DiffBind dba.count() seqfault
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Entering edit mode
em540 • 0
@em540-10722
Last seen 5.4 years ago

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

diffbind dba.count • 748 views
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0
Entering edit mode

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 REPLY
0
Entering edit mode

Hi Gord,

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

 

ADD REPLY
0
Entering edit mode

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

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