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satijalab / azimuth

A Shiny web app for mapping datasets using Seurat v4
https://satijalab.org/azimuth
GNU General Public License v3.0
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Error in `RunAzimuth`: meta.features' must have the same features as 'data' #158

Closed Zepeng-Mu closed 1 year ago

Zepeng-Mu commented 1 year ago

Hello, I encountered this error when running RunAzimuth, but I'm not sure how to trouble shoot given the message here:

Warning: Overwriting miscellanous data for model
Warning: Adding a dimensional reduction (refUMAP) without the associated assay being present
Warning: Adding a dimensional reduction (refUMAP) without the associated assay being present
detected inputs from HUMAN with id type Gene.name
reference rownames detected HUMAN with id type Gene.name
Normalizing query using reference SCT model
Warning: 273 features of the features specified were not present in both the reference query assays. 
Continuing with remaining 4727 features.
Error in validObject(object = value) : 
  invalid class "Assay" object: meta.features' must have the same features as 'data'
─ Session info ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.2.0 (2022-04-22)
 os       Ubuntu 22.04.2 LTS
 system   x86_64, linux-gnu
 ui       RStudio
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       Etc/UTC
 date     2023-06-13
 rstudio  2023.03.1+446 Cherry Blossom (server)
 pandoc   2.19.2 @ /scratch/midway3/zepengmu/miniconda3/envs/R42/bin/pandoc

─ Packages ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 package                     * version    date (UTC) lib source
 abind                         1.4-5      2016-07-21 [1] CRAN (R 4.2.0)
 annotate                      1.74.0     2022-04-26 [1] Bioconductor
 AnnotationDbi                 1.58.0     2022-04-26 [1] Bioconductor
 AnnotationFilter              1.20.0     2022-04-26 [1] Bioconductor
 ArchR                         1.0.3      2023-02-18 [1] Github (GreenleafLab/ArchR@55ab73e)
 assertthat                    0.2.1      2019-03-21 [1] CRAN (R 4.2.0)
 Azimuth                     * 0.4.6.9004 2023-06-13 [1] local
 backports                     1.4.1      2021-12-13 [1] CRAN (R 4.2.0)
 Biobase                       2.56.0     2022-04-26 [1] Bioconductor
 BiocFileCache                 2.4.0      2022-04-26 [1] Bioconductor
 BiocGenerics                  0.42.0     2022-04-26 [1] Bioconductor
 BiocIO                        1.8.0      2022-11-01 [1] Bioconductor
 BiocParallel                  1.30.4     2022-10-11 [1] Bioconductor
 biomaRt                       2.52.0     2022-04-26 [1] Bioconductor
 Biostrings                    2.64.1     2022-08-18 [1] Bioconductor
 bit                           4.0.5      2022-11-15 [1] CRAN (R 4.2.0)
 bit64                         4.0.5      2020-08-30 [1] CRAN (R 4.2.0)
 bitops                        1.0-7      2021-04-24 [1] CRAN (R 4.2.0)
 blob                          1.2.3      2022-04-10 [1] CRAN (R 4.2.0)
 broom                         1.0.1      2022-08-29 [1] CRAN (R 4.2.0)
 BSgenome                      1.66.3     2023-02-16 [1] Bioconductor
 BSgenome.Hsapiens.UCSC.hg38   1.4.5      2023-06-13 [1] Bioconductor
 cachem                        1.0.6      2021-08-19 [1] CRAN (R 4.2.0)
 callr                         3.7.3      2022-11-02 [1] CRAN (R 4.2.0)
 caTools                       1.18.2     2021-03-28 [1] CRAN (R 4.2.0)
 cellranger                    1.1.0      2016-07-27 [1] CRAN (R 4.2.0)
 circlize                      0.4.15     2022-05-10 [1] CRAN (R 4.2.0)
 cli                           3.6.1      2023-03-23 [1] CRAN (R 4.2.0)
