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Question: Gviz failed to fetch ideogram information from UCSC
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gravatar for izzy.yichao.cai
5 months ago by
izzy.yichao.cai0 wrote:

Hi all,

I am trying to use Gviz to plot ideogram tracks. I was able to produce an ideogram in the past few weeks and it suddenly gets no reply from UCSC this week.

The code I used:

> IdeogramTrack(genome="hg19",chromosome="chr16",fontsize=30)
Error in function (type, msg, asError = TRUE)  : Empty reply from server
> traceback()
23: fun(structure(list(message = msg, call = sys.call()), class = c(typeName, 
        "GenericCurlError", "error", "condition")))
22: function (type, msg, asError = TRUE) 
    {
        if (!is.character(type)) {
            i = match(type, CURLcodeValues)
            typeName = if (is.na(i)) 
                character()
            else names(CURLcodeValues)[i]
        }
        typeName = gsub("^CURLE_", "", typeName)
        fun = (if (asError) 
            stop
        else warning)
        fun(structure(list(message = msg, call = sys.call()), class = c(typeName, 
            "GenericCurlError", "error", "condition")))
    }(52L, "Empty reply from server", TRUE)
21: .Call("R_post_form", curl, .opts, .params, TRUE, matchPostStyle(style), 
        PACKAGE = "RCurl")
20: .postForm(curl, .opts, .params, style)
19: postForm(url, .params = .form, .opts = list(..., useragent = "rtracklayer"))
18: httpPost(ucscURL(object, key), .form, ..., cookie = ucscCookie(object))
17: ucscPost(browserSession(query), "tables", c(ucscForm(query, tracks = tracks), 
        list(...)), .parse = .parse)
16: ucscTablePost(query, hgta_enteredUserRegionFile = upload, hgta_enteredUserRegions = "", 
        hgta_doSubmitUserRegions = "submit", hgsid = hgsid)
15: .uploadTableBrowserRanges(object, hgsid)
14: ucscExport(object)
13: .local(object, ...)
12: getTable(query)
11: getTable(query)
10: eval(expression, envir = callEnv)
9: eval(expression, envir = callEnv)
8: eval(expression, envir = callEnv)
7: .doCache(genomesToken, expression({
       if (!genome %in% as.character(genomes[, "db"])) stop("'", 
           genome, "' is not a valid UCSC genome.")
       sessionToken <- paste("session", genome, sep = "_")
       session <- .doCache(sessionToken, expression({
           myUcscUrl <- getOption("Gviz.ucscUrl")
           tmp <- if (is.null(myUcscUrl)) browserSession() else browserSession(url = myUcscUrl)
           genome(tmp) <- genome
           tmp
       }), env, cenv)
       query <- tryCatch(ucscTableQuery(session, "cytoBandIdeo"), 
           error = function(e) {
               warning("There doesn't seem to be any cytoband data available for genome '", 
                   genome, "' at UCSC or the service is temporarily down. Trying to fetch the chromosome length data.")
               tryCatch(ucscTableQuery(session, table = "chromInfo"), 
                   error = function(e) stop("There doesn't seem to be any chromosome length data available for genome '", 
                     genome, "' at UCSC or the service is temporarily down."))
           })
       out <- getTable(query)
       if (all(c("chrom", "size") %in% colnames(out))) {
           out <- data.frame(chrom = out$chrom, chromStart = 0, 
               chromEnd = out$size, name = "", gieStain = "gneg", 
               stringsAsFactors = F)
       }
       out
   }), env, cenv)
6: .cacheGenomes(genome = genome)
5: .local(.Object, ...)
4: initialize(value, ...)
3: initialize(value, ...)
2: new("IdeogramTrack", chromosome = chromosome, genome = genome, 
       name = name, bands = bands, ...)
1: IdeogramTrack(genome = "hg19", chromosome = "chr16", fontsize = 30)

 

 

I've found another thread stating the similar issue: Gviz error 'Expectation Failed'Gviz error 'Expectation Failed'and tried several commands on this:

1. readLines("http://genome.ucsc.edu") --- Returned me a HTML source code

2. IdeogramTrack(genome="hg19",chromosome="chr16",fontsize=30,Gviz.ucscUrl="http://genome-asia.ucsc.edu/cgi-bin") --- Give me the same error: Error in function (type, msg, asError = TRUE) : Empty reply from server. I also tried the euro server and get the same error. http:// or https:// doesn't help me get rid of the error

3.

library(rtracklayer)
session <- browserSession()
genome(session) <- "hg19"

--- No error.

