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Question: makeTxDbFromUCSC: error in Make the TxDb object
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gravatar for DMA1
12 days ago by
DMA10
DMA10 wrote:

Hi GenomicFeatures support,

After I ran

​txdb=makeTxDbFromUCSC(genome="hg19",tablename="refGene")

I got this error which was never happened before. I checked that my input files' chromosomes were from chr1 to chrY, no chr*random included. I ran the same scripts about one month ago and no error happened. Does anyone have any clues ? Thank you very much for your help !

Download the refGene table ... OK
Download the hgFixed.refLink table ... OK
Extract the 'transcripts' data frame ... OK
Extract the 'splicings' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... Error in .check_foreign_key(transcripts_tx_chrom, NA, "transcripts$tx_chrom",  : 
  all the values in 'transcripts$tx_chrom' must be present in 'chrominfo$chrom'



> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS  10.14.1

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/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] grid      parallel  stats4    stats     graphics  grDevices utils     datasets  methods  
[10] base     

other attached packages:
 [1] RMariaDB_1.0.6         BiocInstaller_1.32.1   GenomicFeatures_1.34.1 ChIPseeker_1.18.0     
 [5] ChIPpeakAnno_3.16.0    VennDiagram_1.6.20     futile.logger_1.4.3    GenomicRanges_1.34.0  
 [9] GenomeInfoDb_1.18.0    Biostrings_2.50.1      XVector_0.22.0         org.Hs.eg.db_3.7.0    
[13] AnnotationDbi_1.44.0   IRanges_2.16.0         S4Vectors_0.20.0       Biobase_2.42.0        
[17] BiocGenerics_0.28.0   

loaded via a namespace (and not attached):
  [1] fgsea_1.8.0                             colorspace_1.3-2                       
  [3] seqinr_3.4-5                            ggridges_0.5.1                         
  [5] qvalue_2.14.0                           farver_1.0                             
  [7] urltools_1.7.1                          ggrepel_0.8.0                          
  [9] bit64_0.9-7                             xml2_1.2.0                             
 [11] splines_3.5.1                           GOSemSim_2.8.0                         
 [13] ade4_1.7-13                             jsonlite_1.5                           
 [15] Rsamtools_1.34.0                        gridBase_0.4-7                         
 [17] GO.db_3.7.0                             graph_1.60.0                           
 [19] ggforce_0.1.3                           BiocManager_1.30.3                     
 [21] compiler_3.5.1                          httr_1.3.1                             
 [23] rvcheck_0.1.1                           assertthat_0.2.0                       
 [25] Matrix_1.2-15                           lazyeval_0.2.1                         
 [27] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 limma_3.38.2                           
 [29] tweenr_1.0.0                            formatR_1.5                            
 [31] prettyunits_1.0.2                       tools_3.5.1                            
 [33] bindrcpp_0.2.2                          igraph_1.2.2                           
 [35] gtable_0.2.0                            glue_1.3.0                             
 [37] GenomeInfoDbData_1.2.0                  reshape2_1.4.3                         
 [39] DO.db_2.9                               dplyr_0.7.7                            
 [41] fastmatch_1.1-0                         Rcpp_0.12.19                           
 [43] enrichplot_1.2.0                        multtest_2.38.0                        
 [45] gdata_2.18.0                            rtracklayer_1.42.0                     
 [47] ggraph_1.0.2                            stringr_1.3.1                          
 [49] ensembldb_2.6.1                         gtools_3.8.1                           
 [51] XML_3.98-1.16                           DOSE_3.8.0                             
 [53] idr_1.2                                 europepmc_0.3                          
 [55] zlibbioc_1.28.0                         MASS_7.3-51.1                          
 [57] scales_1.0.0                            BSgenome_1.50.0                        
 [59] hms_0.4.2                               ProtGenerics_1.14.0                    
 [61] SummarizedExperiment_1.12.0             RBGL_1.58.0                            
 [63] AnnotationFilter_1.6.0                  lambda.r_1.2.3                         
 [65] RColorBrewer_1.1-2                      curl_3.2                               
 [67] memoise_1.1.0                           gridExtra_2.3                          
 [69] ggplot2_3.1.0                           UpSetR_1.3.3                           
 [71] biomaRt_2.38.0                          triebeard_0.3.0                        
 [73] stringi_1.2.4                           RSQLite_2.1.1                          
 [75] plotrix_3.7-4                           caTools_1.17.1.1                       
 [77] boot_1.3-20                             BiocParallel_1.16.0                    
 [79] rlang_0.3.0.1                           pkgconfig_2.0.2                        
 [81] matrixStats_0.54.0                      bitops_1.0-6                           
 [83] lattice_0.20-38                         purrr_0.2.5                            
 [85] bindr_0.1.1                             GenomicAlignments_1.18.0               
 [87] cowplot_0.9.3                           bit_1.1-14                             
 [89] tidyselect_0.2.5                        plyr_1.8.4                             
 [91] magrittr_1.5                            R6_2.3.0                               
 [93] gplots_3.0.1                            DelayedArray_0.8.0                     
 [95] DBI_1.0.0                               pillar_1.3.0                           
 [97] units_0.6-1                             survival_2.43-1                        
 [99] RCurl_1.95-4.11                         tibble_1.4.2                           
[101] crayon_1.3.4                            futile.options_1.0.1                   
[103] KernSmooth_2.23-15                      viridis_0.5.1                          
[105] progress_1.2.0                          data.table_1.11.8                      
[107] blob_1.1.1                              digest_0.6.18                          
[109] regioneR_1.14.0                         gridGraphics_0.3-0                     
[111] munsell_0.5.0                           ggplotify_0.0.3                        
[113] viridisLite_0.3.0
ADD COMMENTlink modified 12 days ago • written 12 days ago by DMA10

I also ran into the same issue. Any insights so far?

ADD REPLYlink written 4 days ago by gali.yanovich0
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