Hello,

I am trying to make export files from WGCNA to Cytoscape for network analysis. I have 40 traits. WGCNA analysis identified 57 modules. I want to make a network figure using Cytoscape for all the traits how they are connected. I tried following code in HPC:

lnames = load(file = "dataInput.RData"); 
lnames=load(file = "SignedHybrid-networkConstruction-auto.RData");
softPower <- 7 ;
adjacency <- adjacency(datExpr, power = softPower) ;
TOM <- TOMsimilarity(adjacency) ;
modules = c("bisque4","black","blue","blue2","coral1","coral2","cyan","darkgrey","darkmagenta","darkred","darkseagreen4","darkslateblue","darkturquoise","darkviolet","firebrick4","green","greenyellow","grey","grey60","honeydew1","indianred4","ivory","lavendarblush3","lightcoral","lightcyan1","lightgreen","lightpink4","magenta","maroon","mediumorchid","mediumpurple2","mediumpurple3","navajowhite2","orangered4","palevioletred3","pink","plum1","plum2","plum3","purple","red","royalblue","salmon2","salmon4","skyblue","skyblue1","skyblue3","tan","thistle1 ","thistle2 ","thistle3","turquoise","violet","violetred","white","yellow","yellow4")
probes = colnames(datExpr) 
inModule = is.finite(match(moduleColors, modules));
modProbes = probes[inModule];
modTOM = TOM[inModule, inModule];
dimnames(modTOM) = list(modProbes, modProbes)
cyt = exportNetworkToCytoscape(modTOM,
                               edgeFile = paste("CytoscapeInput-edges0-", paste(modules, collapse="-"), ".txt", sep=""),
                               nodeFile = paste("CytoscapeInput-nodes0-", paste(modules, collapse="-"), ".txt", sep=""),
                               weighted = TRUE,
                               threshold = 0,
                               nodeNames = modProbes,
                               nodeAttr = moduleColors[inModule]);

But it gives error:

/apps/R/3.6/bin/launch_r: line 3:  3725 Killed singularity exec -B /apps,/opt/slurm,/var/run/munge:/run/munge "${HPC_SINGULARITY_IMAGE}" "$@"

You gave way too little info - is this on a cluster? Do you have a log or R output file that shows where exactly the script was aborted? How big is the data? In my experience, jobs run on a cluster get killed mostly because they start consuming more resources than they requested. In this case the offender may be RAM, you may be trying to export a network to cytoscape that is too large (has too many genes).