Entering edit mode
Hi,
I am trying to re-run an analysis that was running fine last week on Seurat V4. There is now an error message that seems to be due to GenomeInfoDb. Do you know if there was an update or something that could explain this error ? Thanks
In:
grange.counts <- StringToGRanges(rownames(atac_counts), sep = c(":", "-"))
grange.use <- seqnames(grange.counts) %in% standardChromosomes(grange.counts)
atac_counts <- atac_counts[as.vector(grange.use), ]
annotations <- GetGRangesFromEnsDb(ensdb = EnsDb.Mmusculus.v79)
seqlevelsStyle(annotations) <- 'UCSC'
genome(annotations) <- "mm10"
# More specifically here #
# seqlevelsStyle(annotations) <- 'UCSC'
# Error in .order_seqlevels(chrom_sizes[, "chrom"]) :
!anyNA(m31) is not TRUE
sessionInfo( )
> sessionInfo( )
R version 4.1.0 (2021-05-18)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19043)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C LC_TIME=English_United States.1252
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] patchwork_1.1.1 SeuratDisk_0.0.0.9019 ggplot2_3.3.5 dplyr_1.0.7 EnsDb.Mmusculus.v79_2.99.0 ensembldb_2.17.0 AnnotationFilter_1.17.0 GenomicFeatures_1.45.0 AnnotationDbi_1.55.1
[10] Biobase_2.53.0 GenomicRanges_1.45.0 GenomeInfoDb_1.29.2 IRanges_2.27.0 S4Vectors_0.31.0 BiocGenerics_0.39.1 Signac_1.2.1 SeuratObject_4.0.2 Seurat_4.0.3
loaded via a namespace (and not attached):
[1] utf8_1.2.1 reticulate_1.20 tidyselect_1.1.1 RSQLite_2.2.7 htmlwidgets_1.5.3 grid_4.1.0 docopt_0.7.1 BiocParallel_1.27.0
[9] Rtsne_0.15 munsell_0.5.0 codetools_0.2-18 ica_1.0-2 future_1.21.0 miniUI_0.1.1.1 withr_2.4.2 colorspace_2.0-2
[17] filelock_1.0.2 knitr_1.33 rstudioapi_0.13 ROCR_1.0-11 tensor_1.5 listenv_0.8.0 MatrixGenerics_1.5.0 slam_0.1-48
[25] GenomeInfoDbData_1.2.6 polyclip_1.10-0 bit64_4.0.5 farver_2.1.0 parallelly_1.26.0 vctrs_0.3.8 generics_0.1.0 xfun_0.24
[33] biovizBase_1.41.0 BiocFileCache_2.1.1 lsa_0.73.2 ggseqlogo_0.1 R6_2.5.0 hdf5r_1.3.3 bitops_1.0-7 spatstat.utils_2.2-0
[41] cachem_1.0.5 DelayedArray_0.19.1 assertthat_0.2.1 promises_1.2.0.1 BiocIO_1.3.0 scales_1.1.1 nnet_7.3-16 gtable_0.3.0
[49] globals_0.14.0 goftest_1.2-2 rlang_0.4.11 RcppRoll_0.3.0 splines_4.1.0 rtracklayer_1.53.0 lazyeval_0.2.2 dichromat_2.0-0
[57] checkmate_2.0.0 spatstat.geom_2.2-0 BiocManager_1.30.16 yaml_2.2.1 reshape2_1.4.4 abind_1.4-5 backports_1.2.1 httpuv_1.6.1
[65] Hmisc_4.5-0 tools_4.1.0 ellipsis_0.3.2 spatstat.core_2.2-0 RColorBrewer_1.1-2 ggridges_0.5.3 Rcpp_1.0.6 plyr_1.8.6
[73] base64enc_0.1-3 progress_1.2.2 zlibbioc_1.39.0 purrr_0.3.4 RCurl_1.98-1.3 prettyunits_1.1.1 rpart_4.1-15 deldir_0.2-10
[81] pbapply_1.4-3 cowplot_1.1.1 zoo_1.8-9 SummarizedExperiment_1.23.1 ggrepel_0.9.1 cluster_2.1.2 magrittr_2.0.1 data.table_1.14.0
[89] scattermore_0.7 lmtest_0.9-38 RANN_2.6.1 SnowballC_0.7.0 ProtGenerics_1.25.0 fitdistrplus_1.1-5 matrixStats_0.59.0 hms_1.1.0
[97] mime_0.11 xtable_1.8-4 XML_3.99-0.6 jpeg_0.1-8.1 sparsesvd_0.2 gridExtra_2.3 compiler_4.1.0 biomaRt_2.49.1
[105] tibble_3.1.2 KernSmooth_2.23-20 crayon_1.4.1 htmltools_0.5.1.1 mgcv_1.8-36 later_1.2.0 Formula_1.2-4 tidyr_1.1.3
[113] DBI_1.1.1 tweenr_1.0.2 dbplyr_2.1.1 MASS_7.3-54 rappdirs_0.3.3 Matrix_1.3-4 cli_2.5.0 parallel_4.1.0
[121] igraph_1.2.6 pkgconfig_2.0.3 GenomicAlignments_1.29.0 foreign_0.8-81 plotly_4.9.4.1 spatstat.sparse_2.0-0 xml2_1.3.2 XVector_0.33.0
[129] VariantAnnotation_1.39.0 stringr_1.4.0 digest_0.6.27 sctransform_0.3.2 RcppAnnoy_0.0.18 spatstat.data_2.1-0 Biostrings_2.61.1 leiden_0.3.8
[137] fastmatch_1.1-0 htmlTable_2.2.1 uwot_0.1.10 restfulr_0.0.13 curl_4.3.2 shiny_1.6.0 Rsamtools_2.9.1 rjson_0.2.20
[145] lifecycle_1.0.0 nlme_3.1-152 jsonlite_1.7.2 BSgenome_1.61.0 viridisLite_0.4.0 fansi_0.5.0 pillar_1.6.1 lattice_0.20-44
[153] KEGGREST_1.33.0 fastmap_1.1.0 httr_1.4.2 survival_3.2-11 glue_1.4.2 qlcMatrix_0.9.7 png_0.1-7 bit_4.0.4
[161] ggforce_0.3.3 stringi_1.6.2 blob_1.2.1 latticeExtra_0.6-29 memoise_2.0.0 irlba_2.3.3 future.apply_1.7.0
I'm seeing the same error when running
The UCSC table is downloaded from
http://hgdownload.cse.ucsc.edu/goldenPath/mm10/database/chromInfo.txt.gzThe table contains the row:The mm10.R file supplied by the
GenomeInfoDbpackage expects that all lines that have there underscore-separated components in the first column will start with a "real" chromosome name such as "chr1", "chrX", etc. This "chrna" breaks this expectation and the parsing fails. It might be better to parse the file yourself and generate the seqinfo object "by hand".