[Bioc-devel] hg19 has two mitochondrial chromosomes in Seqinfo
Tim Triche, Jr.
t|m@tr|che @end|ng |rom gm@||@com
Tue Oct 14 12:48:21 CEST 2025
Thanks Hervé!
--t
> On Oct 14, 2025, at 2:13 AM, Hervé Pagès <hpages.on.github using gmail.com> wrote:
>
> TxDb.Hsapiens.UCSC.hg19.knownGene 3.22.1 now available in BioC 3.22. With this version:
>
> library(TxDb.Hsapiens.UCSC.hg19.knownGene)
> isCircular(seqinfo(TxDb.Hsapiens.UCSC.hg19.knownGene))[c("chrM", "chrMT")]
> # chrM chrMT
> # TRUE TRUE
>
> Likely too late to have an impact on tomorrow's build report. But hopefully the affected packages will go green again on Wednesday.
>
> Cheers,
>
> H.
>
>> On 13/10/2025 16:52, Hervé Pagès wrote:
>> Hi Raymond, Tim,
>>
>> TxDb.Hsapiens.UCSC.hg19.knownGene got updated last week in BioC 3.22 to reflect the current state of UCSC track hg19.knownGene, but the new version of the package (3.22.0) does not carry the correct circularity flag for chrMT, only for chrM. This is on our end and will be addressed shortly.
>>
>> List of packages affected by this: annotatr, decompTumor2Sig, GenomicFeatures, gmapR, MutationalPatterns, OrganismDbi, ProteoDisco, and VariantTools.
>>
>> Sorry for the inconvenience.
>>
>> Best,
>> H.
>>
>>> On 13/10/2025 07:24, Raymond Cavalcante wrote:
>>> I'm sorry, I must have missed the moment where chrM and chrMT were both
>>> included, or they always were and I didn't notice it. To put a finer point
>>> on this issue, the seqinfo from Txdb is inconsistent with that from Seqinfo:
>>>
>>>> txdb = TxDb.Hsapiens.UCSC.hg19.knownGene
>>>> tx_gr = transcripts(txdb, columns = c('TXID','GENEID','TXNAME'))
>>>> seqinfo(tx_gr)[c('chrM','chrMT')]
>>> Seqinfo object with 2 sequences (1 circular) from hg19 genome:
>>> seqnames seqlengths isCircular genome
>>> chrM 16571 TRUE hg19
>>> chrMT 16569 FALSE hg19
>>>
>>> chrMT is circular from Seqinfo but not from TxDb.
>>>
>>> Thanks,
>>> Raymond
>>>
>>> --------------------
>>> Raymond Cavalcante, PhD
>>> Bioinformatics Analyst
>>> Epigenomics Core and Bioinformatics Core
>>> Biomedical Research Core Facilities
>>> University of Michigan Medical School
>>>
>>> rcavalca using umich.edu
>>> rcavalca using med.umich.edu
>>>
>>>
>>> On Sun, Oct 12, 2025 at 10:57 AM Tim Triche, Jr. <tim.triche using gmail.com>
>>> wrote:
>>>
>>>> chrM is the broken old hg19 mitogenome
>>>>
>>>> chrMT is rCRS, same as hg38 chrM
>>>>
>>>> --t
>>>>
>>>>> On Oct 12, 2025, at 12:30 PM, Raymond Cavalcante <rcavalca using umich.edu>
>>>> wrote:
>>>>> Hi,
>>>>>
>>>>> I was testing the annotatr package after fixing the ggplot2 v4 stuff,
>>>> but I
>>>>> got an error in my vignette build and discovered what I think is an error
>>>>> in the result of Seqinfo::seqinfo(genome = 'hg19').
>>>>>
>>>>> There are two mitochondrial chromosomes for hg19. This causes some
>>>>> downstream issues when merging hg19 GRanges.
>>>>>
>>>>>> Seqinfo::Seqinfo(genome='hg19')[c('chrM', 'chrMT')]
>>>>> Seqinfo object with 2 sequences (2 circular) from hg19 genome:
>>>>> seqnames seqlengths isCircular genome
>>>>> chrM 16571 TRUE hg19
>>>>> chrMT 16569 TRUE hg19
>>>>>
>>>>> I checked hg38 on a lark and it appears correct.
>>>>>
>>>>>> Seqinfo::Seqinfo(genome='hg38')[c('chrM', 'chrMT')]
>>>>> Seqinfo object with 2 sequences (1 circular) from 2 genomes (hg38, NA):
>>>>> seqnames seqlengths isCircular genome
>>>>> chrM 16569 TRUE hg38
>>>>> chrMT NA NA <NA>
>>>>>
>>>>> I'm using 0.99.2 of Seqinfo in a Bioconductor devel Docker image.
