I am having trouble retrieving annotation from hg38 using the GenomeInfoDb package.

[gnwwanne]

I am currently working on creating a Signac Pipeline. I keep getting this error when I use the following commands :

extract gene annotations from EnsDb

annotations <- GetGRangesFromEnsDb(ensdb = EnsDb.Hsapiens.v86)

change to UCSC style since the data was mapped to hg38

seqlevelsStyle(annotations) <- 'UCSC'

Error in stop_if(is.null(NCBI_assembly_info), "\"assembly_accession\" field in 'NCBI_LINKER' must ", : Error in UCSC genome registration file 'hg38.R': "assembly_accession" field in 'NCBI_LINKER' must be associated with a registered NCBI assembly

I updated my genomeInfoDb bio conductor package to the newest version but I am still receiving this error.

##############################################R-code and session info################################ library(Signac) library(Seurat) library(GenomeInfoDb) library(EnsDb.Hsapiens.v86) library(ggplot2) library(patchwork) set.seed(1234)

seurat_p function

seurat_p <- function(filtered_data){ filtered_data<-gene.vs.molecule.cell.filter(filtered_data, min.cell.size=500) seurat_p <- CreateSeuratObject(counts = filtered_data, min.cells = 3, min.features = 400) seurat_p[["percent.mt"]] <- PercentageFeatureSet(seurat_p, pattern = "^MT-") seurat_p <- seurat_p[, seurat_p[["nFeature_RNA"]] > 400 & seurat_p[["nFeature_RNA"]] < 7500 & seurat_p[["percent.mt"]] < 20 ] return(seurat_p) }

implement Signac Pipeline on sample

counts <- Read10X_h5(filename = "filtered_feature_bc_matrix.h5")

counts_pks<-counts$Peaks counts_gene<-counts$Gene Expression

create chromatin assay with this function

chrom_assay <- CreateChromatinAssay( counts = counts_pks, sep = c(":", "-"), fragments = 'atac_fragments.tsv.gz', min.cells = 10, min.features = 200 )

create a seurat object after implementing Signac pipeline

K_602A <- CreateSeuratObject( counts = chrom_assay, assay = "peaks", )

extract gene annotations from EnsDb

annotations <- GetGRangesFromEnsDb(ensdb = EnsDb.Hsapiens.v86)

change to UCSC style since the data was mapped to hg38

seqlevelsStyle(annotations) <- 'UCSC'

add the gene information to the object

Annotation(KPMP_602A) <- annotations

sessionInfo() R version 4.2.2 (2022-10-31) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Monterey 12.1

Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.2/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] stats4 stats graphics grDevices utils datasets methods
[8] base

other attached packages: [1] BiocManager_1.30.19 patchwork_1.1.2
[3] ggplot2_3.4.0 EnsDb.Hsapiens.v86_2.99.0 [5] ensembldb_2.22.0 AnnotationFilter_1.22.0
[7] GenomicFeatures_1.50.4 AnnotationDbi_1.60.0
[9] Biobase_2.58.0 GenomicRanges_1.50.2
[11] GenomeInfoDb_1.35.15 IRanges_2.32.0
[13] S4Vectors_0.36.1 BiocGenerics_0.44.0
[15] SeuratObject_4.1.3 Seurat_4.3.0
[17] Signac_1.9.0

