Issue merging SCTransformed Seurat Objects

[genome2020]

I am trying to merge a list of SCTransformed Seurat objects. However, I am getting the following error:

Error in FetchResidualSCTModel(object = object, assay = assay, umi.assay = umi.assay, : object 'chunk_size' not found

Here is the command I used:

all_sample_sct <- merge(x = sample.list_sct[[1]], y = sample.list_sct[2:length(sample.list_sct)], merge.data=TRUE)

I tried the 'Merge_Seurat_List' function from the scCustomize pacakge. However, I am getting the same issue.

Could you please help? The code worked in previous versions of R (v.4.1.3 and 4.2.1) without any issues. I am only seeing this issue now.

sessionInfo() R version 4.3.1 (2023-06-16) Platform: x86_64-conda-linux-gnu (64-bit) Running under: Red Hat Enterprise Linux Server 7.9 (Maipo)

Matrix products: default BLAS/LAPACK: /sysapps/cluster/software/Anaconda3/2023.07-2/envs/R-4.3.1/lib/libopenblasp-r0.3.21.so; LAPACK version 3.9.0

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

time zone: America/Detroit tzcode source: system (glibc)

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

other attached packages: [1] MAST_1.26.0 SingleCellExperiment_1.22.0 [3] SummarizedExperiment_1.30.2 GenomicRanges_1.52.1
[5] GenomeInfoDb_1.36.4 IRanges_2.34.1
[7] S4Vectors_0.38.2 MatrixGenerics_1.12.3
[9] matrixStats_1.2.0 multtest_2.56.0
[11] Biobase_2.60.0 BiocGenerics_0.46.0
[13] harmony_1.0.1 Rcpp_1.0.12
[15] dplyr_1.1.4 scCustomize_2.1.2
[17] RColorBrewer_1.1-3 ggplot2_3.5.0
[19] patchwork_1.2.0 SeuratDisk_0.0.0.9020
[21] Seurat_4.9.9.9067 SeuratObject_5.0.1
[23] sp_2.1-3

loaded via a namespace (and not attached): [1] RcppAnnoy_0.0.22 splines_4.3.1
[3] later_1.3.2 bitops_1.0-7
[5] tibble_3.2.1 R.oo_1.26.0
[7] BPCells_0.1.0 polyclip_1.10-6
[9] janitor_2.2.0 fastDummies_1.7.3
[11] lifecycle_1.0.4 globals_0.16.3
[13] lattice_0.21-8 hdf5r_1.3.10
[15] MASS_7.3-60 magrittr_2.0.3
[17] plotly_4.10.4 httpuv_1.6.15
[19] glmGamPoi_1.12.2 sctransform_0.4.0
[21] spam_2.10-0 spatstat.sparse_3.0-3
[23] reticulate_1.35.0 cowplot_1.1.3
[25] pbapply_1.7-2 lubridate_1.9.2
[27] abind_1.4-5 zlibbioc_1.46.0
[29] Rtsne_0.17 purrr_1.0.2
[31] R.utils_2.12.3 RCurl_1.98-1.14
[33] circlize_0.4.16 GenomeInfoDbData_1.2.10
[35] ggrepel_0.9.5 irlba_2.3.5.1
[37] listenv_0.9.1 spatstat.utils_3.0-4
[39] goftest_1.2-3 RSpectra_0.16-1
[41] spatstat.random_3.1-6 fitdistrplus_1.1-11
[43] parallelly_1.37.1 DelayedMatrixStats_1.22.6 [45] leiden_0.4.3.1 codetools_0.2-19
[47] DelayedArray_0.26.7 tidyselect_1.2.1
[49] shape_1.4.6 spatstat.explore_3.2-3
[51] jsonlite_1.8.8 progressr_0.14.0
[53] ggridges_0.5.6 survival_3.5-7
[55] tools_4.3.1 ica_1.0-3
[57] glue_1.7.0 gridExtra_2.3
[59] withr_3.0.0 fastmap_1.1.1
[61] fansi_1.0.6 digest_0.6.35
[63] timechange_0.2.0 R6_2.5.1
[65] mime_0.12 ggprism_1.0.4
[67] colorspace_2.1-0 scattermore_1.2
[69] tensor_1.5 spatstat.data_3.0-4
[71] R.methodsS3_1.8.2 utf8_1.2.4
[73] tidyr_1.3.1 generics_0.1.3
[75] data.table_1.15.2 httr_1.4.7
[77] htmlwidgets_1.6.4 S4Arrays_1.0.6
[79] uwot_0.1.16 pkgconfig_2.0.3
[81] gtable_0.3.4 lmtest_0.9-40
[83] XVector_0.40.0 htmltools_0.5.7
[85] dotCall64_1.1-1 scales_1.3.0
[87] png_0.1-8 snakecase_0.11.1
[89] reshape2_1.4.4 nlme_3.1-163
[91] zoo_1.8-12 GlobalOptions_0.1.2
[93] stringr_1.5.1 KernSmooth_2.23-22
[95] parallel_4.3.1 miniUI_0.1.1.1
[97] vipor_0.4.7 ggrastr_1.0.2
[99] pillar_1.9.0 grid_4.3.1
[101] vctrs_0.6.5 RANN_2.6.1
[103] promises_1.2.1 xtable_1.8-4
[105] cluster_2.1.4 beeswarm_0.4.0
[107] paletteer_1.6.0 cli_3.6.2
[109] compiler_4.3.1 rlang_1.1.3
[111] crayon_1.5.2 future.apply_1.11.1
[113] rematch2_2.1.2 plyr_1.8.9
[115] forcats_1.0.0 ggbeeswarm_0.7.2
[117] stringi_1.8.3 viridisLite_0.4.2
[119] deldir_2.0-4 munsell_0.5.0
[121] lazyeval_0.2.2 spatstat.geom_3.2-5
[123] Matrix_1.6-5 RcppHNSW_0.6.0
[125] sparseMatrixStats_1.12.2 bit64_4.0.5
[127] future_1.33.2 shiny_1.8.1
[129] ROCR_1.0-11 igraph_2.0.3
[131] bit_4.0.5

[saketkc]

Hi @genome2020, Can you update your Seurat to latest version (5.0.3) and try again? Your current version is Seurat_4.9.9.9067.