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 >>> >>> >>> -- >>> Sent via the guest posting facility at bioconductor.org. >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >> >> NOTICE AND DISCLAIMER >> This e-mail (including any attachments) is intended for > ...{{dropped:16}} >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor