I was running a set of command lines of ChAMP (see below) to normalize methylation beta values from Illumina 450K methylation arrays for 93 individuals. After running for about 3 days, the run stopped with this error message:
"Error: C stack usage 265532545 is too close to the limit"
Anyone knows what the problem is and what is the solution?
Thank you for your help!
Chao
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library(ChAMP)
testDir=champ.load(directory = getwd(), methValue = "B", resultsDir = paste(getwd(),
"resultsChamp", sep = "/"), filterXY = TRUE, filterDetP = TRUE, detPcut = 0.01)
myLoad <- champ.load(directory = testDir)
myNorm <- champ.norm()
batchNorm <- champ.runCombat()
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error log:
Loading required package: minfi
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from ‘package:stats’:
IQR, mad, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, Map, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unlist, unsplit
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: lattice
Loading required package: GenomicRanges
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biostrings
Loading required package: XVector
Loading required package: bumphunter
Loading required package: foreach
Loading required package: iterators
Loading required package: locfit
locfit 1.5-9.1 2013-03-22
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Loading required package: ChAMPdata
Loading required package: Illumina450ProbeVariants.db
Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
2: 'rgl_init' failed, running with rgl.useNULL = TRUE
3: replacing previous import ‘limma::ebayes’ by ‘RPMM::ebayes’ when loading ‘ChAMP’
4: replacing previous import ‘plyr::desc’ by ‘IRanges::desc’ when loading ‘ChAMP’
5: replacing previous import ‘wateRmelon::colnames’ by ‘IRanges::colnames’ when loading ‘ChAMP’
Loading data from /cluster/shared/clai04/A2_Champ_norm
Creating results directory. Results will be saved in /cluster/shared/clai04/A2_Champ_norm/resultsChamp
Loading required package: IlluminaHumanMethylation450kmanifest
The fraction of failed positions per sample:
Filtering probes with a detection p-value above 0.01 in one or more samples has removed 3666 probes from the analysis. If a large number of probes have been removed, ChAMP suggests you look at the failedSample.txt file to identify potentially bad samples.
Filtering probes with a beadcount <3 in at least 5% of samples, has removed 1370 from the analysis.
Filtering probes with SNPs as identified in Nordlund et al, has removed 28566 from the analysis.
Filtering probes that align to multiple locations as identified in Nordlund et al, has removed 8451 from the analysis.
Filtering probes on the X or Y chromosome has removed 11122 from the analysis.
Zeros in your dataset have been replaced with 0.000001
Cluster image is not saved when the number of samples exceeds 60.
The analysis will proceed with 432337 probes and 93 samples.
Error: C stack usage 265532545 is too close to the limit
Execution halted
