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Hi,
I'm running MEDIPS package to analyze methylation sequencing data. I
have many samples (from the same source and preprocessed the same way)
and some of them are performing without problems but for some there is
an error with segfault during the methylProfiling step. For some of
the problematic samples it helps when I manually reload the saved
normalized data object and rerun the code interactively but for one of
the samples I still get the same error.
The code, error and session info are given below. I would be very
grateful for any help!
genome <- c("BSgenome.Hsapiens.UCSC.hg19")
pgenome <- "hg19"
library(BSgenome.Hsapiens.UCSC.hg19)
coverage.resolution <- 50
smoothing.extension <- 400
dat <- MEDIPS.readAlignedSequences(BSgenome=genome, file=paste(aDir,
"/MEDIPS_input/",samples[i], "_MEDIPS-input.tsv", sep=""))
dat <- MEDIPS.genomeVector(data=dat,
bin_size=as.numeric(coverage.resolution),
extend=as.numeric(smoothing.extension))
dat <- MEDIPS.getPositions(data=dat, pattern="CG")
dat <- MEDIPS.couplingVector(data=dat,
fragmentLength=as.numeric(fragment.length), func="count")
dat <- MEDIPS.normalize(data=dat)
roisFile <- paste(aDir, "/promoter_rois.xls", sep="")
if(!file.exists(roisFile)){
library(rtracklayer)
session <- browserSession()
genome(session) <- pgenome
query <- ucscTableQuery(session, "refGene")
refGene <- getTable(query)
sta <- refGene$txStart
sta[refGene$strand=="+"] <- sta[refGene$strand=="+"]-1000
sta[refGene$strand=="-"] <- sta[refGene$strand=="-"]-500
sto <- refGene$txStart
sto[refGene$strand=="+"] <- sta[refGene$strand=="+"]+500
sto[refGene$strand=="-"] <- sta[refGene$strand=="-"]+1000
rois <- unique(data.frame(refGene$chrom, sta, sto,
make.unique(as.character(refGene$name))))
write.table(rois, file=roisFile, sep="\t", quote=F, col.names=F,
row.names=F)
rois <- read.table(roisFile, sep="\t", as.is=T)
colnames(rois) <- c("refGene.chrom", "sta", "sto", "refGene.name")
frames <- MEDIPS.methylProfiling(data1=dat, ROI_file=roisFile,
math=mean, select=2)
Preprocessing...
Reading ROIs...
Extract data according to given ROI...
Methylation profile will be calculated on the ROI data set
Analysed 39041 / 41310
*** caught segfault ***
address 0x2aca1311f900, cause 'memory not mapped'
Traceback:
1: .Call("roiprofile", input, as.numeric(select), as.matrix(ROI2),
as.integer(chr_binposition), data1, data2, environment(wilcox.test),
wilcox.test, environment(var), var, environment(math), math,
t.test, environment(t.test), as.numeric(factor(chr_names(data1))))
2: withCallingHandlers(expr, warning = function(w)
invokeRestart("muffleWarning"))
3: suppressWarnings(.Call("roiprofile", input, as.numeric(select),
as.matrix(ROI2), as.integer(chr_binposition), data1, data2,
environment(wilcox.test), wilcox.test, environment(var), var,
environment(math), math, t.test, environment(t.test),
as.numeric(factor(chr_names(data1)))))
4: MEDIPS.methylProfiling(data1 = dat, ROI_file = roisFile, math =
mean, select = 2)
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection:
-- output of sessionInfo():
R version 2.14.0 (2011-10-31)
Platform: x86_64-redhat-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] MEDIPS_1.4.0
BSgenome.Hsapiens.UCSC.hg19_1.3.17
[3] BSgenome_1.22.0 Biostrings_2.22.0
[5] GenomicRanges_1.6.4 IRanges_1.12.5
loaded via a namespace (and not attached):
[1] gtools_2.6.2
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