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aertslab / SCENIC

SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
http://scenic.aertslab.org
GNU General Public License v3.0
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Error in GENIE3 #123

Closed KabitaBaral1 closed 2 years ago

KabitaBaral1 commented 4 years ago

Hi,

I am running SCENIC on my dataset and the dataset is a big with dimension of 24110 X 28734

When I run my code, it gets stuck at GENIE3 part with the following error message:

Using 1092 TFs as potential regulators... Running GENIE3 part 1 Error in weightMatrix[regulatorNames, ] <- weightMatrix.reg[regulatorNames, : number of items to replace is not a multiple of replacement length Calls: runGenie3 -> -> -> .GENIE3 In addition: Warning message: In mclapply(argsList, FUN, mc.preschedule = preschedule, mc.set.seed = set.seed, : scheduled cores 3, 5, 8, 9, 12, 13, 14, 15, 17, 20, 21, 23, 24, 25, 30, 33, 34 , 37, 39, 41, 42, 43, 44, 46, 48, 49, 52, 54 did not deliver results, all values of the jobs will be affected Execution halted

I did check the previous issue posted with similar error and tried troubleshooting using different number of cores but that didn't work.

Could you please help me with this?

Here is my code snippet :

setwd("/home/kbaral/SCENIC/")

library("Seurat") library("RcisTarget") library("AUCell") library("GENIE3") library("SCENIC")

schwann <- readRDS("skin_nerve.rds") cellInfo <- data.frame(CellType = schwann@active.ident, SC = schwann@meta.data$c lusters, row.names = colnames(schwann)) dir.create("int") saveRDS(cellInfo, file="int/cellInfo.Rds")

colVars <- list(CellType=setNames(c("lightcoral","darkgoldenrod", "springgreen3 ", "steelblue2","magenta2"), c('skin0','nerve1','skin2','nerve3', "nerve4") ), SC= setNames(c("#04C0CC", "#EC7B70"), c("skin", "nerve"))) saveRDS(colVars, file="int/colVars.Rds")

schwann <- schwann@assays$RNA@counts schwann <- as.matrix(schwann) exprMat <- schwann dim(exprMat)

org= "hgnc" dbDir= "/home/kbaral/SCENIC/cisTarget_databases/"

scenicOptions <- initializeScenic(org= org, dbDir=dbDir, nCores=54) scenicOptions@inputDatasetInfo$datasetTitle <- "schwann_cells" scenicOptions@inputDatasetInfo$cellInfo <- "int/cellInfo.Rds" scenicOptions@inputDatasetInfo$colVars <- "int/colVars.Rds" saveRDS(scenicOptions, file="int/scenicOptions.Rds")

genesKept <- geneFiltering(exprMat, scenicOptions=scenicOptions, minCountsPerGene=3.01ncol(exprMat), minSamples=ncol(exprMat)*.01)

exprMat_filtered <- exprMat[genesKept, ] logMat <- log2(exprMat+1) saveRDS(scenicOptions, file="int/scenicOptions.Rds")

exprMat_filtered <- log2(exprMat_filtered+1) dim(exprMat_filtered) options(error = recover) set.seed(123)

runCorrelation(exprMat_filtered, scenicOptions) runGenie3(exprMat_filtered, scenicOptions) runSCENIC_1_coexNetwork2modules(scenicOptions) runSCENIC_2_createRegulons(scenicOptions) runSCENIC_3_scoreCells(scenicOptions, logMat)

Thank you

vbouther commented 4 years ago

Hello, How much memory have you allowed to the job? I had the same issue and resolved it increasing allowed memory. Hope this will work for you too!