BiomaRt and phytozome: error in return results
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Entering edit mode
@lwillianpacheco-18611
Last seen 21 months ago
Brazil/Rio de Janeiro/UFRJ

Hi all

I am trying to use the BiomaRt package to retrieve information from Phytozome, but I am getting the following error:

The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1.

In the step: select()

I believe that this error is associated with long time connection to return the results, am I right? If yes, there is a way to fix it?

I think to clone the database on my PC, but I don't know if this is the best way.

Here is my code:

#BiocManager::install("biomaRt")
library("biomaRt")
mart <- useMart(dataset="phytozome", biomart='phytozome_mart', 
                host = "https://phytozome.jgi.doe.gov", port = 443, ensemblRedirect = F)
keytypes(mart)
columns(mart)
org_ids <- keys(mart,keytype="organism_id")

Step select()

Org<-select(mart, as.character(org_ids), columns = c("organism_id", "organism_name"), "organism_id")
Error in .processResults(postRes, mart = mart, sep = sep, fullXmlQuery = fullXmlQuery,  : 
The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1. 
Please report this on the support site at http://support.bioconductor.org

Session info

> sessionInfo()
R version 3.6.2 (2019-12-12)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 10 (buster)

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.3.5.so
locale:`
 [1] LC_CTYPE=pt_BR.UTF-8       LC_NUMERIC=C               LC_TIME=pt_BR.UTF-8       
 [4] LC_COLLATE=pt_BR.UTF-8     LC_MONETARY=pt_BR.UTF-8    LC_MESSAGES=pt_BR.UTF-8   
 [7] LC_PAPER=pt_BR.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=pt_BR.UTF-8 LC_IDENTIFICATION=C       
attached base packages:

[1] stats     graphics  grDevices utils     datasets  methods   base     
other attached packages:
[1] biomaRt_2.42.0
loaded via a namespace (and not attached):

 [1] Rcpp_1.0.3           compiler_3.6.2       pillar_1.4.3         dbplyr_1.4.2       
 [5] prettyunits_1.1.1    tools_3.6.2          progress_1.2.2       digest_0.6.25       
 [9] bit_1.1-15.2         RSQLite_2.2.0        memoise_1.1.0        BiocFileCache_1.10.2
[13] tibble_2.1.3         pkgconfig_2.0.3      rlang_0.4.4          DBI_1.1.0           
[17] rstudioapi_0.11      curl_4.3             parallel_3.6.2       xml2_1.2.2          
[21] stringr_1.4.0        httr_1.4.1           dplyr_0.8.4          rappdirs_0.3.1      
[25] S4Vectors_0.24.3     vctrs_0.2.3          askpass_1.1          IRanges_2.20.2      
[29] hms_0.5.3            stats4_3.6.2         bit64_0.9-7          tidyselect_1.0.0    
[33] glue_1.3.1           Biobase_2.46.0       R6_2.4.1             AnnotationDbi_1.48.0
[37] XML_3.99-0.3         purrr_0.3.3          blob_1.2.1           magrittr_1.5        
[41] BiocGenerics_0.32.0  assertthat_0.2.1     stringi_1.4.6        openssl_1.4.1       
[45] crayon_1.3.4
Biomart phytozome • 164 views
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Entering edit mode

~~Can you provide an example of the contents of org_ids? If it's really long then just the first few entries would be fine. It'll help with debugging this.~~

Oops, I see it's defined in the code now. I'm a bit confused as to what you're trying to do here. Do you want a table of all organisms with two columns: name and ID ?

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Yeah Mike

I wanted a table of name and ID to select Sorghum bicolor specie, and to get the ENTREZ IDs, but these IDs are not available to this genome.

Willian

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