Again, query error when trying to retrieve attributes from Phytozome via BiomaRt
1
1
Entering edit mode
s.k.tepler ▴ 10
@15b4cabc
Last seen 18 hours ago
United States

Hi there. I'm so sorry to bring up an old error, but for some reason, I just can't get this query to work! I've tried substituting in different Zea mays gene names in "values", trying one attribute at a time in "attributes", and various different "filters". My gene names come from a STAR alignment to the Zm-B73 reference genome.

mart <- useMart(biomart = "phytozome_mart", 
                dataset = "phytozome", 
                host = "https://phytozome.jgi.doe.gov")

b <- getBM(
  attributes=c('gene_name1','organism_name','gene_description', 'peptide_name','kog_desc','go_desc'),
 filters="gene_name_filter",
 values="Zm00001eb069270",
 mart=mart)

Error in .processResults(postRes, mart = mart, hostURLsep = sep, fullXmlQuery = fullXmlQuery,  : 
  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 on the support site at http://support.bioconductor.org


sessionInfo( )
R version 4.1.2 (2021-11-01)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 11.4

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] biomaRt_2.50.1      BiocManager_1.30.16

loaded via a namespace (and not attached):
 [1] KEGGREST_1.34.0        progress_1.2.2         tidyselect_1.1.1      
 [4] purrr_0.3.4            vctrs_0.3.8            generics_0.1.1        
 [7] stats4_4.1.2           BiocFileCache_2.2.0    utf8_1.2.2            
[10] blob_1.2.2             XML_3.99-0.8           rlang_0.4.12          
[13] pillar_1.6.4           withr_2.4.3            glue_1.6.0            
[16] DBI_1.1.2              rappdirs_0.3.3         BiocGenerics_0.40.0   
[19] bit64_4.0.5            dbplyr_2.1.1           lambda.r_1.2.4        
[22] GenomeInfoDbData_1.2.7 lifecycle_1.0.1        stringr_1.4.0         
[25] zlibbioc_1.40.0        Biostrings_2.62.0      futile.logger_1.4.3   
[28] memoise_2.0.1          Biobase_2.54.0         IRanges_2.28.0        
[31] fastmap_1.1.0          GenomeInfoDb_1.30.0    curl_4.3.2            
[34] AnnotationDbi_1.56.2   fansi_1.0.0            Rcpp_1.0.7            
[37] formatR_1.11           filelock_1.0.2         cachem_1.0.6          
[40] S4Vectors_0.32.3       XVector_0.34.0         bit_4.0.4             
[43] hms_1.1.1              png_0.1-7              digest_0.6.29         
[46] stringi_1.7.6          dplyr_1.0.7            tools_4.1.2           
[49] bitops_1.0-7           magrittr_2.0.1         RCurl_1.98-1.5        
[52] RSQLite_2.2.9          tibble_3.1.6           futile.options_1.0.1  
[55] crayon_1.4.2           pkgconfig_2.0.3        ellipsis_0.3.2        
[58] xml2_1.3.3             prettyunits_1.1.1      assertthat_0.2.1      
[61] httr_1.4.2             R6_2.5.1               compiler_4.1.2
Zea_mays Attributes biomaRt Phytozome • 72 views
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1
Entering edit mode
Mike Smith ★ 5.3k
@mike-smith
Last seen 24 minutes ago
EMBL Heidelberg / de.NBI

Version 12 of phytozome was retired in August 2021. The old website still exists, but biomaRt can't query it and you get back a "page not found" which is what leads to this error message.

You need to use the new URL for version 13, which can be done with host = "https://phytozome-next.jgi.doe.gov".

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0
Entering edit mode

Thanks! I knew it was something like that.

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