Issue with SeuratObject version leads to different numbers of observation from FindAllMarkers

[eunksung]

Since I updated Seurat from v4 to v5, I kept getting this error message when I was loading Seurat:
library(Seurat)

Loading required package: SeuratObject
Loading required package: sp
‘SeuratObject’ was built under R 4.3.1 but the current version is 4.3.3; it is
recomended that you reinstall ‘SeuratObject’ as the ABI for R may have changed
‘SeuratObject’ was built with package ‘Matrix’ 1.6.3 but the current version is
1.6.5; it is recomended that you reinstall ‘SeuratObject’ as the ABI for ‘Matrix’ may
have changed

When I ran FindAllMarkers after PrepSCTFindMarkers, the number of observation was changed from 7,141 to 46,367.
This is the code that I used:
ALL.MARKERS.WNN <- FindAllMarkers(seg_status, assay = "SCT", recorrect_umi = FALSE)

My previous version of Seurat and SeuratObject was 4.4.0 and 4.1.4, respectively. The Matrix version was 1.6-5.

I deleted SeuratObject and Matrix package and re-install, and I restarted R whenever I deleted or re-installed them.
I also deleted Seurat and Signac and re-installed them, but it kept giving me the same error.
I even uninstalled R and RStudio and re-downloaded them. After that, I installed Seurat and Signac, non other packages. However, I am still getting same error.

I tried to update my Seurat object. The version of my Seurat object (CF_MultiModal_WNN) was 4.1.4:
seg_status@version

‘4.1.4’

I used this code to update the object:
seg_status <- UpdateSeuratObject(seg_status)

Validating object structure
Updating object slots
Ensuring keys are in the proper structure
Updating matrix keys for DimReduc ‘pca’
Updating matrix keys for DimReduc ‘umap’
Updating matrix keys for DimReduc ‘lsi’
Updating matrix keys for DimReduc ‘umap.atac’
Updating matrix keys for DimReduc ‘harmony’
Updating matrix keys for DimReduc ‘wnn.umap’
Ensuring keys are in the proper structure
Ensuring feature names don't have underscores or pipes
Updating slots in RNA
Updating slots in ATAC
Updating slots in SCT
Updating slots in integrated
Updating slots in integrated_nn
Setting default assay of integrated_nn to integrated
Updating slots in integrated_snn
Setting default assay of integrated_snn to integrated
Updating slots in ATAC_nn
Setting default assay of ATAC_nn to ATAC
Updating slots in ATAC_snn
Setting default assay of ATAC_snn to ATAC
Updating slots in wknn
Cannot find wknn in the object, setting default assay of wknn to ATAC
Updating slots in wsnn
Cannot find wsnn in the object, setting default assay of wsnn to ATAC
Updating slots in pca
Updating slots in umap
Setting umap DimReduc to global
Updating slots in lsi
Updating slots in umap.atac
Setting umap.atac DimReduc to global
Updating slots in harmony
Updating slots in wnn.umap
Setting wnn.umap DimReduc to global
No assay information could be found for FindIntegrationAnchors
No assay information could be found for withCallingHandlers
Setting assay used for ScaleData.integrated to integrated
Setting assay used for RunPCA.integrated to integrated
Setting assay used for FindNeighbors.integrated.pca to integrated
Setting assay used for RunUMAP.integrated.pca to integrated
Setting assay used for RunUMAP.ATAC.lsi to ATAC
Setting assay used for RunUMAP.ATAC.harmony to ATAC
Setting assay used for FindNeighbors.ATAC.harmony to ATAC
No assay information could be found for FindModalityWeights
No assay information could be found for FindMultiModalNeighbors
Setting assay used for RunUMAP.ATAC.pca to integrated
No assay information could be found for FindClusters
Validating object structure for Assay ‘RNA’
Validating object structure for ChromatinAssay ‘ATAC’
Validating object structure for SCTAssay ‘SCT’
Validating object structure for Assay ‘integrated’
Validating object structure for Graph ‘integrated_nn’
Validating object structure for Graph ‘integrated_snn’
Validating object structure for Graph ‘ATAC_nn’
Validating object structure for Graph ‘ATAC_snn’
Validating object structure for Graph ‘wknn’
Validating object structure for Graph ‘wsnn’
Validating object structure for DimReduc ‘pca’
Validating object structure for DimReduc ‘umap’
Validating object structure for DimReduc ‘lsi’
Validating object structure for DimReduc ‘umap.atac’
Validating object structure for DimReduc ‘harmony’
Validating object structure for DimReduc ‘wnn.umap’
Object representation is consistent with the most current Seurat version
Warning messages:
1: Adding a command log without an assay associated with it
2: Adding a command log without an assay associated with it
3: Adding a command log without an assay associated with it
4: Adding a command log without an assay associated with it
5: Adding a command log without an assay associated with it