 cluster                       2.1.4      2022-08-22 [1] CRAN (R 4.2.0)
 CNEr                          1.32.0     2022-04-26 [1] Bioconductor
 codetools                     0.2-18     2020-11-04 [1] CRAN (R 4.2.0)
 colorspace                    2.1-0      2023-01-23 [1] CRAN (R 4.2.0)
 cowplot                       1.1.1      2020-12-30 [1] CRAN (R 4.2.0)
 crayon                        1.5.2      2022-09-29 [1] CRAN (R 4.2.0)
 curl                          4.3.3      2022-10-06 [1] CRAN (R 4.2.0)
 data.table                  * 1.14.6     2022-11-16 [1] CRAN (R 4.2.0)
 DBI                           1.1.3      2022-06-18 [1] CRAN (R 4.2.0)
 dbplyr                        2.1.1      2021-04-06 [1] CRAN (R 4.2.0)
 DelayedArray                  0.22.0     2022-04-26 [1] Bioconductor
 deldir                        1.0-6      2021-10-23 [1] CRAN (R 4.2.0)
 devtools                      2.4.5      2022-10-11 [1] CRAN (R 4.2.0)
 digest                        0.6.31     2022-12-11 [1] CRAN (R 4.2.0)
 DirichletMultinomial          1.38.0     2022-04-26 [1] Bioconductor
 dotCall64                     1.0-2      2022-10-03 [1] CRAN (R 4.2.0)
 dplyr                       * 1.1.1      2023-03-22 [1] CRAN (R 4.2.0)
 DT                            0.26       2022-10-19 [1] CRAN (R 4.2.0)
 edgeR                         3.38.4     2022-08-07 [1] Bioconductor
 ellipsis                      0.3.2      2021-04-29 [1] CRAN (R 4.2.0)
 EnsDb.Hsapiens.v86            2.99.0     2023-06-13 [1] Bioconductor
 ensembldb                     2.20.2     2022-06-16 [1] Bioconductor
 fansi                         1.0.3      2022-03-24 [1] CRAN (R 4.2.0)
 fastDummies                   1.6.3      2020-11-29 [1] CRAN (R 4.2.0)
 fastmap                       1.1.0      2021-01-25 [1] CRAN (R 4.2.0)
 fastmatch                     1.1-3      2021-07-23 [1] CRAN (R 4.2.0)
 filelock                      1.0.2      2018-10-05 [1] CRAN (R 4.2.0)
 fitdistrplus                  1.1-8      2022-03-10 [1] CRAN (R 4.2.0)
 forcats                     * 0.5.2      2022-08-19 [1] CRAN (R 4.2.0)
 fs                            1.5.2      2021-12-08 [1] CRAN (R 4.2.0)
 future                        1.28.0     2022-09-02 [1] CRAN (R 4.2.0)
 future.apply                  1.9.1      2022-09-07 [1] CRAN (R 4.2.0)
 gargle                        1.2.0      2021-07-02 [1] CRAN (R 4.2.0)
 generics                      0.1.3      2022-07-05 [1] CRAN (R 4.2.0)
 GenomeInfoDb                  1.34.9     2023-02-02 [1] Bioconductor
 GenomeInfoDbData              1.2.8      2022-09-10 [1] Bioconductor
 GenomicAlignments             1.32.1     2022-07-24 [1] Bioconductor
 GenomicFeatures               1.50.2     2022-11-03 [1] Bioconductor
 GenomicRanges                 1.48.0     2022-04-26 [1] Bioconductor
 ggplot2                     * 3.4.2      2023-04-03 [1] CRAN (R 4.2.0)
 ggprism                       1.0.3      2021-06-08 [1] CRAN (R 4.2.0)
 ggrepel                       0.9.2.9999 2022-12-12 [1] Github (slowkow/ggrepel@e9bcb75)
 ggridges                      0.5.4      2022-09-26 [1] CRAN (R 4.2.0)
 ggtext                        0.1.2      2022-09-16 [1] CRAN (R 4.2.0)
 GlobalOptions                 0.1.2      2020-06-10 [1] CRAN (R 4.2.0)
 globals                       0.16.1     2022-08-28 [1] CRAN (R 4.2.0)
 glue                          1.6.2      2022-02-24 [1] CRAN (R 4.2.0)
 GO.db                         3.15.0     2022-09-10 [1] Bioconductor
 goftest                       1.2-3      2021-10-07 [1] CRAN (R 4.2.0)
 googledrive                   2.0.0      2021-07-08 [1] CRAN (R 4.2.0)
