Hello!

I am currently trying to annotate some whole genome bisulfite sequencing data with the annotatr package. However, when trying to use the hg38_basicgenes annotation, I run into a warning saying that the GRanges object contains out-of-bound ranges (please see below for the code and the warning).

Originally, I had tried to use an older version of annotatr, because our server is still running R 3.6. I thought that not using the latest version of R, Bioconductor and the annotatr package could be the problem and thus also tried with R 4.0.1. This produced less warnings than before, but still indicated 120 out-of-bound ranges.

Can anybody help with this?

> annots <- c("hg38_cpgs", "hg38_basicgenes", "hg38_genes_intergenic")
> annotations <- build_annotations(genome="hg38", annotations=annots)

'select()' returned 1:1 mapping between keys and columns
Building promoters...
[...]
Building inter-CpG-islands...
Warning message:
In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 120 out-of-bound ranges located on sequences
  chr1_GL383518v1_alt, chr1_KQ458384v1_alt, chr2_GL383522v1_alt,
  chr4_GL000257v2_alt, chr5_GL339449v2_alt, chr5_KI270795v1_alt,
  chr5_KI270898v1_alt, chr5_KV575244v1_fix, chr6_KI270797v1_alt,
  chr6_KI270798v1_alt, chr6_KI270801v1_alt, chr7_GL383534v2_alt,
  chr7_KI270803v1_alt, chr7_KI270806v1_alt, chr7_KI270809v1_alt,
  chr7_KZ208912v1_fix, chr9_GL383540v1_alt, chr9_GL383541v1_alt,
  chr11_KI270902v1_alt, chr12_GL383551v1_alt, chr12_GL383553v2_alt,
  chr12_KI270834v1_alt, chr14_KI270847v1_alt, chr15_KI270848v1_alt,
  chr15_KI270850v1_alt, chr15_KI270851v1_alt, chr15_KI270906v1_alt,
  chr16_GL383556v1_alt, chr16_KI270854v1_alt, chr17_JH159146v1_alt,
  chr17_JH159147v1_alt, chr17_KI270857v1_alt, chr17_KI270860v1_alt,
  chr17_KV575245v1_fix, chr17_KV766196v1_fix, chr17_KV766198v1_alt,
  chr19_GL383575v2_alt, chr19_GL383576v1_alt, chr19_KI270866v1_alt,
  chr19_KI270884v1_alt, chr19_KI270885v1_alt, chr19_KI270889v1_al [... truncated]

My SessionInfo:

R version 4.0.1 (2020-06-06)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux

Matrix products: default
BLAS:   /mnt/254b78b9-76b4-422d-84b1-cc632bff60f7/Software/install/R-4.0.1/installation/lib64/R/lib/libRblas.so
LAPACK: /mnt/254b78b9-76b4-422d-84b1-cc632bff60f7/Software/install/R-4.0.1/installation/lib64/R/lib/libRlapack.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    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] org.Hs.eg.db_3.11.4
 [2] TxDb.Hsapiens.UCSC.hg38.knownGene_3.10.0
 [3] GenomicFeatures_1.40.0
 [4] AnnotationDbi_1.50.0
 [5] Biobase_2.48.0
 [6] GenomicRanges_1.40.0
 [7] GenomeInfoDb_1.24.2
 [8] IRanges_2.22.2
 [9] S4Vectors_0.26.1
[10] BiocGenerics_0.34.0
[11] annotatr_1.14.0

loaded via a namespace (and not attached):
 [1] httr_1.4.1                    regioneR_1.20.1
 [3] bit64_0.9-7                   AnnotationHub_2.20.2
 [5] shiny_1.5.0                   assertthat_0.2.1
 [7] interactiveDisplayBase_1.26.3 askpass_1.1
 [9] BiocManager_1.30.10           BiocFileCache_1.12.0
[11] blob_1.2.1                    BSgenome_1.56.0
[13] GenomeInfoDbData_1.2.3        Rsamtools_2.4.0
[15] yaml_2.2.1                    progress_1.2.2
[17] BiocVersion_3.11.1            pillar_1.4.4
[19] RSQLite_2.2.0                 lattice_0.20-41
[21] glue_1.4.1                    digest_0.6.25
[23] promises_1.1.1                XVector_0.28.0
[25] colorspace_1.4-1              plyr_1.8.6
[27] htmltools_0.5.0               httpuv_1.5.4
[29] Matrix_1.2-18                 XML_3.99-0.3
[31] pkgconfig_2.0.3               biomaRt_2.44.1
[33] zlibbioc_1.34.0               purrr_0.3.4
[35] xtable_1.8-4                  scales_1.1.1
[37] later_1.1.0.1                 BiocParallel_1.22.0
[39] tibble_3.0.1                  openssl_1.4.1
[41] generics_0.0.2                ggplot2_3.3.2
[43] ellipsis_0.3.1                SummarizedExperiment_1.18.1
[45] magrittr_1.5                  crayon_1.3.4
[47] mime_0.9                      memoise_1.1.0
[49] tools_4.0.1                   prettyunits_1.1.1
[51] hms_0.5.3                     lifecycle_0.2.0
[53] matrixStats_0.56.0            stringr_1.4.0
[55] munsell_0.5.0                 DelayedArray_0.14.0
[57] Biostrings_2.56.0             compiler_4.0.1
[59] rlang_0.4.6                   grid_4.0.1
[61] RCurl_1.98-1.2                rappdirs_0.3.1
[63] bitops_1.0-6                  gtable_0.3.0
[65] DBI_1.1.0                     curl_4.3
[67] reshape2_1.4.4                R6_2.4.1
[69] GenomicAlignments_1.24.0      dplyr_1.0.0
[71] rtracklayer_1.48.0            fastmap_1.0.1
[73] bit_1.1-15.2                  readr_1.4.0
[75] stringi_1.4.6                 Rcpp_1.0.4.6
[77] vctrs_0.3.1                   dbplyr_1.4.4
[79] tidyselect_1.1.0