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Bioconductor / GenomeInfoDb

Utilities for manipulating chromosome names, including modifying them to follow a particular naming style
https://bioconductor.org/packages/GenomeInfoDb
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Issue with seqlevelStyle() #31

Closed yuhsinhsieh-josch closed 3 years ago

yuhsinhsieh-josch commented 3 years ago

I was doing scATAC analysis using Signac, where I need a GenomeInfoDb and EnsDb.Hsapiens.v86 to annotate my data. It worked nicely at the beginning of last week, but then I ran into the issue with the following code:

annotations <- GetGRangesFromEnsDb(ensdb = EnsDb.Hsapiens.v86)
seqlevelsStyle(annotations) <- 'UCSC'
genome(annotations) <- "hg38"

Here is the error message I received:

Error in .order_seqlevels(chrom_sizes[, "chrom"]) : 
  !anyNA(m32) is not TRUE

I would appreciate if you can have a look and give me some feedback

Here's my R sessionInfo():

R version 4.1.1 (2021-08-10)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /fast/work/users/yhsieh_m/miniconda3/envs/Signac/lib/libopenblasp-r0.3.18.so

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

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

other attached packages:
 [1] dplyr_1.0.7               EnsDb.Hsapiens.v86_2.99.0
 [3] ensembldb_2.17.4          AnnotationFilter_1.17.1  
 [5] GenomicFeatures_1.45.2    AnnotationDbi_1.55.1     
 [7] Biobase_2.53.0            GenomicRanges_1.45.0     
 [9] GenomeInfoDb_1.29.8       IRanges_2.27.2           
[11] S4Vectors_0.31.5          BiocGenerics_0.39.2      
[13] patchwork_1.1.1           ggplot2_3.3.5            
[15] SeuratObject_4.0.2        Seurat_4.0.5             
[17] Signac_1.4.0             

