Question: makeTxDbFromUCSC: error in Make the TxDb object
1
gravatar for DMA1
6 months ago by
DMA110
DMA110 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 6 months ago • written 6 months ago by DMA110

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

ADD REPLYlink written 6 months ago by gali.yanovich0

I also got this problem.Anyone know how to deal with it?

ADD REPLYlink written 3 months ago by alanchenslm0
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