RStudio crashing with convertFormat - Anndata to Seurat

[sarakn97]

I am working on a remote server and activated a conda environment : scRNAsaran. I am running the convertFormat command shown below and it will run for 15 minutes before my Rstudio session crashes unexpectedly so I am unsure of what is happening. My session info is posted below. Any suggestions?

ibrary(anndata)
library(reticulate)
library(sceasy)
loompy <- reticulate::import('loompy')
use_condaenv('scRNAsaran')

ad <- read_h5ad("./t-cells.h5ad")
sceasy::convertFormat("./t-cells.h5ad", from="anndata", to="seurat",
                      outFile='./tcells.rds')

R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.5 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /home/saran/.local/share/r-miniconda/envs/r-reticulate/lib/libmkl_rt.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               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    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] sceasy_0.0.7       reticulate_1.20    anndata_0.7.5.2    SeuratObject_4.0.2 Seurat_4.0.3      

loaded via a namespace (and not attached):
  [1] nlme_3.1-152            matrixStats_0.63.0-9003 spatstat.sparse_2.0-0   RcppAnnoy_0.0.19       
  [5] RColorBrewer_1.1-2      httr_1.4.2              sctransform_0.3.3       tools_4.1.0            
  [9] utf8_1.2.2              R6_2.5.0                irlba_2.3.3             rpart_4.1-15           
 [13] KernSmooth_2.23-20      uwot_0.1.10             mgcv_1.8-35             DBI_1.1.1              
 [17] lazyeval_0.2.2          colorspace_2.0-2        tidyselect_1.1.1        gridExtra_2.3          
 [21] compiler_4.1.0          plotly_4.9.4.1          scales_1.1.1            lmtest_0.9-38          
 [25] spatstat.data_2.1-0     ggridges_0.5.3          pbapply_1.5-0           rappdirs_0.3.3         
 [29] goftest_1.2-2           stringr_1.4.0           digest_0.6.27           spatstat.utils_2.2-0   
 [33] pkgconfig_2.0.3         htmltools_0.5.1.1       parallelly_1.27.0       fastmap_1.1.0          
 [37] htmlwidgets_1.5.3       rlang_0.4.11            shiny_1.6.0             generics_0.1.0         
 [41] zoo_1.8-9               jsonlite_1.7.2          ica_1.0-2               dplyr_1.0.7            
 [45] magrittr_2.0.1          patchwork_1.1.1         Matrix_1.3-3            Rcpp_1.0.7             
 [49] munsell_0.5.0           fansi_0.5.0             abind_1.4-5             lifecycle_1.0.0        
 [53] stringi_1.7.3           MASS_7.3-54             Rtsne_0.15              plyr_1.8.6             
 [57] grid_4.1.0              parallel_4.1.0          listenv_0.8.0           promises_1.2.0.1       
 [61] ggrepel_0.9.1           crayon_1.4.1            miniUI_0.1.1.1          deldir_0.2-10          
 [65] lattice_0.20-44         cowplot_1.1.1           splines_4.1.0           tensor_1.5             
 [69] pillar_1.6.2            igraph_1.2.6            spatstat.geom_2.2-2     future.apply_1.7.0     
 [73] reshape2_1.4.4          codetools_0.2-18        leiden_0.3.9            glue_1.4.2             
 [77] data.table_1.14.0       png_0.1-7               vctrs_0.3.8             httpuv_1.6.1           
 [81] gtable_0.3.0            RANN_2.6.1              purrr_0.3.4             spatstat.core_2.3-0    
 [85] polyclip_1.10-0         tidyr_1.1.3             scattermore_0.7         future_1.21.0          
 [89] assertthat_0.2.1        ggplot2_3.3.5           mime_0.11               xtable_1.8-4           
 [93] later_1.2.0             survival_3.2-11         viridisLite_0.4.0       tibble_3.1.3           
 [97] cluster_2.1.2           globals_0.14.0          fitdistrplus_1.1-5      ellipsis_0.3.2         
[101] ROCR_1.0-11  

[prete]

How large is the file? Is it possible that your remote server is crashing because it's running out of memory?