loaded via a namespace (and not attached):
  [1] utf8_1.2.2                  reticulate_1.22            
  [3] tidyselect_1.1.1            RSQLite_2.2.8              
  [5] htmlwidgets_1.5.4           grid_4.1.1                 
  [7] docopt_0.7.1                BiocParallel_1.27.17       
  [9] Rtsne_0.15                  munsell_0.5.0              
 [11] codetools_0.2-18            ica_1.0-2                  
 [13] future_1.22.1               miniUI_0.1.1.1             
 [15] withr_2.4.2                 colorspace_2.0-2           
 [17] filelock_1.0.2              knitr_1.36                 
 [19] rstudioapi_0.13             ROCR_1.0-11                
 [21] tensor_1.5                  listenv_0.8.0              
 [23] MatrixGenerics_1.5.4        slam_0.1-48                
 [25] GenomeInfoDbData_1.2.7      polyclip_1.10-0            
 [27] bit64_4.0.5                 farver_2.1.0               
 [29] parallelly_1.28.1           vctrs_0.3.8                
 [31] generics_0.1.0              xfun_0.26                  
 [33] biovizBase_1.41.0           BiocFileCache_2.1.1        
 [35] lsa_0.73.2                  ggseqlogo_0.1              
 [37] R6_2.5.1                    hdf5r_1.3.4                
 [39] bitops_1.0-7                spatstat.utils_2.2-0       
 [41] cachem_1.0.6                DelayedArray_0.19.4        
 [43] assertthat_0.2.1            promises_1.2.0.1           
 [45] BiocIO_1.3.0                scales_1.1.1               
 [47] nnet_7.3-16                 gtable_0.3.0               
 [49] globals_0.14.0              goftest_1.2-3              
 [51] rlang_0.4.11                RcppRoll_0.3.0             
 [53] splines_4.1.1               rtracklayer_1.53.1         
 [55] lazyeval_0.2.2              dichromat_2.0-0            
 [57] checkmate_2.0.0             spatstat.geom_2.3-0        
 [59] yaml_2.2.1                  reshape2_1.4.4             
 [61] abind_1.4-5                 backports_1.2.1            
 [63] httpuv_1.6.3                Hmisc_4.6-0                
 [65] tools_4.1.1                 ellipsis_0.3.2             
 [67] spatstat.core_2.3-0         RColorBrewer_1.1-2         
 [69] ggridges_0.5.3              Rcpp_1.0.7                 
 [71] plyr_1.8.6                  base64enc_0.1-3            
 [73] progress_1.2.2              zlibbioc_1.39.0            
 [75] purrr_0.3.4                 RCurl_1.98-1.5             
 [77] prettyunits_1.1.1           rpart_4.1-15               
 [79] deldir_1.0-5                pbapply_1.5-0              
 [81] cowplot_1.1.1               zoo_1.8-9                  
 [83] SummarizedExperiment_1.23.5 ggrepel_0.9.1              
 [85] cluster_2.1.2               magrittr_2.0.1             
 [87] data.table_1.14.2           scattermore_0.7            
 [89] lmtest_0.9-38               RANN_2.6.1                 
 [91] SnowballC_0.7.0             ProtGenerics_1.25.1        
 [93] fitdistrplus_1.1-6          matrixStats_0.61.0         
 [95] hms_1.1.1                   mime_0.12                  
 [97] xtable_1.8-4                XML_3.99-0.8               
 [99] jpeg_0.1-9                  sparsesvd_0.2              
[101] gridExtra_2.3               compiler_4.1.1             
[103] biomaRt_2.49.6              tibble_3.1.5               
[105] KernSmooth_2.23-20          crayon_1.4.1               
[107] htmltools_0.5.2             mgcv_1.8-38                
[109] later_1.3.0                 Formula_1.2-4              
[111] tidyr_1.1.4                 DBI_1.1.1                  
[113] tweenr_1.0.2                dbplyr_2.1.1               
[115] MASS_7.3-54                 rappdirs_0.3.3             
[117] Matrix_1.3-4                parallel_4.1.1             
[119] igraph_1.2.7                pkgconfig_2.0.3            
[121] GenomicAlignments_1.29.0    foreign_0.8-81             
[123] plotly_4.10.0               spatstat.sparse_2.0-0      
[125] xml2_1.3.2                  XVector_0.33.0             
[127] VariantAnnotation_1.39.0    stringr_1.4.0              
[129] digest_0.6.28               sctransform_0.3.2          
[131] RcppAnnoy_0.0.19            spatstat.data_2.1-0        
[133] Biostrings_2.61.2           leiden_0.3.9               
[135] fastmatch_1.1-3             htmlTable_2.3.0            
[137] uwot_0.1.10                 restfulr_0.0.13            
[139] curl_4.3.2                  shiny_1.7.1                
[141] Rsamtools_2.9.1             rjson_0.2.20               
[143] lifecycle_1.0.1             nlme_3.1-153               
[145] jsonlite_1.7.2              BSgenome_1.61.0            
[147] viridisLite_0.4.0           fansi_0.5.0                
[149] pillar_1.6.3                lattice_0.20-45            
[151] KEGGREST_1.33.0             fastmap_1.1.0              
[153] httr_1.4.2                  survival_3.2-13            
[155] glue_1.4.2                  qlcMatrix_0.9.7            
[157] png_0.1-7                   bit_4.0.4                  
[159] ggforce_0.3.3               stringi_1.7.5              
[161] blob_1.2.2                  latticeExtra_0.6-29        
[163] memoise_2.0.0               irlba_2.3.3                
[165] future.apply_1.8.1
hpages commented 3 years ago

Hi,

This is just another manifestation of issue #30. It's now fixed in GenomeInfoDb 1.29.10 (see commit c460a6278710f3e2b31f6e67d99b17ce89609959) but unfortunately the fix cannot be backported to BioC 3.13 (see issue #30 for why).

Cheers, H.