Reduce max nodes from 50 to 45 for parallel processing

r.scripts/sc-TissueMapper.R

@@ -91,7 +91,7 @@ scCellCycle <- function(sc10x){
   genes.s <- genes.cc[1:43]
   genes.g2m <- genes.cc[44:97]
   sc10x <- NormalizeData(object=sc10x)
-  sc10x <- ScaleData(object=sc10x,display.progress=FALSE,do.par=TRUE,num.cores=50)
+  sc10x <- ScaleData(object=sc10x,display.progress=FALSE,do.par=TRUE,num.cores=45)
   sc10x <- CellCycleScoring(object=sc10x,s.genes=genes.s,g2m.genes=genes.g2m,set.ident=TRUE)
   
   postscript("./analysis/qc/cc/Ridge_cc.Raw.eps")
@@ -110,7 +110,7 @@ scCellCycle <- function(sc10x){
   plot(plot)
   dev.off()
   gc()
-  sc10x <- ScaleData(object=sc10x,vars.to.regress=c("S.Score","G2M.Score"),display.progress=FALSE,do.par=TRUE,num.cores=50)
+  sc10x <- ScaleData(object=sc10x,vars.to.regress=c("S.Score","G2M.Score"),display.progress=FALSE,do.par=TRUE,num.cores=45)
   gc()
   sc10x <- RunPCA(object=sc10x,pc.genes=c(genes.s,genes.g2m),do.print=FALSE,pcs.store=2)
   postscript("./analysis/qc/cc/PCA_cc.Norm.eps")
@@ -225,9 +225,9 @@ scPC <- function(sc10x,lx=0.15,hx=3.5,ly=0.75,cc=FALSE,pc=50,hpc=0.75,file="pre.
   if (cca==FALSE){
     gc()
     if (cc==TRUE){
-      sc10x <- ScaleData(object=sc10x,vars.to.regress=c("nUMI","percent.mito","S.Score","G2M.Score"),display.progress=FALSE,do.par=TRUE,num.cores=50)
+      sc10x <- ScaleData(object=sc10x,vars.to.regress=c("nUMI","percent.mito","S.Score","G2M.Score"),display.progress=FALSE,do.par=TRUE,num.cores=45)
     } else {
-      sc10x <- ScaleData(object=sc10x,vars.to.regress=c("nUMI","percent.mito"),display.progress=FALSE,do.par=TRUE,num.cores=50)
+      sc10x <- ScaleData(object=sc10x,vars.to.regress=c("nUMI","percent.mito"),display.progress=FALSE,do.par=TRUE,num.cores=45)
     }
     gc()
   }
@@ -982,17 +982,17 @@ scDEG <- function(sc10x,i="Lin",g.1="Epi",g.2="St",pct=0.25,t=2){
 scCCA <-  function(sc10x.1,sc10x.2,nm.1="D17",nm.2="D27",cc=FALSE){
   gc()
   if (cc==TRUE){
-    sc10x.1 <- ScaleData(object=sc10x.1,vars.to.regress=c("nUMI","percent.mito","S.Score","G2M.Score"),display.progress=FALSE,do.par=TRUE,num.cores=50)
+    sc10x.1 <- ScaleData(object=sc10x.1,vars.to.regress=c("nUMI","percent.mito","S.Score","G2M.Score"),display.progress=FALSE,do.par=TRUE,num.cores=45)
   } else {
-    sc10x.1 <- ScaleData(object=sc10x.1,vars.to.regress=c("nUMI","percent.mito"),display.progress=FALSE,do.par=TRUE,num.cores=50)
+    sc10x.1 <- ScaleData(object=sc10x.1,vars.to.regress=c("nUMI","percent.mito"),display.progress=FALSE,do.par=TRUE,num.cores=45)
   }
   gc()
   
   gc()
   if (cc==TRUE){
-    sc10x.2 <- ScaleData(object=sc10x.2,vars.to.regress=c("nUMI","percent.mito","S.Score","G2M.Score"),display.progress=FALSE,do.par=TRUE,num.cores=50)
+    sc10x.2 <- ScaleData(object=sc10x.2,vars.to.regress=c("nUMI","percent.mito","S.Score","G2M.Score"),display.progress=FALSE,do.par=TRUE,num.cores=45)
   } else {
-    sc10x.2 <- ScaleData(object=sc10x.2,vars.to.regress=c("nUMI","percent.mito"),display.progress=FALSE,do.par=TRUE,num.cores=50)
+    sc10x.2 <- ScaleData(object=sc10x.2,vars.to.regress=c("nUMI","percent.mito"),display.progress=FALSE,do.par=TRUE,num.cores=45)
   }
   gc()
   
@@ -1052,25 +1052,25 @@ scCCA <-  function(sc10x.1,sc10x.2,nm.1="D17",nm.2="D27",cc=FALSE){
 sc3CCA <-  function(sc10x.1,sc10x.2,sc10x.3,nm.1="D17",nm.2="D27",nm.3="D35",cc=FALSE){
   gc()
   if (cc==TRUE){
-    sc10x.1 <- ScaleData(object=sc10x.1,vars.to.regress=c("nUMI","percent.mito","S.Score","G2M.Score"),display.progress=FALSE,do.par=TRUE,num.cores=50)
+    sc10x.1 <- ScaleData(object=sc10x.1,vars.to.regress=c("nUMI","percent.mito","S.Score","G2M.Score"),display.progress=FALSE,do.par=TRUE,num.cores=45)
   } else {
-    sc10x.1 <- ScaleData(object=sc10x.1,vars.to.regress=c("nUMI","percent.mito"),display.progress=FALSE,do.par=TRUE,num.cores=50)
+    sc10x.1 <- ScaleData(object=sc10x.1,vars.to.regress=c("nUMI","percent.mito"),display.progress=FALSE,do.par=TRUE,num.cores=45)
   }
   gc()
   
   gc()
   if (cc==TRUE){
-    sc10x.2 <- ScaleData(object=sc10x.2,vars.to.regress=c("nUMI","percent.mito","S.Score","G2M.Score"),display.progress=FALSE,do.par=TRUE,num.cores=50)
+    sc10x.2 <- ScaleData(object=sc10x.2,vars.to.regress=c("nUMI","percent.mito","S.Score","G2M.Score"),display.progress=FALSE,do.par=TRUE,num.cores=45)
   } else {
-    sc10x.2 <- ScaleData(object=sc10x.2,vars.to.regress=c("nUMI","percent.mito"),display.progress=FALSE,do.par=TRUE,num.cores=50)
+    sc10x.2 <- ScaleData(object=sc10x.2,vars.to.regress=c("nUMI","percent.mito"),display.progress=FALSE,do.par=TRUE,num.cores=45)
   }
   gc()
   
   gc()
   if (cc==TRUE){
-    sc10x.3 <- ScaleData(object=sc10x.3,vars.to.regress=c("nUMI","percent.mito","S.Score","G2M.Score"),display.progress=FALSE,do.par=TRUE,num.cores=50)
+    sc10x.3 <- ScaleData(object=sc10x.3,vars.to.regress=c("nUMI","percent.mito","S.Score","G2M.Score"),display.progress=FALSE,do.par=TRUE,num.cores=45)
   } else {
-    sc10x.3 <- ScaleData(object=sc10x.3,vars.to.regress=c("nUMI","percent.mito"),display.progress=FALSE,do.par=TRUE,num.cores=50)
+    sc10x.3 <- ScaleData(object=sc10x.3,vars.to.regress=c("nUMI","percent.mito"),display.progress=FALSE,do.par=TRUE,num.cores=45)
   }
   gc()