Question: "error: C stack usage 265532545 is too close to the limit" with running ChAMP
0
gravatar for chaoqiang.lai
3.4 years ago by
chaoqiang.lai0 wrote:

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

________________________________________________

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()

__________________________________

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

champ • 748 views
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