Bioconductor / GenomeInfoDb

Utilities for manipulating chromosome names, including modifying them to follow a particular naming style
https://bioconductor.org/packages/GenomeInfoDb
31 stars 13 forks source link

`Seqinfo` is now broken with UCSC hg38 (v1.34.7) #83

Closed mjsteinbaugh closed 1 year ago

mjsteinbaugh commented 1 year ago

It looks like UCSC has changed some things on their server related to hg38 that is causing issues with the latest stable version of GenomeInfoDb (v1.34.7).

packageVersion("GenomeInfoDb")
## [1] ‘1.34.7’
suppressPackageStartupMessages({
    library(GenomeInfoDb)
})
Seqinfo(genome = "hg38")
## Error in .order_seqlevels(chrom_sizes[, "chrom"]) :
##   !anyNA(m32) is not TRUE
## Calls: Seqinfo ... FETCH_ORDERED_CHROM_SIZES -> .order_seqlevels -> stopifnot
## Backtrace:
##     ▆
##  1. └─GenomeInfoDb::Seqinfo(genome = "hg38")
##  2.   └─GenomeInfoDb:::.make_Seqinfo_from_genome(genome)
##  3.     └─GenomeInfoDb::getChromInfoFromUCSC(genome, as.Seqinfo = TRUE)
##  4.       └─GenomeInfoDb:::.get_chrom_info_for_registered_UCSC_genome(...)
##  5.         └─GenomeInfoDb:::.get_raw_chrom_info_for_registered_UCSC_genome(...)
##  6.           └─GenomeInfoDb:::.fetch_raw_chrom_info_from_UCSC(...)
##  7.             └─GenomeInfoDb (local) FETCH_ORDERED_CHROM_SIZES(goldenPath.url = goldenPath.url)
##  8.               └─GenomeInfoDb (local) .order_seqlevels(chrom_sizes[, "chrom"]) at registered/UCSC_genomes/hg38.R:69:4
##  9.                 └─base::stopifnot(!anyNA(m32)) at registered/UCSC_genomes/hg38.R:37:4
Seqinfo(genome = "hg19")
## Seqinfo object with 298 sequences (2 circular) from hg19 genome:
##   seqnames           seqlengths isCircular genome
##   chr1                249250621      FALSE   hg19
##   chr2                243199373      FALSE   hg19
##   chr3                198022430      FALSE   hg19
##   chr4                191154276      FALSE   hg19
##   chr5                180915260      FALSE   hg19
##   ...                       ...        ...    ...
##   chr21_gl383580_alt      74652      FALSE   hg19
##   chr21_gl383581_alt     116690      FALSE   hg19
##   chr22_gl383582_alt     162811      FALSE   hg19
##   chr22_gl383583_alt      96924      FALSE   hg19
##   chr22_kb663609_alt      74013      FALSE   hg19

See related:

Best, Mike

mjsteinbaugh commented 1 year ago

@hpages OK reading through the comments in the other thread, sounds like this should be fixed in 1.34.8. Will reopen if I'm still having issues. Thanks!