[BioC] Caught segfault when running MEDIPS package
chavez
chavez at molgen.mpg.de
Tue Jan 10 23:53:16 CET 2012
Hi,
indeed there might be a problem with a region of interest included in your
ROI file ('rois'). The MEDIPS output indicates that there is a problem with
the given roi at line 39041 (see your output below). It might be worthwhile
to check this roi (or the immediate neighbours) for consistency.
It is likely that
- the roi is of length 0 or of negative length (i.e. if start position <=
stop position)
- the genomic coordinates of the roi are outside of the length of the
chromosome
- the chromosome of the roi is not represented by the MeDIP-seq data (e.g.
there are no chrM short reads given but you have chrM in your ROIs).
Unfortunately, these cases are not caught internally by MEDIPS and the R
session quits what is a very ugly behaviour. Please apologise this 'bad
programming' (but we are working on an improved and completely revised
version).
In case to cannot narrow down your error to a suspicious roi, please post
again and we will try to figure out the reason in detail.
Best,
Lukas
On Tue, 10 Jan 2012 14:38:39 +0000, Oscar Rueda
<Oscar.Rueda at cancer.org.uk>
wrote:
> Hi Asta,
>
> I've had a similar error in the past; It was caused by chromosome names
in
> the roi file not found in your data file. I would check that.
>
> Cheers,
> Oscar
>
>
> Oscar M. Rueda, PhD.
> Postdoctoral Research Fellow, Breast Cancer Functional Genomics.
> Cancer Research UK Cambridge Research Institute.
> Li Ka Shing Centre, Robinson Way.
> Cambridge CB2 0RE
> England
>
>
>
>
>
> On 10/1/12 14:13, "Asta Laiho [guest]" <guest at bioconductor.org> wrote:
>
>>
>>
>> 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
>>
>>
>> --
>> Sent via the guest posting facility at bioconductor.org.
>>
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