Error in minimum.spanning.tree(gp) : d_indheap reserve failed, Out of memory

Greetings to you.

Firstly, I would like to thank you for creating this wonderful tool.

I am trying to use monocle 2 for performing pseudotime analysis for 10x scRNA-Seq libraries.

If I run the test with 25K cells, it runs smoothly but takes long time (~45 hrs). However, when the number of cells increases to 32K cells, the analysis crashes and the error displayed is:

"Error in minimum.spanning.tree(gp) : At heap.c:560 : d_indheap reserve failed, Out of memory"

The scripts i used are as follows:

cellranger_pipestance_path <- "/home/user1/10x_libraries/" gbm <- load_cellranger_matrix(cellranger_pipestance_path) fd <- fData(gbm) colnames(fd)[2] <- "gene_short_name" gbm_cds <- newCellDataSet(exprs(gbm), phenoData = new("AnnotatedDataFrame", data = > pData(gbm)), featureData = new("AnnotatedDataFrame", data = fd), lowerDetectionLimit = 0.5, expressionFamily = negbinomial.size()) gbm_cds <- estimateSizeFactors(gbm_cds) gbm_cds <- estimateDispersions(gbm_cds) gbm_cds <- detectGenes(gbm_cds, min_expr = 0.1) expressed_genes <- row.names(subset(fData(gbm_cds), num_cells_expressed >= 10));diff_test_res <- differentialGeneTest(gbm_cds[expressed_genes,], fullModelFormulaStr = "~Size_Factor") ordering_genes <- row.names (subset(diff_test_res, qval < 0.01)) gbm_cds <- setOrderingFilter(gbm_cds, ordering_genes) gbm_cds <- reduceDimension(gbm_cds, max_components = 2, method = 'DDRTree', cores = 10);gbm_cds <- orderCells(gbm_cds)

My guess is that it is crashing while the "reduceDimensions" script is running.

My session info is as follows: R version 3.4.1 (2017-06-30) Platform: x86_64-redhat-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

Matrix products: default BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so

locale: [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C
[3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8
[5] LC_MONETARY=en_US.utf8 LC_MESSAGES=en_US.utf8
[7] LC_PAPER=en_US.utf8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C

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

other attached packages: [1] cellrangerRkit_2.0.0 Rmisc_1.5 plyr_1.8.4
[4] lattice_0.20-35 bit64_0.9-7 bit_1.1-12
[7] RColorBrewer_1.1-2 monocle_2.6.1 DDRTree_0.1.5
[10] irlba_2.3.1 VGAM_1.0-4 ggplot2_2.2.1
[13] Biobase_2.38.0 BiocGenerics_0.24.0 Matrix_1.2-12

loaded via a namespace (and not attached): [1] slam_0.1-42 reshape2_1.4.3 rhdf5_2.22.0
[4] colorspace_1.3-2 fastICA_1.2-1 viridisLite_0.2.0
[7] rlang_0.1.6 pillar_1.0.1 glue_1.2.0
[10] HSMMSingleCell_0.112.0 bindrcpp_0.2 matrixStats_0.52.2
[13] bindr_0.1 zlibbioc_1.24.0 stringr_1.2.0
[16] munsell_0.4.3 combinat_0.0-8 gtable_0.2.0
[19] Rcpp_0.12.14 scales_0.5.0 limma_3.34.5
[22] densityClust_0.3 FNN_1.1 gridExtra_2.3
[25] RANN_2.5.1 stringi_1.1.6 Rtsne_0.13
[28] qlcMatrix_0.9.5 dplyr_0.7.4 ggrepel_0.7.0
[31] grid_3.4.1 tools_3.4.1 magrittr_1.5
[34] lazyeval_0.2.1 tibble_1.4.1 cluster_2.0.6
[37] pkgconfig_2.0.1 pheatmap_1.0.8 data.table_1.10.4-3
[40] assertthat_0.2.0 viridis_0.4.0 R6_2.2.2
[43] igraph_1.1.2 compiler_3.4.1

Could you kindly help me rectify the issue?

Thank you.

Best Wishes,

Chadi

cole-trapnell-lab / monocle-release

Error in minimum.spanning.tree(gp) : d_indheap reserve failed, Out of memory #102