celldex ensembl gene annotation issue
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immuno.dh ▴ 20
@6554a238
Last seen 3.1 years ago
United States

Anyone know how I can fix this?


> ref.data <- celldex::HumanPrimaryCellAtlasData(ensembl = T)
snapshotDate(): 2021-10-18
see ?celldex and browseVignettes('celldex') for documentation
loading from cache
see ?celldex and browseVignettes('celldex') for documentation
loading from cache
snapshotDate(): 2021-10-20
loading from cache
Error: failed to load resource
  name: AH73881
  title: Ensembl 97 EnsDb for Homo sapiens
  reason: Table gene is missing required columns canonical_transcript!
SingleR celldex HumanPrimaryCellAtlasData ensembl • 3.7k views
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I met with the same issues. I intend to annotate Mus musculus.

ah <- AnnotationHub() ens.mm.98 <- query(ah, c("Mus musculus", "Ensembl", 98))[[1]]

But R console showed that

loading from cache Error: failed to load resource name: AH75036 title: Ensembl 98 EnsDb for Mus musculus reason: Table gene is missing required columns canonical_transcript!

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Also running into this issue using tximeta...

Error: failed to load resource
name: AH78783
title: Ensembl 99 EnsDb for Homo sapiens
reason: Table gene is missing required columns canonical_transcript!
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I’ve reported this also here:

ensembldb support for Ensembl's transcript_name column

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Session information?

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This is mine:

> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19043)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252 LC_NUMERIC=C                           LC_TIME=English_United States.1252    

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

other attached packages:
 [1] ensembldb_2.18.1            AnnotationFilter_1.18.0     GenomicFeatures_1.46.1      AnnotationDbi_1.56.1        DESeq2_1.34.0               SummarizedExperiment_1.24.0 Biobase_2.54.0             
 [8] MatrixGenerics_1.6.0        matrixStats_0.61.0          GenomicRanges_1.46.0        GenomeInfoDb_1.30.0         IRanges_2.28.0              S4Vectors_0.32.1            BiocGenerics_0.40.0        
[15] tximeta_1.12.0              readxl_1.3.1                ggrepel_0.9.1               forcats_0.5.1               stringr_1.4.0               dplyr_1.0.7                 purrr_0.3.4                
[22] readr_2.0.2                 tidyr_1.1.4                 tibble_3.1.5                ggplot2_3.3.5               tidyverse_1.3.1            

loaded via a namespace (and not attached):
  [1] colorspace_2.0-2              rjson_0.2.20                  ellipsis_0.3.2                XVector_0.34.0                fs_1.5.0                      rstudioapi_0.13               bit64_4.0.5                  
  [8] interactiveDisplayBase_1.32.0 fansi_0.5.0                   lubridate_1.8.0               xml2_1.3.2                    splines_4.1.2                 tximport_1.22.0               cachem_1.0.6                 
 [15] geneplotter_1.72.0            knitr_1.36                    jsonlite_1.7.2                Rsamtools_2.10.0              annotate_1.72.0               broom_0.7.10                  dbplyr_2.1.1                 
 [22] png_0.1-7                     shiny_1.7.1                   BiocManager_1.30.16           compiler_4.1.2                httr_1.4.2                    backports_1.3.0               lazyeval_0.2.2               
 [29] assertthat_0.2.1              Matrix_1.3-4                  fastmap_1.1.0                 cli_3.1.0                     later_1.3.0                   htmltools_0.5.2               prettyunits_1.1.1            
 [36] tools_4.1.2                   gtable_0.3.0                  glue_1.5.0                    GenomeInfoDbData_1.2.7        rappdirs_0.3.3                Rcpp_1.0.7                    cellranger_1.1.0             
 [43] vctrs_0.3.8                   Biostrings_2.62.0             rtracklayer_1.54.0            xfun_0.28                     rvest_1.0.2                   mime_0.12                     lifecycle_1.0.1              
 [50] restfulr_0.0.13               XML_3.99-0.8                  AnnotationHub_3.2.0           zlibbioc_1.40.0               scales_1.1.1                  vroom_1.5.5                   ProtGenerics_1.26.0          
 [57] hms_1.1.1                     promises_1.2.0.1              parallel_4.1.2                RColorBrewer_1.1-2            yaml_2.2.1                    curl_4.3.2                    memoise_2.0.0                
 [64] biomaRt_2.50.0                stringi_1.7.5                 RSQLite_2.2.8                 genefilter_1.76.0             BiocVersion_3.14.0            BiocIO_1.4.0                  filelock_1.0.2               
 [71] BiocParallel_1.28.0           rlang_0.4.12                  pkgconfig_2.0.3               bitops_1.0-7                  lattice_0.20-45               evaluate_0.14                 GenomicAlignments_1.30.0     
 [78] bit_4.0.4                     tidyselect_1.1.1              magrittr_2.0.1                R6_2.5.1                      generics_0.1.1                DelayedArray_0.20.0           DBI_1.1.1                    
 [85] pillar_1.6.4                  haven_2.4.3                   withr_2.4.2                   survival_3.2-13               KEGGREST_1.34.0               RCurl_1.98-1.5                modelr_0.1.8                 
 [92] crayon_1.4.2                  utf8_1.2.2                    BiocFileCache_2.2.0           tzdb_0.2.0                    rmarkdown_2.11                progress_1.2.2                locfit_1.5-9.4               
 [99] grid_4.1.2                    blob_1.2.2                    reprex_2.0.1                  digest_0.6.28                 xtable_1.8-4                  httpuv_1.6.3                  munsell_0.5.0
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Aaron Lun ★ 28k
@alun
Last seen 8 hours ago
The city by the bay