>>>>>
>>>>> My session info:
>>>>>
>>>>>> devtools::session_info()
>>>>> ─ Session info
>>>>>
>>>> ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
>>>>> setting value
>>>>> version R version 4.5.1 (2025-06-13)
>>>>> os Ubuntu 24.04.3 LTS
>>>>> system x86_64, linux-gnu
>>>>> ui X11
>>>>> language (EN)
>>>>> collate en_US.UTF-8
>>>>> ctype en_US.UTF-8
>>>>> tz Etc/UTC
>>>>> date 2025-10-12
>>>>> pandoc 3.8.1 @ /usr/bin/pandoc
>>>>> quarto 1.7.32 @ /usr/local/bin/quarto
>>>>>
>>>>> ─ Packages
>>>>>
>>>> ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
>>>>> ! package * version date (UTC) lib source
>>>>> abind 1.4-8 2024-09-12 [1] RSPM (R
>>>>> 4.5.0)
>>>>> AnnotationDbi * 1.71.1 2025-10-07 [1]
>>>>> Bioconductor 3.22 (R 4.5.1)
>>>>> AnnotationHub 3.99.6 2025-10-07 [1]
>>>>> Bioconductor 3.22 (R 4.5.1)
>>>>> VP annotatr * 1.35.1 2025-05-13 [?]
>>>>> Bioconductor 3.22 (R 4.5.0) (on disk 1.35.0)
>>>>> Biobase * 2.69.1 2025-10-07 [1]
>>>>> Bioconductor 3.22 (R 4.5.1)
>>>>> BiocFileCache 2.99.6 2025-10-07 [1]
>>>>> Bioconductor 3.22 (R 4.5.1)
>>>>> BiocGenerics * 0.55.3 2025-10-09 [1]
>>>>> Bioconductor 3.22 (R 4.5.1)
>>>>> BiocIO 1.19.0 2025-04-15 [1]
>>>>> Bioconductor 3.22 (R 4.5.0)
>>>>> BiocManager 1.30.26 2025-06-05 [1] CRAN (R
>>>>> 4.5.1)
>>>>> BiocParallel 1.43.4 2025-10-07 [1]
>>>>> Bioconductor 3.22 (R 4.5.1)
>>>>> BiocVersion 3.22.0 2025-10-07 [1]
>>>>> Bioconductor 3.22 (R 4.5.1)
>>>>> Biostrings 2.77.2 2025-10-07 [1]
>>>>> Bioconductor 3.22 (R 4.5.1)
>>>>> bit 4.6.0 2025-03-06 [1] RSPM (R
>>>>> 4.5.0)
>>>>> bit64 4.6.0-1 2025-01-16 [1] RSPM (R
>>>>> 4.5.0)
>>>>> bitops 1.0-9 2024-10-03 [1] RSPM (R
>>>>> 4.5.0)
>>>>> blob 1.2.4 2023-03-17 [1] RSPM (R
>>>>> 4.5.0)
>>>>> brio 1.1.5 2024-04-24 [1] RSPM (R
>>>>> 4.5.0)
>>>>> BSgenome 1.77.2 2025-10-07 [1]
>>>>> Bioconductor 3.22 (R 4.5.1)
>>>>> cachem 1.1.0 2024-05-16 [1] RSPM (R
>>>>> 4.5.0)
>>>>> cli 3.6.5 2025-04-23 [1] RSPM (R
>>>>> 4.5.0)
>>>>> codetools 0.2-20 2024-03-31 [2] CRAN (R
>>>>> 4.5.1)
>>>>> crayon 1.5.3 2024-06-20 [1] RSPM (R
>>>>> 4.5.0)
>>>>> curl 7.0.0 2025-08-19 [1] RSPM (R
>>>>> 4.5.0)
>>>>> DBI 1.2.3 2024-06-02 [1] RSPM (R
>>>>> 4.5.0)
>>>>> dbplyr 2.5.1 2025-09-10 [1] RSPM (R
>>>>> 4.5.0)
>>>>> DelayedArray 0.35.3 2025-10-07 [1]
>>>>> Bioconductor 3.22 (R 4.5.1)
>>>>> desc 1.4.3 2023-12-10 [1] RSPM (R
>>>>> 4.5.0)
>>>>> devtools 2.4.6 2025-10-03 [1] RSPM (R
>>>>> 4.5.0)
>>>>> dplyr 1.1.4 2023-11-17 [1] RSPM (R
>>>>> 4.5.0)
>>>>> ellipsis 0.3.2 2021-04-29 [1] RSPM (R
>>>>> 4.5.0)
>>>>> farver 2.1.2 2024-05-13 [1] RSPM (R
