Dear All, I come back to DiffBind and tried the new version, I am analyzing some 5hmc and mc Seq experiments in a HPC server. I have both biological replicates and two different peak callers, I first extracted consensus peakset for each replicate. I am facing some problems when I call dba.count I think I have some problems with the server, here is the message: *** caught segfault *** address 0x1, cause 'memory not mapped' Traceback: 1: .Call("croi_load_reads", as.character(bamfile), as.integer(insertLength)) 2: FUN("bed/sample_10_sorted_paired_RD_10.bed.gz"[[1L]], ...) 3: lapply(X = S, FUN = FUN, ...) 4: doTryCatch(return(expr), name, parentenv, handler) 5: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 6: tryCatchList(expr, classes, parentenv, handlers) 7: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L msg <- conditionMessage(e) sm <- strsplit(msg, "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && identical(getOption("show.error.messages"), TRUE)) { cat(msg, file = stderr()) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))}) 8: try(lapply(X = S, FUN = FUN, ...), silent = TRUE) 9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) 10: FUN(1:12[[12L]], ...) 11: lapply(seq_len(cores), inner.do) 12: mclapply(arglist, fn, ..., mc.preschedule = TRUE, mc.allow.recursive = TRUE) 13: config$lapplyFun(config, params, arglist, fn, ...) 14: dba.parallel.lapply(pv$config, params, todo, pv.getCounts, bed, insertLength, bWithoutDupes = bWithoutDupes, bLowMem, yieldSize, mode, singleEnd, scanbamparam) 15: pv.counts(DBA, peaks = peaks, minOverlap = minOverlap, defaultScore = score, bLog = bLog, insertLength = insertLength, bOnlyCounts = T, bCalledMasks = bCalledMasks, minMaxval = filter, bParallel = bParallel, bUseLast = bUseLast, bWithoutDupes = bRemoveDuplicates, bScaleControl = bScaleControl, filterFun = filterFun, bLowMem = bLowMem) 16: dba.count(testsave, peaks = conspeaks) Possible actions: 1: abort (with core dump, if enabled) 2: normal R exit 3: exit R without saving workspace 4: exit R saving workspace Any suggestion? Thanks again, Paolo [[alternative HTML version deleted]]

Hello Paolo- This is most likely one of two things: 1. Insufficient memory. There ware two ways to check for this and get around this problem. The first is to run dba.count in non-parallel mode (bParallel=FALSE). This will take a lot longer, but has the added benefit that it will tell you exactly if only a specific read file is causing the failure. The second way in the latest version is to set bLowMem=TRUE, which will take a bit longer but use only 1GB per core. (You can also lower the number of parallel operations going on simultaneously by setting DBA$config$cores = n, where n is the number of concurrent parallel counting processes). 2. Something wrong with the format of the bed file. If you can rule out insufficient memory, we can have a look at sample_10_sorted_paired_RD_10.bed.gz it to see if there an issue. If you can share this bed file (and another one if there are some that work), say on Dropbox, along with a saved DBA object (and conspeaks), that would be most helpful. Cheers- Rory From: Paolo Kunderfranco <paolo.kunderfranco@gmail.com<mailto:paolo.kunderfranco@gmail.com>> Date: Thu, 16 May 2013 12:27:32 +0200 To: "bioconductor@r-project.org<mailto:bioconductor@r-project.org>" <bioconductor@r-project.org<mailto:bioconductor@r-project.org>>, Rory Stark <rory.stark@cancer.org.uk<mailto:rory.stark@cancer.org.uk>>, Gordon Brown <gordon.brown@cancer.org.uk<mailto:gordon.brown@cancer.org.uk>> Subject: DiffBind - error dba-count Resent-From: Rory Stark <rory.stark@cancer.org.uk<mailto:rory.stark@cancer.org.uk>> Dear All, I come back to DiffBind and tried the new version, I am analyzing some 5hmc and mc Seq experiments in a HPC server. I have both biological replicates and two different peak callers, I first extracted consensus peakset for each replicate. I am facing some problems when I call dba.count I think I have some problems with the server, here is the message: *** caught segfault *** address 0x1, cause 'memory not mapped' Traceback: 1: .Call("croi_load_reads", as.character(bamfile), as.integer(insertLength)) 2: FUN("bed/sample_10_sorted_paired_RD_10.bed.gz"[[1L]], ...) 3: lapply(X = S, FUN = FUN, ...) 4: doTryCatch(return(expr), name, parentenv, handler) 5: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 6: tryCatchList(expr, classes, parentenv, handlers) 7: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L msg <- conditionMessage(e) sm <- strsplit(msg, "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if is.na<http: is.na="">(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && identical(getOption("show.error.messages"), TRUE)) { cat(msg, file = stderr()) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))}) 8: try(lapply(X = S, FUN = FUN, ...), silent = TRUE) 9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) 10: FUN(1:12[[12L]], ...) 11: lapply(seq_len(cores), inner.do) 12: mclapply(arglist, fn, ..., mc.preschedule = TRUE, mc.allow.recursive = TRUE) 13: config$lapplyFun(config, params, arglist, fn, ...) 14: dba.parallel.lapply(pv$config, params, todo, pv.getCounts, bed, insertLength, bWithoutDupes = bWithoutDupes, bLowMem, yieldSize, mode, singleEnd, scanbamparam) 15: pv.counts(DBA, peaks = peaks, minOverlap = minOverlap, defaultScore = score, bLog = bLog, insertLength = insertLength, bOnlyCounts = T, bCalledMasks = bCalledMasks, minMaxval = filter, bParallel = bParallel, bUseLast = bUseLast, bWithoutDupes = bRemoveDuplicates, bScaleControl = bScaleControl, filterFun = filterFun, bLowMem = bLowMem) 16: dba.count(testsave, peaks = conspeaks) Possible actions: 1: abort (with core dump, if enabled) 2: normal R exit 3: exit R without saving workspace 4: exit R saving workspace Any suggestion? Thanks again, Paolo NOTICE AND DISCLAIMER This e-mail (including any attachments) is intended for ...{{dropped:20}}