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Question: possible Rtracklayer issue: TxDb errors in GenomicFeatures package-- cannot load TxDb with standard params from UCSC (issue began last night)
1
gravatar for james.dalgleish
6 days ago by
james.dalgleish10 wrote:

I've been running code that used this for a long time and it just started breaking last night. Another colleague also is having issues on version 31 of GenomicFeatures.

> hg19.refseq.db<-GenomicFeatures::makeTxDbFromUCSC(genome="hg19", table="refGene")
Error in names(trackIds) <- sub("^ ", "", sapply(nodes, xmlValue)) : 
  'names' attribute [211] must be the same length as the vector [209]

> biomarttxdb<-GenomicFeatures::makeTxDbFromBiomart()
Download and preprocess the 'transcripts' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... FAILED! (=> skipped)
Download and preprocess the 'splicings' data frame ... OK
Download and preprocess the 'genes' data frame ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Warning messages:
1: In download.file(url, destfile, quiet = TRUE) :
  InternetOpenUrl failed: 'The login request was denied
'
2: In .warning_on_BioMart_data_anomaly(bm_result, idx, id_prefix, msg) :
  BioMart data anomaly: in the following transcripts, 
  the CDS length inferred from the CDS/UTR genomic 
  coordinates doesn't match the "cds_length" attribute.
  1. Transcript ENST00000595423:
       strand rank exon_chrom_start exon_chrom_end ensembl_exon_id genomic_coding_start genomic_coding_end 5_utr_start 5_utr_end
     1      1    1         18637057       18637137 ENSE00003008180             18637057           18637137          NA        NA
     2      1    2         18664261       18664443 ENSE00003555092             18664261           18664443          NA        NA
       3_utr_start 3_utr_end cds_start cds_end cds_length
     1          NA        NA         1      81        554
     2          NA        NA        82     264        554
3: In .makeTxDb_normarg_chrominfo(chrominfo, transcripts$tx_chrom,  :
  chromosome lengths and circularity flags are not available for this TxDb object

 

session info:

> sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

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

other attached packages:
 [1] rtracklayer_1.38.1         biomaRt_2.34.0             GenomicFeatures_1.30.0     AnnotationDbi_1.40.0      
 [5] data.table_1.10.4-3        Gviz_1.22.0                GenomicInteractions_1.12.0 InteractionSet_1.6.0      
 [9] SummarizedExperiment_1.8.0 DelayedArray_0.4.1         matrixStats_0.52.2         Biobase_2.38.0            
[13] GenomicRanges_1.30.0       GenomeInfoDb_1.14.0        IRanges_2.12.0             S4Vectors_0.16.0          
[17] BiocGenerics_0.24.0       

loaded via a namespace (and not attached):
 [1] ProtGenerics_1.10.0           bitops_1.0-6                  bit64_0.9-7                   RColorBrewer_1.1-2           
 [5] progress_1.1.2                httr_1.3.1                    tools_3.4.3                   backports_1.1.1              
 [9] R6_2.2.2                      rpart_4.1-11                  Hmisc_4.0-3                   DBI_0.7                      
[13] lazyeval_0.2.1                colorspace_1.3-2              nnet_7.3-12                   gridExtra_2.3                
[17] prettyunits_1.0.2             RMySQL_0.10.13                curl_3.0                      bit_1.1-12                   
[21] compiler_3.4.3                htmlTable_1.11.0              scales_0.5.0                  checkmate_1.8.5              
[25] stringr_1.2.0                 digest_0.6.12                 Rsamtools_1.30.0              foreign_0.8-69               
[29] XVector_0.18.0                base64enc_0.1-3               dichromat_2.0-0               pkgconfig_2.0.1              
[33] htmltools_0.3.6               ensembldb_2.2.0               BSgenome_1.46.0               htmlwidgets_0.9              
[37] rlang_0.1.4                   rstudioapi_0.7                RSQLite_2.0                   BiocInstaller_1.28.0         
[41] shiny_1.0.5                   bindr_0.1                     BiocParallel_1.12.0           acepack_1.4.1                
[45] dplyr_0.7.4                   VariantAnnotation_1.24.2      RCurl_1.95-4.8                magrittr_1.5                 
[49] GenomeInfoDbData_0.99.1       Formula_1.2-2                 Matrix_1.2-12                 Rcpp_0.12.14                 
[53] munsell_0.4.3                 stringi_1.1.6                 yaml_2.1.15                   zlibbioc_1.24.0              
[57] plyr_1.8.4                    AnnotationHub_2.10.1          blob_1.1.0                    lattice_0.20-35              
[61] Biostrings_2.46.0             splines_3.4.3                 knitr_1.17                    igraph_1.1.2                 
[65] XML_3.98-1.9                  glue_1.2.0                    biovizBase_1.26.0             latticeExtra_0.6-28          
[69] httpuv_1.3.5                  gtable_0.2.0                  purrr_0.2.4                   tidyr_0.7.2                  
[73] assertthat_0.2.0              ggplot2_2.2.1                 mime_0.5                      xtable_1.8-2                 
[77] AnnotationFilter_1.2.0        survival_2.41-3               tibble_1.3.4                  GenomicAlignments_1.14.1     
[81] memoise_1.1.0                 bindrcpp_0.2                  cluster_2.0.6                 interactiveDisplayBase_1.16.0

ADD COMMENTlink modified 1 day ago by Michael Lawrence9.8k • written 6 days ago by james.dalgleish10
0
gravatar for james.dalgleish
5 days ago by
james.dalgleish10 wrote:

It turns out it's an rtracklayer bug. I received the following response on the GenomicFeatures github site:

Hi @jamesdalg,

Thanks for the report. The error is actually happening in the rtracklayer package. It's easy to reproduce with:

library(rtracklayer)
session <- browserSession()
genome(session) <- "hg38"
track_names <- trackNames(session)
genome(session) <- "hg19"
track_names <- trackNames(session)
# Error in names(trackIds) <- sub("^ ", "", sapply(nodes, xmlValue)) : 
#   'names' attribute [210] must be the same length as the vector [208]

Seems like something has changed on the UCSC side that breaks trackNames() on hg19. Would you mind reporting this issue on the Bioconductor support site (https://support.bioconductor.org/) or here https://github.com/lawremi/rtracklayer ?

Thanks,
H.

ADD COMMENTlink written 5 days ago by james.dalgleish10
0
gravatar for Michael Lawrence
1 day ago by
United States
Michael Lawrence9.8k wrote:

Should be fixed in 1.38.2, already available.

ADD COMMENTlink written 1 day ago by Michael Lawrence9.8k
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