>>>>> 4.5.0)
>>>>> fastmap 1.2.0 2024-05-15 [1] RSPM (R
>>>>> 4.5.0)
>>>>> filelock 1.0.3 2023-12-11 [1] RSPM (R
>>>>> 4.5.0)
>>>>> fs 1.6.6 2025-04-12 [1] RSPM (R
>>>>> 4.5.0)
>>>>> generics * 0.1.4 2025-05-09 [1] RSPM (R
>>>>> 4.5.0)
>>>>> GenomeInfoDb 1.45.12 2025-10-07 [1]
>>>>> Bioconductor 3.22 (R 4.5.1)
>>>>> GenomicAlignments 1.45.4 2025-10-07 [1]
>>>>> Bioconductor 3.22 (R 4.5.1)
>>>>> GenomicFeatures * 1.61.6 2025-10-07 [1]
>>>>> Bioconductor 3.22 (R 4.5.1)
>>>>> GenomicRanges * 1.61.5 2025-10-07 [1]
>>>>> Bioconductor 3.22 (R 4.5.1)
>>>>> ggplot2 4.0.0 2025-09-11 [1] RSPM (R
>>>>> 4.5.0)
>>>>> glue 1.8.0 2024-09-30 [1] RSPM (R
>>>>> 4.5.0)
>>>>> gtable 0.3.6 2024-10-25 [1] RSPM (R
>>>>> 4.5.0)
>>>>> hms 1.1.3 2023-03-21 [1] RSPM (R
>>>>> 4.5.0)
>>>>> httr 1.4.7 2023-08-15 [1] RSPM (R
>>>>> 4.5.0)
>>>>> httr2 1.2.1 2025-07-22 [1] RSPM (R
>>>>> 4.5.0)
>>>>> IRanges * 2.43.5 2025-10-07 [1]
>>>>> Bioconductor 3.22 (R 4.5.1)
>>>>> jsonlite 2.0.0 2025-03-27 [1] RSPM (R
>>>>> 4.5.0)
>>>>> KEGGREST 1.49.2 2025-10-10 [1]
>>>>> Bioconductor 3.22 (R 4.5.1)
>>>>> lattice 0.22-7 2025-04-02 [2] CRAN (R
>>>>> 4.5.1)
>>>>> lifecycle 1.0.4 2023-11-07 [1] RSPM (R
>>>>> 4.5.0)
>>>>> magrittr 2.0.4 2025-09-12 [1] RSPM (R
>>>>> 4.5.0)
>>>>> Matrix 1.7-4 2025-08-28 [1] RSPM (R
>>>>> 4.5.0)
>>>>> MatrixGenerics 1.21.0 2025-04-15 [1]
>>>>> Bioconductor 3.22 (R 4.5.0)
>>>>> matrixStats 1.5.0 2025-01-07 [1] RSPM (R
>>>>> 4.5.0)
>>>>> memoise 2.0.1 2021-11-26 [1] RSPM (R
>>>>> 4.5.0)
>>>>> org.Hs.eg.db * 3.22.0 2025-10-11 [1]
>>>>> Bioconductor
>>>>> pillar 1.11.1 2025-09-17 [1] RSPM (R
>>>>> 4.5.0)
>>>>> pkgbuild 1.4.8 2025-05-26 [1] RSPM (R
>>>>> 4.5.0)
>>>>> pkgconfig 2.0.3 2019-09-22 [1] RSPM (R
>>>>> 4.5.0)
>>>>> pkgload 1.4.1 2025-09-23 [1] RSPM (R
>>>>> 4.5.0)
>>>>> plyr 1.8.9 2023-10-02 [1] RSPM (R
>>>>> 4.5.0)
>>>>> png 0.1-8 2022-11-29 [1] RSPM (R
>>>>> 4.5.0)
>>>>> purrr 1.1.0 2025-07-10 [1] RSPM (R
>>>>> 4.5.0)
>>>>> R6 2.6.1 2025-02-15 [1] RSPM (R
>>>>> 4.5.0)
>>>>> rappdirs 0.3.3 2021-01-31 [1] RSPM (R
>>>>> 4.5.0)
>>>>> RColorBrewer 1.1-3 2022-04-03 [1] RSPM (R
>>>>> 4.5.0)
>>>>> Rcpp 1.1.0 2025-07-02 [1] RSPM (R
>>>>> 4.5.0)
>>>>> RCurl 1.98-1.17 2025-03-22 [1] RSPM (R
>>>>> 4.5.0)
>>>>> readr 2.1.5 2024-01-10 [1] RSPM (R
>>>>> 4.5.0)
>>>>> regioneR 1.41.3 2025-10-07 [1]
>>>>> Bioconductor 3.22 (R 4.5.1)
>>>>> remotes 2.5.0 2024-03-17 [1] RSPM (R
>>>>> 4.5.0)
>>>>> reshape2 1.4.4 2020-04-09 [1] RSPM (R
>>>>> 4.5.0)
>>>>> restfulr 0.0.16 2025-06-27 [1] RSPM (R
>>>>> 4.5.1)
>>>>> rjson 0.2.23 2024-09-16 [1] RSPM (R
