[Bioc-devel] UCSC Table Query Failing For Large Ranges

Dario Strbenac dstr7320 at uni.sydney.edu.au
Thu Sep 5 04:00:17 CEST 2013


I get an error :

> session <- browserSession("UCSC")
> consQuery <- ucscTableQuery(session, "Conservation", GRangesForUCSCGenome("hg9", "chr1", IRanges(100000000, 101000000)), "phyloP46wayPlacental")
> consQuery
Get table 'phyloP46wayPlacental' from track 'Conservation' within hg19:chr1:100000000-101000000
> conservation <- track(consQuery)
Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") : 
  solving row 100001: range cannot be determined from the supplied arguments (too many NAs)

> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-pc-linux-gnu (64-bit)

 [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8    
 [7] LC_PAPER=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            

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

other attached packages:
[1] rtracklayer_1.20.4   GenomicRanges_1.12.5 IRanges_1.18.3      
[4] BiocGenerics_0.6.0  

loaded via a namespace (and not attached):
[1] Biostrings_2.28.0 bitops_1.0-6      BSgenome_1.28.0   RCurl_1.95-4.1   
[5] Rsamtools_1.12.4  stats4_3.0.1      tools_3.0.1       XML_3.98-1.1     
[9] zlibbioc_1.6.0   

This could be because of a limit on the size of the results from the UCSC server. It works with a smaller width query 1000 bases wide. It could fail with a more informative error, and provide a warning about this in the help file of ucscTableQuery. I wish we could convince UCSC to remove these restrictions from a time when computing power was much less.

Dario Strbenac
PhD Student
University of Sydney
Camperdown NSW 2050

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