 googlesheets4                 1.0.0      2021-07-21 [1] CRAN (R 4.2.0)
 gridExtra                     2.3        2017-09-09 [1] CRAN (R 4.2.0)
 gridtext                      0.1.5      2022-09-16 [1] CRAN (R 4.2.0)
 gtable                        0.3.1      2022-09-01 [1] CRAN (R 4.2.0)
 gtools                        3.9.4      2022-11-27 [1] CRAN (R 4.2.0)
 haven                         2.5.0      2022-04-15 [1] CRAN (R 4.2.0)
 hdf5r                         1.3.8      2023-01-21 [1] CRAN (R 4.2.0)
 hms                           1.1.2      2022-08-19 [1] CRAN (R 4.2.0)
 htmltools                     0.5.4      2022-12-07 [1] CRAN (R 4.2.2)
 htmlwidgets                   1.5.4      2021-09-08 [1] CRAN (R 4.2.0)
 httpuv                        1.6.11     2023-05-11 [1] CRAN (R 4.2.3)
 httr                          1.4.4      2022-08-17 [1] CRAN (R 4.2.0)
 ica                           1.0-3      2022-07-08 [1] CRAN (R 4.2.0)
 igraph                        1.3.4      2022-07-19 [1] CRAN (R 4.2.0)
 IRanges                       2.30.1     2022-08-18 [1] Bioconductor
 irlba                         2.3.5.1    2022-10-03 [1] CRAN (R 4.2.0)
 JASPAR2020                    0.99.10    2023-06-13 [1] Bioconductor
 jsonlite                      1.8.4      2022-12-06 [1] CRAN (R 4.2.0)
 KEGGREST                      1.36.3     2022-07-12 [1] Bioconductor
 KernSmooth                    2.23-20    2021-05-03 [1] CRAN (R 4.2.1)
 later                         1.3.1      2023-05-02 [1] CRAN (R 4.2.3)
 lattice                       0.20-45    2021-09-22 [1] CRAN (R 4.2.0)
 lazyeval                      0.2.2      2019-03-15 [1] CRAN (R 4.2.0)
 leiden                        0.4.2      2022-05-09 [1] CRAN (R 4.2.0)
 lifecycle                     1.0.3      2022-10-07 [1] CRAN (R 4.2.0)
 limma                         3.52.4     2022-09-27 [1] Bioconductor
 listenv                       0.8.0      2019-12-05 [1] CRAN (R 4.2.0)
 lmtest                        0.9-40     2022-03-21 [1] CRAN (R 4.2.0)
 locfit                        1.5-9.6    2022-07-11 [1] CRAN (R 4.2.0)
 lubridate                     1.8.0      2021-10-07 [1] CRAN (R 4.2.0)
 magrittr                      2.0.3      2022-03-30 [1] CRAN (R 4.2.0)
 MASS                          7.3-58.1   2022-08-03 [1] CRAN (R 4.2.0)
 Matrix                        1.5-3      2022-11-11 [1] CRAN (R 4.2.0)
 MatrixGenerics                1.8.1      2022-06-26 [1] Bioconductor
 matrixStats                   0.63.0     2022-11-18 [1] CRAN (R 4.2.0)
 memoise                       2.0.1      2021-11-26 [1] CRAN (R 4.2.0)
 mime                          0.12       2021-09-28 [1] CRAN (R 4.2.0)
 miniUI                        0.1.1.1    2018-05-18 [1] CRAN (R 4.2.0)
 modelr                        0.1.8      2020-05-19 [1] CRAN (R 4.2.0)
 munsell                       0.5.0      2018-06-12 [1] CRAN (R 4.2.0)
 nlme                          3.1-160    2022-10-10 [1] CRAN (R 4.2.0)
 parallelly                    1.32.1     2022-07-21 [1] CRAN (R 4.2.0)
 patchwork                     1.1.2.9000 2023-02-20 [1] Github (thomasp85/patchwork@c14c960)
 pbapply                       1.7-0      2023-01-13 [1] CRAN (R 4.2.0)
 pillar                        1.8.1      2022-08-19 [1] CRAN (R 4.2.0)
 pkgbuild                      1.4.0      2022-11-27 [1] CRAN (R 4.2.0)
 pkgconfig                     2.0.3      2019-09-22 [1] CRAN (R 4.2.0)
 pkgload                       1.3.2      2022-11-16 [1] CRAN (R 4.2.0)
 plotly                        4.10.1     2022-11-07 [1] CRAN (R 4.2.0)
 plyr                          1.8.8      2022-11-11 [1] CRAN (R 4.2.0)
 plyranges                     1.13.1     2023-03-15 [1] Github (sa-lee/plyranges@c82b7eb)