I don't really know what the cause might be; looks like the same error is occurring on the BioC build machines, despite the lack of any recent changes to celldex. I don't have a copy of the latest BioC release right now, but I would guess that cached versions of various EnsDb objects are not compatible with the latest ensembldb. This can be tested by running:

library(AnnotationHub)
AnnotationHub()[["AH78783"]] # should fail 
AnnotationHub()[["AH78783", force=TRUE]] # might work. or not.

If the second one also fails, then ensembldb is busted and I'll need to complain to someone.
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Thanks! Just tested and they both still fail for me – might be a problem with ensembldb then!

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I'd suggest making a new question with this example, or posting this on the ensembldb GitHub repo; otherwise the ensembldb maintainers won't see it.

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Just to add that Johannes Rainer, who kindly provides the EnsDb objects at the AnnotationHub, indicated that the field canonical_transcript has been add to the EnsDb objects starting from Ensembl release 102 onwards. In other words, you may need to use a more recent version of the EndDb object...?

See: https://github.com/jorainer/ensembldb/issues/109#issuecomment-726741705

<<added>> I noticed on this list that also the package txmeta seems to be affected by the same issue/bug... so it looks like it is an issue with ensembldb rather than the EnsDb objects?? ensembldb support for Ensembl's transcript_name column

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Johannes is aware of this and has an issue here:

https://github.com/jorainer/ensembldb/issues/122

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Hi, Michael and Aaron,

Thank you!

I tried to repeat the following codes just now.

ah <- AnnotationHub()

ens.mm.98 <- query(ah, c("Homo sapiens", "Ensembl", 98))[[1]]

ens.mm.98 <- query(ah, c("Mus musculus", "Ensembl", 98))[[1]]

But, I still get following errors.

Error: failed to load resource

name: AH75011

title: Ensembl 98 EnsDb for Homo sapiens

reason: Table gene is missing required columns canonical_transcript!

My session info is as followings

R version 4.1.1 (2021-08-10) 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.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

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

other attached packages: [1] ggvenn_0.1.9 patchwork_1.1.1 forcats_0.5.1
[4] stringr_1.4.0 dplyr_1.0.7 purrr_0.3.4
[7] readr_2.0.2 tidyr_1.1.4 tibble_3.1.5
[10] tidyverse_1.3.1 BiocParallel_1.28.0 AnnotationHub_3.2.0
[13] BiocFileCache_2.2.0 dbplyr_2.1.1 ensembldb_2.18.1
[16] AnnotationFilter_1.18.0 GenomicFeatures_1.46.1 AnnotationDbi_1.56.1
[19] scater_1.22.0 ggplot2_3.3.5 scuttle_1.4.0
[22] DropletUtils_1.14.0 SingleCellExperiment_1.16.0 SummarizedExperiment_1.24.0 [25] Biobase_2.54.0 GenomicRanges_1.46.0 GenomeInfoDb_1.30.0
[28] IRanges_2.28.0 S4Vectors_0.32.1 BiocGenerics_0.40.0
[31] MatrixGenerics_1.6.0 matrixStats_0.61.0 Matrix_1.3-4