loaded via a namespace (and not attached): [1] utf8_1.2.3 spatstat.explore_3.0-6
[3] reticulate_1.28 tidyselect_1.2.0
[5] RSQLite_2.2.20 htmlwidgets_1.6.1
[7] grid_4.2.2 BiocParallel_1.32.5
[9] Rtsne_0.16 munsell_0.5.0
[11] codetools_0.2-19 ica_1.0-3
[13] interp_1.1-3 future_1.31.0
[15] miniUI_0.1.1.1 withr_2.5.0
[17] spatstat.random_3.1-3 colorspace_2.1-0
[19] progressr_0.13.0 filelock_1.0.2
[21] knitr_1.42 rstudioapi_0.14
[23] ROCR_1.0-11 tensor_1.5
[25] listenv_0.9.0 MatrixGenerics_1.10.0
[27] GenomeInfoDbData_1.2.9 polyclip_1.10-4
[29] bit64_4.0.5 rprojroot_2.0.3
[31] parallelly_1.34.0 vctrs_0.5.2
[33] generics_0.1.3 xfun_0.37
[35] biovizBase_1.46.0 BiocFileCache_2.6.0
[37] R6_2.5.1 hdf5r_1.3.8
[39] bitops_1.0-7 spatstat.utils_3.0-1
[41] cachem_1.0.6 DelayedArray_0.24.0
[43] assertthat_0.2.1 promises_1.2.0.1
[45] BiocIO_1.8.0 scales_1.2.1
[47] nnet_7.3-18 gtable_0.3.1
[49] globals_0.16.2 processx_3.8.0
[51] goftest_1.2-3 rlang_1.0.6
[53] RcppRoll_0.3.0 splines_4.2.2
[55] rtracklayer_1.58.0 lazyeval_0.2.2
[57] dichromat_2.0-0.1 checkmate_2.1.0
[59] spatstat.geom_3.0-6 yaml_2.3.7
[61] reshape2_1.4.4 abind_1.4-5
[63] backports_1.4.1 httpuv_1.6.8
[65] Hmisc_4.7-2 tools_4.2.2
[67] ellipsis_0.3.2 RColorBrewer_1.1-3
[69] ggridges_0.5.4 Rcpp_1.0.10
[71] plyr_1.8.8 base64enc_0.1-3
[73] progress_1.2.2 zlibbioc_1.44.0
[75] purrr_1.0.1 RCurl_1.98-1.10
[77] ps_1.7.2 prettyunits_1.1.1
[79] rpart_4.1.19 deldir_1.0-6
[81] pbapply_1.7-0 cowplot_1.1.1
[83] zoo_1.8-11 SummarizedExperiment_1.28.0 [85] ggrepel_0.9.2 cluster_2.1.4
[87] magrittr_2.0.3 data.table_1.14.6
[89] scattermore_0.8 lmtest_0.9-40
[91] RANN_2.6.1 ProtGenerics_1.30.0
[93] fitdistrplus_1.1-8 matrixStats_0.63.0
[95] hms_1.1.2 mime_0.12
[97] xtable_1.8-4 XML_3.99-0.13
[99] jpeg_0.1-10 gridExtra_2.3
[101] compiler_4.2.2 biomaRt_2.54.0
[103] tibble_3.1.8 KernSmooth_2.23-20
[105] crayon_1.5.2 htmltools_0.5.4
[107] later_1.3.0 Formula_1.2-4
[109] tidyr_1.3.0 DBI_1.1.3
[111] dbplyr_2.3.0 MASS_7.3-58.2
[113] rappdirs_0.3.3 Matrix_1.5-3
[115] cli_3.6.0 parallel_4.2.2
[117] igraph_1.3.5 pkgconfig_2.0.3
[119] GenomicAlignments_1.34.0 foreign_0.8-84
[121] sp_1.6-0 plotly_4.10.1
[123] spatstat.sparse_3.0-0 xml2_1.3.3
[125] XVector_0.38.0 VariantAnnotation_1.44.0
[127] stringr_1.5.0 callr_3.7.3
[129] digest_0.6.31 sctransform_0.3.5
[131] RcppAnnoy_0.0.20 spatstat.data_3.0-0
[133] Biostrings_2.66.0 leiden_0.4.3
[135] fastmatch_1.1-3 htmlTable_2.4.1
[137] uwot_0.1.14 restfulr_0.0.15
[139] curl_5.0.0 shiny_1.7.4
[141] Rsamtools_2.14.0 rjson_0.2.21
[143] lifecycle_1.0.3 nlme_3.1-162
[145] jsonlite_1.8.4 BSgenome_1.66.2
[147] desc_1.4.2 viridisLite_0.4.1
[149] fansi_1.0.4 pillar_1.8.1
[151] lattice_0.20-45 pkgbuild_1.4.0
[153] KEGGREST_1.38.0 fastmap_1.1.0
[155] httr_1.4.4 survival_3.5-0
[157] glue_1.6.2 remotes_2.4.2
[159] png_0.1-8 bit_4.0.5
[161] stringi_1.7.12 blob_1.2.3
[163] latticeExtra_0.6-30 memoise_2.0.1
[165] dplyr_1.1.0 irlba_2.3.5.1
[167] future.apply_1.10.0

[hpages]

Please take a look at https://github.com/Bioconductor/GenomeInfoDb/issues/82#issuecomment-1413895055

[gnwwanne]

Ok thanks but now I am getting this error:

seqlevelsStyle(annotations) <- 'UCSC' Error in function (type, msg, asError = TRUE) : Could not resolve host: ftp.ncbi.nlm.nih.gov

[hpages]

You have an internet problem or ftp.ncbi.nlm.nih.gov was temporarily unresponsive. This has not much to do with the latest changes in GenomeInfoDb.

Does this link work for you? https://ftp.ncbi.nlm.nih.gov/

If it does then try seqlevelsStyle(annotations) <- 'UCSC' again.