4. Access the http://genome.ucsc.edu/cgi-bin through browser. --- Error 404: Page Not Found on Our Server

 

Does anyone have a clue on what happened?

Thank you so much!

Yichao

 

This is my sessioninfo:

R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.0
LAPACK: /usr/lib/lapack/liblapack.so.3.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_SG.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_SG.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_SG.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_SG.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
 [1] grid      parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] rtracklayer_1.36.3                      org.Hs.eg.db_3.4.1                      TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
 [4] GenomicFeatures_1.28.1                  AnnotationDbi_1.38.1                    Biobase_2.36.2                         
 [7] Gviz_1.20.0                             GenomicRanges_1.28.3                    GenomeInfoDb_1.12.1                    
[10] IRanges_2.10.2                          S4Vectors_0.14.3                        BiocGenerics_0.22.0                    
[13] optparse_1.3.2                          Sushi_1.14.0                            biomaRt_2.32.0                         
[16] zoo_1.8-0                               RColorBrewer_1.1-2                     

loaded via a namespace (and not attached):
 [1] httr_1.2.1                    AnnotationHub_2.8.1           splines_3.4.0                 assertthat_0.2.0             
 [5] shiny_1.0.3                   Formula_1.2-1                 interactiveDisplayBase_1.14.0 latticeExtra_0.6-28          
 [9] BSgenome_1.44.0               GenomeInfoDbData_0.99.0       Rsamtools_1.28.0              yaml_2.1.14                  
[13] RSQLite_1.1-2                 backports_1.1.0               lattice_0.20-35               biovizBase_1.24.0            
[17] digest_0.6.12                 XVector_0.16.0                checkmate_1.8.2               colorspace_1.3-2             
[21] httpuv_1.3.3                  htmltools_0.3.6               Matrix_1.2-10                 plyr_1.8.4                   
[25] XML_3.98-1.7                  zlibbioc_1.22.0               xtable_1.8-2                  scales_0.4.1                 
[29] getopt_1.20.0                 BiocParallel_1.10.1           htmlTable_1.9                 tibble_1.3.3                 
[33] AnnotationFilter_1.0.0        ggplot2_2.2.1                 SummarizedExperiment_1.6.3    nnet_7.3-12                  
[37] lazyeval_0.2.0                mime_0.5                      survival_2.41-3               magrittr_1.5                 
[41] memoise_1.1.0                 foreign_0.8-68                BiocInstaller_1.26.0          tools_3.4.0                  
[45] data.table_1.10.4             matrixStats_0.52.2            stringr_1.2.0                 munsell_0.4.3                
[49] cluster_2.0.6                 DelayedArray_0.2.5            ensembldb_2.0.3               Biostrings_2.44.1            
[53] compiler_3.4.0                rlang_0.1.1                   RCurl_1.95-4.8                dichromat_2.0-0              
[57] VariantAnnotation_1.22.1      htmlwidgets_0.8               bitops_1.0-6                  base64enc_0.1-3              
[61] gtable_0.2.0                  curl_2.6                      DBI_0.6-1                     R6_2.2.1                     
[65] GenomicAlignments_1.12.1      gridExtra_2.2.1               dplyr_0.5.0                   knitr_1.16                   
[69] Hmisc_4.0-3                   ProtGenerics_1.8.0            stringi_1.1.5                 Rcpp_0.12.11                 
[73] rpart_4.1-11                  acepack_1.4.1   
ADD COMMENTlink written 5 months ago by izzy.yichao.cai0
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