Entering edit mode
I've been using liftover for years, but I've never encountered this error. Is there something wrong with my chain? I downloaded my chain from https://hgdownload.cse.ucsc.edu/goldenpath/hg19/liftOver/
library(liftOver)
#Loading required package: gwascat
#Registered S3 methods overwritten by 'dbplyr':
# method from
# print.tbl_lazy
# print.tbl_sql
#gwascat loaded. Use makeCurrentGwascat() to extract current image.
#from EBI. The data folder of this package has some legacy extracts.
#Loading required package: GenomicRanges
#Loading required package: stats4
#Loading required package: BiocGenerics
#Attaching package: ‘BiocGenerics’
#The following objects are masked from ‘package:stats’:
# IQR, mad, sd, var, xtabs
#The following objects are masked from ‘package:base’:
# anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
#match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min
#Loading required package: S4Vectors
#Attaching package: ‘S4Vectors’
#The following objects are masked from ‘package:base’:
# expand.grid, I, unname
# Loading required package: IRanges
#Attaching package: ‘IRanges’
#The following object is masked from ‘package:grDevices’:
# windows
#Loading required package: GenomeInfoDb
#Attaching package: ‘GenomicRanges’
#The following object is masked from ‘package:magrittr’:
# subtract
#Loading required package: rtracklayer
#Loading required package: Homo.sapiens
#Loading required package: AnnotationDbi
#Loading required package: Biobase
#Welcome to Bioconductor
# Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'.
#Loading required package: OrganismDbi
#Loading required package: GenomicFeatures
#Loading required package: GO.db
#Loading required package: org.Hs.eg.db
#Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene
library(rtracklayer)
chain_file=rtracklayer::import.chain("hg19ToHg38.over.chain.gz")
#Error in .local(con, format, text, ...) :
# expected 11 elements in header, got 1, on line 1
sessionInfo( )
R version 4.2.0 (2022-04-22 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8 LC_MONETARY=English_United States.utf8 LC_NUMERIC=C LC_TIME=English_United States.utf8
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] liftOver_1.20.0 Homo.sapiens_1.3.1 TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 org.Hs.eg.db_3.15.0 GO.db_3.15.0
[6] OrganismDbi_1.38.0 GenomicFeatures_1.48.0 AnnotationDbi_1.58.0 Biobase_2.56.0 rtracklayer_1.56.0
[11] GenomicRanges_1.48.0 GenomeInfoDb_1.32.1 IRanges_2.30.0 S4Vectors_0.34.0 BiocGenerics_0.42.0
[16] gwascat_2.28.0 magrittr_2.0.3
loaded via a namespace (and not attached):
[1] bitops_1.0-7 matrixStats_0.62.0 bit64_4.0.5 filelock_1.0.2 progress_1.2.2 httr_1.4.3 tools_4.2.0
[8] utf8_1.2.2 R6_2.5.1 DBI_1.1.2 tidyselect_1.1.2 prettyunits_1.1.1 bit_4.0.4 curl_4.3.2
[15] compiler_4.2.0 graph_1.74.0 cli_3.3.0 xml2_1.3.3 DelayedArray_0.22.0 readr_2.1.2 RBGL_1.72.0
[22] rappdirs_0.3.3 stringr_1.4.0 digest_0.6.29 Rsamtools_2.12.0 XVector_0.36.0 pkgconfig_2.0.3 MatrixGenerics_1.8.0
[29] highr_0.9 dbplyr_2.1.1 fastmap_1.1.0 BSgenome_1.64.0 rlang_1.0.2 RSQLite_2.2.14 BiocIO_1.6.0
[36] generics_0.1.2 BiocParallel_1.30.0 dplyr_1.0.9 VariantAnnotation_1.42.0 RCurl_1.98-1.6 GenomeInfoDbData_1.2.8 Matrix_1.4-1
[43] Rcpp_1.0.8.3 fansi_1.0.3 lifecycle_1.0.1 stringi_1.7.6 yaml_2.3.5 SummarizedExperiment_1.26.1 zlibbioc_1.42.0
[50] BiocFileCache_2.4.0 grid_4.2.0 blob_1.2.3 parallel_4.2.0 snpStats_1.46.0 crayon_1.5.1 lattice_0.20-45
[57] Biostrings_2.64.0 splines_4.2.0 hms_1.1.1 KEGGREST_1.36.0 knitr_1.39 pillar_1.7.0 rjson_0.2.21
[64] biomaRt_2.52.0 XML_3.99-0.9 glue_1.6.2 evaluate_0.15 data.table_1.14.2 BiocManager_1.30.17 png_0.1-7
[71] vctrs_0.4.1 tzdb_0.3.0 purrr_0.3.4 tidyr_1.2.0 assertthat_0.2.1 cachem_1.0.6 xfun_0.30
[78] restfulr_0.0.13 survival_3.3-1 tibble_3.1.7 GenomicAlignments_1.32.0 memoise_2.0.1 ellipsis_0.3.2
You could also try using one of the chain files in
AnnotationHub
, which gets auto-cached: