Error "cannot map the following UCSC seqlevel(s) to an NCBI seqlevel" in package GenomeDbInfo
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foehn ▴ 60
@foehn-16281
Last seen 2 days ago
United States

Dear all,

I have the following code that once worked:

> library("GenomeInfoDb")
Loading required package: BiocGenerics 
Loading required package: parallel 
...
> Seqinfo(genome = "hg19") 
Error in FUN(genome = names(SUPPORTED_UCSC_GENOMES)[idx], circ_seqs = supported_genome$circ_seqs,  :    
cannot map the following UCSC seqlevel(s) to an NCBI seqlevel:   
chr1_jh636052_fix, chrX_jh806600_fix, chrX_jh806587_fix,   
chr7_jh159134_fix, chrX_jh159150_fix, chrX_jh806590_fix,   
chr10_jh591181_fix, chr1_jh636053_fix, chr5_gl339449_alt,   
chr14_kb021645_fix, chrX_jh720453_fix, chrX_jh806601_fix,   
chr7_gl582971_fix, chrX_jh806599_fix, chr19_gl949749_alt,   
chr19_gl949750_alt, chr19_gl949748_alt, chr19_kb021647_fix,   
chrX_jh806597_fix, chr10_ke332501_fix, chr19_gl949751_alt,   
chr19_gl949746_alt, chr19_gl949752_alt, chrX_jh806598_fix,   
chrX_jh720451_fix, chrX_jh806591_fix, chr11_jh806581_fix,   
chrX_jh806588_fix, chrX_jh806592_fix, chr19_gl949753_alt,   
chr1_jh636054_fix, chrX_jh720454_fix, chr19_gl949747_alt,   
chr7_jh636058_fix, chrX_jh806602_fix, chr17_gl383561_fix,   
chr8_gl949743_fix, chr2_kb663603_fix, chr19_gl582977_fix,   
chr19_ke332505_fix, chr11_jh159140_fix, chr5_ke332497_fix,   
chr17_gl383560_fix, chrX_jh720452_fix, chr4_ke332496_fix,   
chr6_kb663604_fix, chr

Here is the session info:

> sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: x86_64-apple-darwin18.7.0 (64-bit)
Running under: macOS  10.15.3

Matrix products: default
BLAS: $HOME/Applications/R/3.5.2/lib/R/lib/libRblas.dylib
LAPACK: $HOME/Applications/R/3.5.2/lib/R/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
[1] GenomeInfoDb_1.18.2 IRanges_2.16.0      S4Vectors_0.20.1   
[4] BiocGenerics_0.28.0

loaded via a namespace (and not attached):
[1] compiler_3.5.2         GenomeInfoDbData_1.2.0 RCurl_1.95-4.12       
[4] bitops_1.0-6

Note that my GenomeInfoDb is not the most updated version, but it is the last available for bioc 3.8/R 3.5 which I have to stick to for a while.

I suspect it might be caused by some recent update of the UCSC database... Does anybody know? Thanks.

genomeinfodb hg19 ucsc seqlevel genomicfeatures • 389 views
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I believe this was fixed in devel but not ported to release.

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Looks like has already been brought up: https://support.bioconductor.org/p/117808.

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@james-w-macdonald-5106
Last seen 2 days ago
United States

No, this was fixed in release as well. Just not all releases. Only the current one.

We don't support old releases, so if you are stuck using Bioc3.8, you'll likely have to get the sources and then emulate the changes that Herve made. Assuming of course that there aren't other breaking changes.

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