I am trying to export my network to cytoscape for visualization. I have a very large dataset. When I run a subset of my data on my personal computer it works just fine, making the files necessary for cytoscape. I can't run the program with my whole dataset on my PC and so I run it on my universities cluster. After about 5hr I get the error:
*** caught segfault ***
address 0x7f559183f610, cause 'memory not mapped'
Traceback:
1: .Call("tomSimilarity_call", datExpr, as.integer(corTypeC), as.integer(netwo$
2: TOMsimilarityFromExpr(datExpr, power = 3)
An irrecoverable exception occurred. R is aborting now ...
/global/opt/slurm_state/slurmd/job2756987/slurm_script: line 14: 124588 Segment$
It it a memory issue with recalculating the topo overlap? Is there a way around this? In the tutorial it says "Recalculate topological overlap if needed", what is the alternative?
the output I get is:
Allowing multi-threading with up to 40 threads.
TOM calculation: adjacency..
..will use 40 parallel threads.
Fraction of slow calculations: 0.000000
..connectivity..
The script I am running:
library(WGCNA);
options(stringsAsFactors = FALSE);
allowWGCNAThreads();
lnames = load(file = "Lda-TRAIT_dataInput.RData");
lnames=load(file = "Lda-02-networkConstruction-block.RData");
TOM = TOMsimilarityFromExpr(datExpr, power = 3);
annot = read.csv(file = "Lda_Genes_DONE.csv");
module = c("lavenderblush3", "bisque4", "mediumorchid", "darkmagenta", "grey");
probes = names(datExpr)
inModule = is.finite(match(moduleColors, modules));
modProbes = probes[inModule];
modGenes = annot$Gene_ID[match(modProbes, annot$Contig)];
modTOM = TOM[inModule, inModule];
dimnames(modTOM) = list(modProbes, modProbes)
cyt = exportNetworkToCytoscape(modTOM,
edgeFile = paste("CytoscapeInput-edges-", paste(module, collapse="-"), ".txt$
nodeFile = paste("CytoscapeInput-nodes-", paste(module, collapse="-"), ".txt$
weighted = TRUE,
threshold = 0.02,
nodeNames = modProbes,
altNodeNames = modGenes,
nodeAttr = moduleColors[inModule]);
Thank you!!
Jessica
