runSCENIC_2_createRegulons(scenicOptions) cannot proceed after scoring database (don't know if it is really running)

[parkjooyoung99]

<--

downsampled <- readRDS('./ad_seurat_fastmnn_fibro_downsampled.rds')

cellInfo <- data.frame(seuratCluster=Idents(downsampled))
sce <- as.SingleCellExperiment(downsampled)
exprMat <- as.matrix(downsampled@assays$RNA@counts)

scenicOptions <- readRDS('./scenic/scenicOptions.Rds')

### Co-expression network
genesKept <- geneFiltering(exprMat, scenicOptions)
exprMat_filtered <- exprMat[genesKept, ]
runCorrelation(exprMat_filtered, scenicOptions)
exprMat_filtered_log <- log2(exprMat_filtered+1) 
runGenie3(exprMat_filtered_log, scenicOptions)

### Build and score the GRN 
scenicOptions@settings$verbose <- TRUE
scenicOptions@settings$nCores <- 5
scenicOptions@settings$seed <- 123

exprMat_log <- log2(exprMat+1)
runSCENIC_1_coexNetwork2modules(scenicOptions)
runSCENIC_2_createRegulons(scenicOptions) 
runSCENIC_3_scoreCells(scenicOptions, exprMat_log)

-->

i am trying to run the above code which is a code of SCENIC 1.1.2 rmd file. i have only 400 cells so it does not have to consume more than a day for step 2 but it is running for over a day,, my r version is 4.2.0

If you need more information, please let me know. Thank you

[parkjooyoung99]

scenicOptions.Rds.zip ad_seurat_fastmnn_fibro_downsampled.rds.zip

these are my data

[tfguinan]

Hi there, are you running this in R studio by any chance?

The authors recommend using an R console or HPC for GENIE3, perhaps this would help with runSCENIC_2...?