[BioC] Caught segfault when running MEDIPS package
Asta Laiho
asta.laiho at btk.fi
Wed Jan 11 11:17:53 CET 2012
Hi,
Many thanks for your advice, the problem indeed seems to be related to coordinates missing for the specific sample.
- Asta
On Jan 11, 2012, at 12:53 AM, chavez wrote:
>
> 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
>>>
>>>
>>> --
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>>>
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>>
>>
>>
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