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

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