[BioC] Caught segfault when running MEDIPS package

[Oscar Rueda]

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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