Monocle2 *** caught segfault ***

[elusito]

Hi, I'm trying (for the first time) to run Monocle2 on a human dataset of 60.000 cells and 14.000 genes pre-filtered using Seurat3. I accurately followed the instructions here http://cole-trapnell-lab.github.io/monocle-release/docs/ but when I try to cluster cells the following error occurs:

       my_cds <- clusterCells(cds, num_clusters = 6)

Distance cutoff calculated to 4.824363

caught segfault address 0xfffffffe22b47030, cause 'memory not mapped'

Traceback: 1: findDistValueByRowColInd(x$distance, attr(x$distance, "Size"), i, higherDensity) 2: findClusters.densityCluster(dataClust, rho = rho_threshold, delta = delta_threshold, peaks = peaks) 3: densityClust::findClusters(dataClust, rho = rho_threshold, delta = delta_threshold, peaks = peaks) 4: clusterCells(cds, num_clusters = 15)

Possible actions: 1: abort (with core dump, if enabled) 2: normal R exit 3: exit R without saving workspace 4: exit R saving workspace

I tried to run monocle2 on a toy subset of cells (around 8000) and it works perfectly. I suppose my dataset is too big. I also tried to run it on a cluster using 10 cores but without success. Can anyone help me please?

[simoncchu]

We met the similar issue: caught segfault address 0x2b1a28320040, cause 'memory not mapped'

Traceback: 1: findDistValueByRowColInd(x$distance, attr(x$distance, "Size"), i, higherDensity) 2: findClusters.densityCluster(dataClust, rho = rho_threshold, delta = delta_threshold, peaks = peaks) 3: densityClust::findClusters(dataClust, rho = rho_threshold, delta = delta_threshold, peaks = peaks) 4: clusterCells(my_cds_subset, verbose = FALSE) An irrecoverable exception occurred. R is aborting now ... /1614157616.8684932: line 8: 105707 Segmentation fault Rscript test.R

Any suggestions?

[SlatitudeChou]

Did you solve the problem? I had the same error.

[NiklasTR]

same error here. sources I found online suggest different potential fixes:

• increase available memory
• check whether the Rcpp installation was touched since you've installed the package