seqlevelsStyle() not working
2
0
Entering edit mode
Kai Hu ▴ 70
@kai
Last seen 5 weeks ago
Worcester

I got the following error when invoking seqlevelsStyle():

 seqlevelsStyle(annoData) <- "UCSC"

Error in download.file(url, destfile, quiet = TRUE) : 
  cannot open URL 'https://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz'

Seems that the URL is no longer valid, and has been replaced with: https://hgdownload2.cse.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz

The following link seems to work as well: https://hgdownload2.soe.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz

Any input on how to solve this and which link should be used for downloading?

ensembldb genomei GenomeInfoDb • 493 views
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2
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@kentriemondy-14219
Last seen 8 hours ago
Denver, University of Colorado Anschutz…

An update to the GenomeDbInfo package was pushed to Bioconductor 3.18 recently that should fix this and will be available in a day or two. In the meantime you can change the domain used by seqlevelsStyle() by setting this option in your session:

options(UCSC.goldenPath.url="https://hgdownload.soe.ucsc.edu/goldenPath")
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0
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Ty, this works for me!

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@james-w-macdonald-5106
Last seen 8 hours ago
United States

Do you need to update your versions of R/Bioconductor?

> gr <- GRanges("1:100-1000")
> seqlevelsStyle(gr) <- "UCSC"
> gr
GRanges object with 1 range and 0 metadata columns:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  [1]     chr1  100-1000      *
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths
> sessionInfo()
R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 22621)

Matrix products: default


locale:
[1] LC_COLLATE=English_United States.utf8 
[2] LC_CTYPE=English_United States.utf8   
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

time zone: America/New_York
tzcode source: internal

attached base packages:
[1] stats4    stats     graphics 
[4] grDevices utils     datasets 
[7] methods   base     

other attached packages:
[1] GenomicFeatures_1.54.1
[2] AnnotationDbi_1.64.1  
[3] Biobase_2.62.0        
[4] GenomicRanges_1.54.1  
[5] GenomeInfoDb_1.38.5   
[6] IRanges_2.36.0        
[7] S4Vectors_0.40.2      
[8] BiocGenerics_0.48.1   

loaded via a namespace (and not attached):
 [1] KEGGREST_1.42.0            
 [2] SummarizedExperiment_1.32.0
 [3] rjson_0.2.21               
 [4] lattice_0.22-5             
 [5] vctrs_0.6.5                
 [6] tools_4.3.1                
 [7] bitops_1.0-7               
 [8] generics_0.1.3             
 [9] curl_5.2.0                 
[10] parallel_4.3.1             
[11] tibble_3.2.1               
[12] fansi_1.0.6                
[13] RSQLite_2.3.5              
[14] blob_1.2.4                 
[15] pkgconfig_2.0.3            
[16] Matrix_1.6-5               
[17] dbplyr_2.4.0               
[18] lifecycle_1.0.4            
[19] GenomeInfoDbData_1.2.11    
[20] compiler_4.3.1             
[21] stringr_1.5.1              
[22] Rsamtools_2.18.0           
[23] Biostrings_2.70.2          
[24] progress_1.2.3             
[25] codetools_0.2-19           
[26] RCurl_1.98-1.14            
[27] yaml_2.3.8                 
[28] pillar_1.9.0               
[29] crayon_1.5.2               
[30] BiocParallel_1.36.0        
[31] DelayedArray_0.28.0        
[32] cachem_1.0.8               
[33] abind_1.4-5                
[34] tidyselect_1.2.0           
[35] digest_0.6.34              
[36] stringi_1.8.3              
[37] dplyr_1.1.4                
[38] restfulr_0.0.15            
[39] grid_4.3.1                 
[40] biomaRt_2.58.1             
[41] fastmap_1.1.1              
[42] SparseArray_1.2.3          
[43] cli_3.6.2                  
[44] magrittr_2.0.3             
[45] S4Arrays_1.2.0             
[46] XML_3.99-0.16.1            
[47] utf8_1.2.4                 
[48] prettyunits_1.2.0          
[49] filelock_1.0.3             
[50] rappdirs_0.3.3             
[51] bit64_4.0.5                
[52] XVector_0.42.0             
[53] httr_1.4.7                 
[54] matrixStats_1.2.0          
[55] bit_4.0.5                  
[56] png_0.1-8                  
[57] hms_1.1.3                  
[58] memoise_2.0.1              
[59] BiocIO_1.12.0              
[60] BiocFileCache_2.10.1       
[61] rtracklayer_1.62.0         
[62] rlang_1.1.3                
[63] glue_1.7.0                 
[64] DBI_1.2.1                  
[65] xml2_1.3.6                 
[66] R6_2.5.1                   
[67] MatrixGenerics_1.14.0      
[68] GenomicAlignments_1.38.2   
[69] zlibbioc_1.48.0            
>

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