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Question: DiffBind dba.count() seqfault
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gravatar for em540
18 months ago by
em5400
em5400 wrote:

HI All,

I have been using DiffBind for several analyses. But lately I am having problems with a dataset. Please see the terminal log file below.

~$ R

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> library(DiffBind)
Loading required package: GenomicRanges
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from ‘package:stats’:

    xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
    duplicated, eval, evalq, Filter, Find, get, intersect, is.unsorted,
    lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames,
    sapply, setdiff, sort, table, tapply, union, unique, unlist

Loading required package: IRanges
Loading required package: XVector
> diffAnalysis = dba(sampleSheet="dataInfo.csv")
1 KO1 H3K4me1 KnockOut  1 raw
2 KO2 H3K4me1 KnockOut  2 raw
3 WT1 H3K4me1 WildType  1 raw
4 WT2 H3K4me1 WildType  2 raw
> diffAnalysis = dba.count(diffAnalysis, minOverlap=2)

 *** caught segfault ***
address 0xfffffffc7824c980, cause 'memory not mapped'

Traceback:
 1: .Call("croi_count_reads", bamfile, as.integer(insertLength),     as.integer(fileType), as.integer(bufferSize), as.character(intervals[[1]]),     as.integer(intervals[[2]]), as.integer(intervals[[3]]), as.integer(icount),     as.logical(bWithoutDupes), counts.croi)
 2: FUN(X[[i]], ...)
 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(X[[i]], ...)
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, readFormat)
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 = bUseSummarizeOverlaps, readFormat = readFormat)
16: dba.count(diffAnalysis, minOverlap = 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: 
 *** caught segfault ***
address 0x113a5b2a8, cause 'memory not mapped'

Traceback:
 1: .Call("croi_count_reads", bamfile, as.integer(insertLength),     as.integer(fileType), as.integer(bufferSize), as.character(intervals[[1]]),     as.integer(intervals[[2]]), as.integer(intervals[[3]]), as.integer(icount),     as.logical(bWithoutDupes), counts.croi)
 2: FUN(X[[i]], ...)
 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(X[[i]], ...)
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, readFormat)
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 = bUseSummarizeOverlaps, readFormat = readFormat)
16: dba.count(diffAnalysis, minOverlap = 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: 

I am having the same issue even with 6 column bed file as advised earlier on similar problems in discussion forums.

Please help me in solving this issue.

Here is the sessionInfo()

> sessionInfo()

R version 3.3.0 (2016-05-03)

Platform: x86_64-pc-linux-gnu (64-bit)

Running under: Ubuntu 14.04.4 LTS

 

locale:

 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              

 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    

 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   

 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                 

 [9] LC_ADDRESS=C               LC_TELEPHONE=C            

[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

 

attached base packages:

[1] parallel  stats     graphics  grDevices utils     datasets  methods  

[8] base     

 

other attached packages:

[1] DiffBind_1.8.5       GenomicRanges_1.14.4 XVector_0.2.0       

[4] IRanges_1.20.7       BiocGenerics_0.8.0  

 

loaded via a namespace (and not attached):

 [1] edgeR_3.4.2        gtools_3.5.0       bitops_1.0-6       stats4_3.3.0      

 [5] KernSmooth_2.23-15 amap_0.8-14        gplots_3.0.1       zlibbioc_1.8.0    

 [9] gdata_2.17.0       limma_3.18.13      RColorBrewer_1.1-2 caTools_1.17.1    

many thanks

ADD COMMENTlink written 18 months ago by em5400

Hi,

Your sessionInfo shows DiffBind version 1.8.5, which is very out of date.  Please upgrade to the current version that goes with R 3.3 (which is DiffBind version 2.0.2) and let us know what happens.  (You'll probably have to upgrade a number of other packages too.)

Cheers,

 - Gord

ADD REPLYlink written 18 months ago by Gord Brown540

Hi Gord,

It is still the same with upgraded DiffBind version 2.0.2. Any more suggestions please?

 

ADD REPLYlink written 18 months ago by em5400

Hi,

Have you upgraded all other packages as well?

Try running dba.count with "bUseSummarizeOverlaps=TRUE" to use different counting code.  If it still fails, there's something wrong with your read files.  What format are they in?  Also, if you could send or attach your sample sheet, I can see if there's something not quite right there.

Cheers,

 - Gord

ADD REPLYlink written 18 months ago by Gord Brown540
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