>>>>> 4.5.0)
>>>>> rlang 1.1.6 2025-04-11 [1] RSPM (R
>>>>> 4.5.0)
>>>>> rprojroot 2.1.1 2025-08-26 [1] RSPM (R
>>>>> 4.5.0)
>>>>> Rsamtools 2.25.3 2025-10-07 [1]
>>>>> Bioconductor 3.22 (R 4.5.1)
>>>>> RSQLite 2.4.3 2025-08-20 [1] RSPM (R
>>>>> 4.5.0)
>>>>> rstudioapi 0.17.1 2024-10-22 [1] RSPM (R
>>>>> 4.5.0)
>>>>> rtracklayer * 1.69.1 2025-10-07 [1]
>>>>> Bioconductor 3.22 (R 4.5.1)
>>>>> S4Arrays 1.9.1 2025-10-07 [1]
>>>>> Bioconductor 3.22 (R 4.5.1)
>>>>> S4Vectors * 0.47.4 2025-10-07 [1]
>>>>> Bioconductor 3.22 (R 4.5.1)
>>>>> S7 0.2.0 2024-11-07 [1] RSPM (R
>>>>> 4.5.0)
>>>>> scales 1.4.0 2025-04-24 [1] RSPM (R
>>>>> 4.5.0)
>>>>> Seqinfo * 0.99.2 2025-10-07 [1]
>>>>> Bioconductor 3.22 (R 4.5.1)
>>>>> sessioninfo 1.2.3 2025-02-05 [1] RSPM (R
>>>>> 4.5.0)
>>>>> SparseArray 1.9.1 2025-10-07 [1]
>>>>> Bioconductor 3.22 (R 4.5.1)
>>>>> stringi 1.8.7 2025-03-27 [1] RSPM (R
>>>>> 4.5.0)
>>>>> stringr 1.5.2 2025-09-08 [1] RSPM (R
>>>>> 4.5.0)
>>>>> SummarizedExperiment 1.39.2 2025-10-07 [1]
>>>>> Bioconductor 3.22 (R 4.5.1)
>>>>> testthat * 3.2.3 2025-01-13 [1] RSPM (R
>>>>> 4.5.0)
>>>>> tibble 3.3.0 2025-06-08 [1] RSPM (R
>>>>> 4.5.0)
>>>>> tidyselect 1.2.1 2024-03-11 [1] RSPM (R
>>>>> 4.5.0)
>>>>> TxDb.Hsapiens.UCSC.hg19.knownGene * 3.22.0 2025-10-11 [1]
>>>>> Bioconductor
>>>>> tzdb 0.5.0 2025-03-15 [1] RSPM (R
>>>>> 4.5.0)
>>>>> UCSC.utils 1.5.0 2025-04-17 [1]
>>>>> Bioconductor 3.22 (R 4.5.0)
>>>>> usethis 3.2.1 2025-09-06 [1] RSPM (R
>>>>> 4.5.0)
>>>>> vctrs 0.6.5 2023-12-01 [1] RSPM (R
>>>>> 4.5.0)
>>>>> withr 3.0.2 2024-10-28 [1] RSPM (R
>>>>> 4.5.0)
>>>>> XML 3.99-0.19 2025-08-22 [1] RSPM (R
>>>>> 4.5.0)
>>>>> XVector 0.49.1 2025-10-07 [1]
>>>>> Bioconductor 3.22 (R 4.5.1)
>>>>> yaml 2.3.10 2024-07-26 [1] RSPM (R
>>>>> 4.5.0)
>>>>>
>>>>> Thanks!
>>>>>
>>>>> --------------------
>>>>> Raymond Cavalcante, PhD
>>>>> Bioinformatics Analyst
>>>>> Epigenomics Core and Bioinformatics Core
>>>>> Biomedical Research Core Facilities
>>>>> University of Michigan Medical School
>>>>>
>>>>> rcavalca using umich.edu
>>>>> rcavalca using med.umich.edu
>>>>>
>>>>> [[alternative HTML version deleted]]
>>>>>
>>>>> _______________________________________________
>>>>> Bioc-devel using r-project.org mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>> [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
>>> Bioc-devel using r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
> --
> Hervé Pagès
>
> Bioconductor Core Team
> hpages.on.github using gmail.com
>
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