 png                           0.1-8      2022-11-29 [1] CRAN (R 4.2.0)
 polyclip                      1.10-0     2019-03-14 [1] CRAN (R 4.2.0)
 poweRlaw                      0.70.6     2020-04-25 [1] CRAN (R 4.2.0)
 pracma                        2.4.2      2022-09-22 [1] CRAN (R 4.2.0)
 presto                        1.0.0      2023-06-13 [1] Github (immunogenomics/presto@31dc97f)
 prettyunits                   1.1.1      2020-01-24 [1] CRAN (R 4.2.0)
 processx                      3.8.0      2022-10-26 [1] CRAN (R 4.2.0)
 profvis                       0.3.7      2020-11-02 [1] CRAN (R 4.2.0)
 progress                      1.2.2      2019-05-16 [1] CRAN (R 4.2.0)
 progressr                     0.11.0     2022-09-02 [1] CRAN (R 4.2.0)
 promises                      1.2.0.1    2021-02-11 [1] CRAN (R 4.2.1)
 ProtGenerics                  1.28.0     2022-04-26 [1] Bioconductor
 ps                            1.7.2      2022-10-26 [1] CRAN (R 4.2.0)
 purrr                       * 1.0.1      2023-01-10 [1] CRAN (R 4.2.0)
 R.methodsS3                   1.8.2      2022-06-13 [1] CRAN (R 4.2.0)
 R.oo                          1.25.0     2022-06-12 [1] CRAN (R 4.2.0)
 R.utils                       2.12.2     2022-11-11 [1] CRAN (R 4.2.0)
 R6                            2.5.1      2021-08-19 [1] CRAN (R 4.2.0)
 RANN                          2.6.1      2019-01-08 [1] CRAN (R 4.2.0)
 rappdirs                      0.3.3      2021-01-31 [1] CRAN (R 4.2.0)
 RColorBrewer                  1.1-3      2022-04-03 [1] CRAN (R 4.2.0)
 Rcpp                          1.0.10     2023-01-22 [1] CRAN (R 4.2.0)
 RcppAnnoy                     0.0.20     2022-10-27 [1] CRAN (R 4.2.0)
 RcppHNSW                      0.4.1      2022-07-18 [1] CRAN (R 4.2.0)
 RcppRoll                      0.3.0      2018-06-05 [1] CRAN (R 4.2.0)
 RCurl                         1.98-1.9   2022-10-03 [1] CRAN (R 4.2.0)
 readr                       * 2.1.3      2022-10-01 [1] CRAN (R 4.2.0)
 readxl                        1.4.0      2022-03-28 [1] CRAN (R 4.2.0)
 remotes                       2.4.2      2021-11-30 [1] CRAN (R 4.2.0)
 reprex                        2.0.1      2021-08-05 [1] CRAN (R 4.2.0)
 reshape2                      1.4.4      2020-04-09 [1] CRAN (R 4.2.0)
 restfulr                      0.0.15     2022-06-16 [1] CRAN (R 4.2.0)
 reticulate                    1.30       2023-06-09 [1] CRAN (R 4.2.0)
 rhdf5                         2.40.0     2022-04-26 [1] Bioconductor
 rhdf5filters                  1.8.0      2022-04-26 [1] Bioconductor
 Rhdf5lib                      1.18.2     2022-05-15 [1] Bioconductor
 rjson                         0.2.21     2022-01-09 [1] CRAN (R 4.2.0)
 rlang                         1.1.0      2023-03-14 [1] CRAN (R 4.2.0)
 ROCR                          1.0-11     2020-05-02 [1] CRAN (R 4.2.0)
 Rsamtools                     2.12.0     2022-04-26 [1] Bioconductor
 RSpectra                      0.16-1     2022-04-24 [1] CRAN (R 4.2.0)
 RSQLite                       2.2.19     2022-11-24 [1] CRAN (R 4.2.0)
 rstudioapi                    0.14       2022-08-22 [1] CRAN (R 4.2.0)
 rtracklayer                   1.56.1     2022-06-23 [1] Bioconductor
 Rtsne                         0.16       2022-04-17 [1] CRAN (R 4.2.0)
 rvest                         1.0.2      2021-10-16 [1] CRAN (R 4.2.0)
 S4Vectors                     0.34.0     2022-04-26 [1] Bioconductor
 scales                        1.2.1      2022-08-20 [1] CRAN (R 4.2.0)
 scattermore                   0.8        2022-02-14 [1] CRAN (R 4.2.0)
 sctransform                   0.3.5      2022-09-21 [1] CRAN (R 4.2.0)