loaded via a namespace (and not attached): [1] snow_0.4-4 readxl_1.3.1 backports_1.2.1
[4] lazyeval_0.2.2 digest_0.6.28 htmltools_0.5.2
[7] viridis_0.6.2 fansi_0.5.0 magrittr_2.0.1
[10] memoise_2.0.0 ScaledMatrix_1.2.0 tzdb_0.1.2
[13] limma_3.50.0 Biostrings_2.62.0 modelr_0.1.8
[16] R.utils_2.11.0 prettyunits_1.1.1 colorspace_2.0-2
[19] rvest_1.0.2 blob_1.2.2 rappdirs_0.3.3
[22] ggrepel_0.9.1 haven_2.4.3 crayon_1.4.2
[25] RCurl_1.98-1.5 jsonlite_1.7.2 glue_1.4.2
[28] gtable_0.3.0 zlibbioc_1.40.0 XVector_0.34.0
[31] DelayedArray_0.20.0 BiocSingular_1.10.0 Rhdf5lib_1.16.0
[34] HDF5Array_1.22.0 scales_1.1.1 DBI_1.1.1
[37] edgeR_3.36.0 Rcpp_1.0.7 viridisLite_0.4.0
[40] xtable_1.8-4 progress_1.2.2 dqrng_0.3.0
[43] bit_4.0.4 rsvd_1.0.5 httr_1.4.2
[46] ellipsis_0.3.2 pkgconfig_2.0.3 XML_3.99-0.8
[49] R.methodsS3_1.8.1 locfit_1.5-9.4 utf8_1.2.2
[52] tidyselect_1.1.1 rlang_0.4.11 later_1.3.0
[55] cellranger_1.1.0 munsell_0.5.0 BiocVersion_3.14.0
[58] tools_4.1.1 cachem_1.0.6 cli_3.0.1
[61] generics_0.1.1 RSQLite_2.2.8 broom_0.7.10
[64] fastmap_1.1.0 yaml_2.2.1 fs_1.5.0
[67] bit64_4.0.5 KEGGREST_1.34.0 sparseMatrixStats_1.6.0
[70] mime_0.12 R.oo_1.24.0 xml2_1.3.2
[73] biomaRt_2.50.0 compiler_4.1.1 rstudioapi_0.13
[76] beeswarm_0.4.0 filelock_1.0.2 curl_4.3.2
[79] png_0.1-7 interactiveDisplayBase_1.32.0 reprex_2.0.1
[82] stringi_1.7.5 lattice_0.20-44 ProtGenerics_1.26.0
[85] vctrs_0.3.8 pillar_1.6.4 lifecycle_1.0.1
[88] rhdf5filters_1.6.0 BiocManager_1.30.16 BiocNeighbors_1.12.0
[91] bitops_1.0-7 irlba_2.3.3 httpuv_1.6.3
[94] rtracklayer_1.54.0 R6_2.5.1 BiocIO_1.4.0
[97] promises_1.2.0.1 gridExtra_2.3 vipor_0.4.5
[100] assertthat_0.2.1 rhdf5_2.38.0 rjson_0.2.20
[103] withr_2.4.2 GenomicAlignments_1.30.0 Rsamtools_2.10.0
[106] GenomeInfoDbData_1.2.7 parallel_4.1.1 hms_1.1.1
[109] beachmat_2.10.0 DelayedMatrixStats_1.16.0 lubridate_1.8.0
[112] shiny_1.7.1 ggbeeswarm_0.6.0 restfulr_0.0.13

I am very new to this. I hope to know how to annotate scRNAseq matrix.tsv file.

Thank you very much!

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This bug has been solved in ensembldb version 2.18.2, so you will need to update (you are (still) using version 2.18.1).

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Hi, Guido,

Thank you so much! I re-installed ensembldb and then it works!!

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