broken chain import in liftOver
Entering edit mode
Last seen 18 days ago
United States

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

#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,, basename, cbind, colnames, dirname,, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
    #match, mget, order, paste, pmax,, pmin,, 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:

#Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene
#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

[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                     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
lifto liftOver • 92 views
Entering edit mode

You could also try using one of the chain files in AnnotationHub, which gets auto-cached:

query(ah <- AnnotationHub(), "hg19ToHg38")
Entering edit mode
Last seen 2 days ago
United States

You have to uncompress first:

> download.file("", "hg19ToHg38.over.chain.gz")
trying URL ''
Content type 'application/x-gzip' length 227698 bytes (222 KB)
downloaded 222 KB

> system("gzip -d hg19ToHg38.over.chain.gz")
[1] 0
> import.chain("hg19ToHg38.over.chain.gz")
Error in .local(con, format, text, ...) : 
  expected 11 elements in header, got 1, on line 1
> z <- import.chain("hg19ToHg38.over.chain")
## success!

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