calls: useEnsembl -> useMart -> listMarts
> Execution halted
> 
> Message #2 (Archive version changes but error message stays the same here)
> Error in listMarts(host = host, path = path, port = port, includeHosts = TRUE,  : 
>   Unexpected format to the list of available marts.
> Please check the following URL manually, and try ?listMarts for advice.
> http://jan2020.archive.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt <http://jan2020.archive.ensembl.org/biomart/martservice?type=registry&requestid=biomaRt>
> Calls: useEnsembl -> useMart -> listMarts
> Execution halted
> 
> Message #3
> Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  : 
>   line 1 did not have 3 elements
> Calls: getBM -> read.table -> scan
> Execution halted
> 
> Message #4
> Error in useMart(biomart = biomart, dataset = dataset, host = host, verbose = verbose) : 
>   Incorrect BioMart name, use the listMarts function to see which BioMart databases are available
> Calls: useEnsembl -> useMart
> Execution halted
> 
> Message #5 (In this case it continues to the following lines without any problem)
> Note: requested host was redirected from
> http://jan2020.archive.ensembl.org <http://jan2020.archive.ensembl.org/> to http://www.ensembl.org:80/biomart/martservice <http://www.ensembl.org/biomart/martservice>
> This often occurs when connecting to the archive URL for the current Ensembl release
> You can check the current version number using listEnsemblArchives()
> 
> sessionInfo()
> R version 3.5.2 (2018-12-20)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Red Hat Enterprise Linux
> 
> Matrix products: default
> BLAS: /gpfs/gpfs0/RHEL7-Tools/Software/R/3.5.2/lib64/R/lib/libRblas.so
> LAPACK: /gpfs/gpfs0/RHEL7-Tools/Software/R/3.5.2/lib64/R/lib/libRlapack.so
> 
> locale:
>  [1] LC_CTYPE=C                 LC_NUMERIC=C              
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
> [11] 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_2.38.0  forcats_0.4.0   stringr_1.4.0   dplyr_0.8.3    
>  [5] purrr_0.3.2     readr_1.3.1     tidyr_0.8.3     tibble_2.1.3   
>  [9] ggplot2_3.2.0   tidyverse_1.2.1
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