broken chain import in liftOver
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Entering edit mode
@jamesdalgleish-23638
Last seen 7 weeks 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 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
lifto liftOver • 120 views
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Entering edit mode

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

library(AnnotationHub)
query(ah <- AnnotationHub(), "hg19ToHg38")
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Entering edit mode
@james-w-macdonald-5106
Last seen 8 hours ago
United States

You have to uncompress first:

> download.file("https://hgdownload.soe.ucsc.edu/gbdb/hg19/liftOver/hg19ToHg38.over.chain.gz", "hg19ToHg38.over.chain.gz")
trying URL 'https://hgdownload.soe.ucsc.edu/gbdb/hg19/liftOver/hg19ToHg38.over.chain.gz'
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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