Hi, I am trying to execute Preprocess_DNAmethylation function of MethylMix using R script. The aws cloud instance (c4 large,60Gb RAM)is not able to handle the high load and its failing after 4 hrs.Please let me know which kind of system configuration needed to execute successfully Preprocess_CancerSite_Methylation450k().
Rscript used:
print("starting ++++++++");
library(MethylMix);
library(parallel);
library(doParallel);
cancerSite <- "STAD";
targetDirectory <- paste0(getwd(), "/");
cl <- makeCluster(16);
registerDoParallel(cl);
t1 <- Sys.time();
print(t1) ;
METdirectories <- Download_DNAmethylation(cancerSite,targetDirectory, TRUE);
METProcessedData <- Preprocess_DNAmethylation(cancerSite,METdirectories)
print("Completed methylation preprocessed data+++++++");
# Saving methylation processed data
saveRDS(METProcessedData, file = paste0(targetDirectory, "MET_", cancerSite, "_Processed.rds"))
stopCluster(cl);
difftime(Sys.time(),t1)
# scrpt end
The log file details
Standardizing Data across genes
Fitting L/S model and finding priors
Finding nAdjusting the Data
LoadiAdjusting the Data
Loading data for 450k.
Read 0.0% of 485578 rows
Read 2.1% of 485578 rows
-----
-----
Cluster size 1761 broken into 933 828
Done cluster 933
Done cluster 828
Done cluster 1761
Done cluster 3363
Done cluster 5312
Done cluster 13325
Done cluster 31982
Done cluster 126245
Done cluster 192925
Batch correction for the cancer samples.
Reading Sample Information File
Reading Expression Data File
Found 16 batches
Found 0 covariate(s)
Standardizing Data across genes
Fitting L/S model and finding priors
Finding nonparametric adjustments
+++The log stop here.++++++++
