RStudio Crashes with LoadH5Seurat()
sarakn97 opened this issue · 1 comments
sarakn97 commented
I am trying to run the following script so I can use the h5ad file in seurat. The Convert() function successfully ran and now my RStudio crashes every-time that I run the LoadH5Seurat() command.
# scrna analysis h5ad t-cells
library(Seurat)
library(SeuratDisk)
library(devtools)
library(SeuratData)
Convert("./t-cells.h5ad", dest = "h5seurat", overwrite = TRUE)
Tcells <- LoadH5Seurat("./t-cells.h5seurat")
Tcells@meta.data
It begins to run and spits out :
Validating h5seurat file
Initializing RNA with data
.... Then it Crashes. "RStudio Session Aborted."
RStudio Session Info:
R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.3 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C
[3] LC_TIME=C.UTF-8 LC_COLLATE=C.UTF-8
[5] LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods
[7] base
other attached packages:
[1] SeuratData_0.2.2 devtools_2.4.4 usethis_2.1.6
[4] SeuratDisk_0.0.0.9020 SeuratObject_4.1.3 Seurat_4.3.0
loaded via a namespace (and not attached):
[1] Rtsne_0.16 colorspace_2.0-3
[3] deldir_1.0-6 ellipsis_0.3.2
[5] ggridges_0.5.4 fs_1.5.2
[7] rstudioapi_0.13 spatstat.data_3.0-0
[9] leiden_0.4.3 listenv_0.8.0
[11] remotes_2.4.2 ggrepel_0.9.2
[13] bit64_4.0.5 fansi_1.0.3
[15] codetools_0.2-18 splines_4.1.2
[17] cachem_1.0.6 pkgload_1.3.0
[19] polyclip_1.10-4 jsonlite_1.8.3
[21] ica_1.0-3 cluster_2.1.2
[23] png_0.1-8 uwot_0.1.14
[25] shiny_1.7.3 sctransform_0.3.5
[27] spatstat.sparse_3.0-0 compiler_4.1.2
[29] httr_1.4.4 assertthat_0.2.1
[31] Matrix_1.5-3 fastmap_1.1.0
[33] lazyeval_0.2.2 cli_3.4.1
[35] later_1.3.0 prettyunits_1.1.1
[37] htmltools_0.5.3 tools_4.1.2
[39] igraph_1.3.5 gtable_0.3.1
[41] glue_1.6.2 RANN_2.6.1
[43] reshape2_1.4.4 dplyr_1.0.10
[45] rappdirs_0.3.3 Rcpp_1.0.9
[47] scattermore_0.8 vctrs_0.5.1
[49] spatstat.explore_3.0-5 nlme_3.1-153
[51] progressr_0.11.0 lmtest_0.9-40
[53] spatstat.random_3.0-1 stringr_1.4.1
[55] ps_1.7.1 globals_0.16.2
[57] mime_0.12 miniUI_0.1.1.1
[59] lifecycle_1.0.3 irlba_2.3.5.1
[61] goftest_1.2-3 future_1.29.0
[63] MASS_7.3-54 zoo_1.8-11
[65] scales_1.2.1 promises_1.2.0.1
[67] spatstat.utils_3.0-1 parallel_4.1.2
[69] RColorBrewer_1.1-3 memoise_2.0.1
[71] reticulate_1.26 pbapply_1.6-0
[73] gridExtra_2.3 ggplot2_3.4.0
[75] stringi_1.7.8 pkgbuild_1.3.1
[77] rlang_1.0.6 pkgconfig_2.0.3
[79] matrixStats_0.63.0 lattice_0.20-45
[81] ROCR_1.0-11 purrr_0.3.5
[83] tensor_1.5 patchwork_1.1.2
[85] htmlwidgets_1.5.4 processx_3.7.0
[87] cowplot_1.1.1 bit_4.0.5
[89] tidyselect_1.2.0 parallelly_1.32.1
[91] RcppAnnoy_0.0.20 plyr_1.8.8
[93] magrittr_2.0.3 R6_2.5.1
[95] profvis_0.3.7 generics_0.1.3
[97] DBI_1.1.3 pillar_1.8.1
[99] withr_2.5.0 fitdistrplus_1.1-8
[101] survival_3.2-13 abind_1.4-5
[103] sp_1.5-1 tibble_3.1.8
[105] future.apply_1.10.0 crayon_1.5.2
[107] hdf5r_1.3.7 KernSmooth_2.23-20
[109] utf8_1.2.2 spatstat.geom_3.0-3
[111] plotly_4.10.1 urlchecker_1.0.1
[113] grid_4.1.2 data.table_1.14.6
[115] callr_3.7.1 digest_0.6.30
[117] xtable_1.8-4 tidyr_1.2.1
[119] httpuv_1.6.6 munsell_0.5.0
[121] viridisLite_0.4.1 sessioninfo_1.2.2
I set 32GB as the memory for this RStudio Session and before running ReadH5Seurat() I have only used 20%.
sarakn97 commented
Nevermind, Its a very large file so I was running out of memory and had to allot more space.