The version of the object changed to 5.0.1, but this didn't help me to solve the issue.

This is my sessionInfo:

R version 4.3.3 (2024-02-29)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.4

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0

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

time zone: US/Pacific
tzcode source: internal

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

other attached packages:
[1] Seurat_5.0.3 SeuratObject_5.0.1 sp_2.1-3

loaded via a namespace (and not attached):
[1] deldir_2.0-4 pbapply_1.7-2 gridExtra_2.3
[4] rlang_1.1.3 magrittr_2.0.3 RcppAnnoy_0.0.22
[7] matrixStats_1.2.0 ggridges_0.5.6 compiler_4.3.3
[10] spatstat.geom_3.2-9 png_0.1-8 vctrs_0.6.5
[13] reshape2_1.4.4 stringr_1.5.1 pkgconfig_2.0.3
[16] fastmap_1.1.1 utf8_1.2.4 promises_1.2.1
[19] purrr_1.0.2 jsonlite_1.8.8 goftest_1.2-3
[22] later_1.3.2 spatstat.utils_3.0-4 irlba_2.3.5.1
[25] parallel_4.3.3 cluster_2.1.6 R6_2.5.1
[28] ica_1.0-3 stringi_1.8.3 RColorBrewer_1.1-3
[31] spatstat.data_3.0-4 reticulate_1.35.0 parallelly_1.37.1
[34] lmtest_0.9-40 scattermore_1.2 Rcpp_1.0.12
[37] tensor_1.5 future.apply_1.11.2 zoo_1.8-12
[40] sctransform_0.4.1 httpuv_1.6.15 Matrix_1.6-5
[43] splines_4.3.3 igraph_2.0.3 tidyselect_1.2.1
[46] rstudioapi_0.16.0 abind_1.4-5 spatstat.random_3.2-3
[49] codetools_0.2-19 miniUI_0.1.1.1 spatstat.explore_3.2-7
[52] listenv_0.9.1 lattice_0.22-5 tibble_3.2.1
[55] plyr_1.8.9 shiny_1.8.1 ROCR_1.0-11
[58] Rtsne_0.17 future_1.33.2 fastDummies_1.7.3
[61] survival_3.5-8 polyclip_1.10-6 fitdistrplus_1.1-11
[64] pillar_1.9.0 KernSmooth_2.23-22 plotly_4.10.4
[67] generics_0.1.3 RcppHNSW_0.6.0 ggplot2_3.5.0
[70] munsell_0.5.0 scales_1.3.0 globals_0.16.3
[73] xtable_1.8-4 glue_1.7.0 pheatmap_1.0.12
[76] lazyeval_0.2.2 tools_4.3.3 data.table_1.15.2
[79] RSpectra_0.16-1 RANN_2.6.1 leiden_0.4.3.1
[82] dotCall64_1.1-1 cowplot_1.1.3 grid_4.3.3
[85] tidyr_1.3.1 colorspace_2.1-0 nlme_3.1-164
[88] patchwork_1.2.0 cli_3.6.2 spatstat.sparse_3.0-3
[91] spam_2.10-0 fansi_1.0.6 viridisLite_0.4.2
[94] dplyr_1.1.4 uwot_0.1.16 gtable_0.3.4
[97] digest_0.6.35 progressr_0.14.0 ggrepel_0.9.5
[100] htmlwidgets_1.6.4 htmltools_0.5.8 lifecycle_1.0.4
[103] httr_1.4.7 mime_0.12 MASS_7.3-60.0.1