 seqLogo                       1.62.0     2022-04-26 [1] Bioconductor
 sessioninfo                   1.2.2      2021-12-06 [1] CRAN (R 4.2.0)
 Seurat                      * 4.9.9.9049 2023-06-12 [1] Github (satijalab/seurat@3a826c5)
 SeuratData                    0.2.2.9001 2023-06-13 [1] Github (satijalab/seurat-data@dd7d0df)
 SeuratDisk                    0.0.0.9020 2023-06-12 [1] Github (mojaveazure/seurat-disk@9b89970)
 SeuratObject                * 4.9.9.9084 2023-06-12 [1] Github (mojaveazure/seurat-object@185884a)
 shape                         1.4.6      2021-05-19 [1] CRAN (R 4.2.0)
 shiny                         1.7.4      2022-12-15 [1] CRAN (R 4.2.2)
 shinyBS                     * 0.61.1     2022-04-17 [1] CRAN (R 4.2.0)
 shinydashboard                0.7.2      2021-09-30 [1] CRAN (R 4.2.0)
 shinyjs                       2.1.0      2021-12-23 [1] CRAN (R 4.2.0)
 Signac                        1.10.0     2023-06-13 [1] Github (stuart-lab/signac@2ad6c3c)
 sp                          * 1.5-0      2022-06-05 [1] CRAN (R 4.2.0)
 spam                          2.9-1      2022-08-07 [1] CRAN (R 4.2.0)
 sparseMatrixStats             1.8.0      2022-04-26 [1] Bioconductor
 spatstat.data                 3.0-0      2022-10-21 [1] CRAN (R 4.2.0)
 spatstat.explore              3.0-6      2023-01-26 [1] CRAN (R 4.2.0)
 spatstat.geom                 3.0-6      2023-01-30 [1] CRAN (R 4.2.0)
 spatstat.random               3.1-3      2023-01-25 [1] CRAN (R 4.2.0)
 spatstat.sparse               3.0-0      2022-10-21 [1] CRAN (R 4.2.0)
 spatstat.utils                3.0-1      2022-10-19 [1] CRAN (R 4.2.0)
 stringi                       1.7.8      2022-07-11 [1] CRAN (R 4.2.0)
 stringr                     * 1.5.0      2022-12-02 [1] CRAN (R 4.2.0)
 SummarizedExperiment          1.26.1     2022-04-29 [1] Bioconductor
 survival                      3.4-0      2022-08-09 [1] CRAN (R 4.2.0)
 tensor                        1.5        2012-05-05 [1] CRAN (R 4.2.0)
 TFBSTools                     1.36.0     2022-11-01 [1] Bioconductor
 TFMPvalue                     0.0.9      2022-10-21 [1] CRAN (R 4.2.0)
 tibble                      * 3.2.1      2023-03-20 [1] CRAN (R 4.2.0)
 tidyr                       * 1.3.0      2023-01-24 [1] CRAN (R 4.2.0)
 tidyselect                    1.2.0      2022-10-10 [1] CRAN (R 4.2.0)
 tidyverse                   * 1.3.1      2021-04-15 [1] CRAN (R 4.2.0)
 tzdb                          0.3.0      2022-03-28 [1] CRAN (R 4.2.0)
 urlchecker                    1.0.1      2021-11-30 [1] CRAN (R 4.2.0)
 usethis                       2.1.6      2022-05-25 [1] CRAN (R 4.2.0)
 utf8                          1.2.2      2021-07-24 [1] CRAN (R 4.2.0)
 uwot                          0.1.14     2022-08-22 [1] CRAN (R 4.2.0)
 vctrs                         0.6.1      2023-03-22 [1] CRAN (R 4.2.0)
 viridisLite                   0.4.1      2022-08-22 [1] CRAN (R 4.2.0)
 withr                         2.5.0      2022-03-03 [1] CRAN (R 4.2.0)
 XML                           3.99-0.9   2022-02-24 [1] CRAN (R 4.2.0)
 xml2                          1.3.3      2021-11-30 [1] CRAN (R 4.2.0)
 xtable                        1.8-4      2019-04-21 [1] CRAN (R 4.2.1)
 XVector                       0.36.0     2022-04-26 [1] Bioconductor
 yaml                          2.3.6      2022-10-18 [1] CRAN (R 4.2.0)
 zlibbioc                      1.42.0     2022-04-26 [1] Bioconductor
 zoo                           1.8-10     2022-04-15 [1] CRAN (R 4.2.0)

 [1] /scratch/midway3/zepengmu/miniconda3/envs/R42/lib/R/library
Zepeng-Mu commented 1 year ago

Turned out its due to some problems with the query Seurat object.