[BioC] About the DiffBind dba.count() crash problems

Tue May 28 11:35:22 CEST 2013

Hi, Ken,

This bug is fixed in the current version of DiffBind, so if you upgrade,
it should go away.  If upgrading is not feasible, ensure that the bed
files all have 6 columns to work around the bug.

Cheers,

 - Gord

>Message: 23
>Date: Sat, 25 May 2013 16:55:00 +0900
>From: <kentanaka at chiba-u.jp>
>To: <bioconductor at r-project.org>
>Subject: [BioC] About the DiffBind dba.count() crash problems
>Message-ID: <20130525075500.0000701E.0473 at chiba-u.jp>
>Content-Type: text/plain; charset=UTF-8
>
>Hi, I'm Ken Tanaka.
>
>I'm currently interested in analyzing the DiffBind analysis by using the
>ChIP-seq data from Th2 immune cell samples.
>
>To be more specific, I would like to analyze this data (GSE28292) by
>using DiffBind analysis.
>
>I have questions regarding the dba.count().
>When I execute the dba.count(), it crashes.
>
>The bed data which I'm using doesn't include the 6th strand column.
>So, I suppose the crash problem doesn't originate from the problems
>regarding the columns.
>
>I would like to know how to modify the bed data which the DiffBind can
>read the bed file specifications.
>If you can inform me of these DiffBind bed file specifications which can
>read the bed data, I think I will be able to make the perl script for
>conversions. 
>So, could you kindly please let me know of these DiffBind bed file
>specifications which can read the bed data?
>
>I attached below the data and logs which I used for this analysis as
>follows. 
>
>My Best Regards, 
>Ken Tanaka
>
>----------------------------------------------------------------
># ChIP-seq bed data files.
>GSM773482_Th2_GATA3_Ab.bed.gz
>GSM773480_Th2_control_Ab.bed.gz
>GSM773484_Th2_WCE.bed.gz     (The 2 bed files listed above are the
>controls.)
>
>GSM773486_Th2_WT_anti_H3K27me3.bed.gz
>GSM773490_Th2_WT_anti_H3K9Ac.bed.gz
>GSM773492_Th2_WT_anti_H3K4me3.bed.gz
>GSM773488_Th2_WT_input.bed.gz (The 3 bed files listed above are the
>controls.)
>
>
># macs14 1.4.2 20120305 peak calling output files.
>GATA3_Ab_peaks.bed
>control_Ab_peaks.bed
>
>H3K27me3_peaks.bed
>H3K4me3_peaks.bed
>H3K9Ac_peaks.bed
>
>
># DiffBind sampleSheet file.
>%cat th2diffbind.csv
>SampleID,Tissue,Factor,Condition,Treatment,Replicate,bamReads,bamControl,
>ControlID,Peaks,PeakCaller,PeakFormat
>GATA3_Ab,GATA3_Ab,Th2,Resistant,Full_Media,1,databed/Th2_GATA3_Ab.bed.gz,
>databed/Th2_WCE.bed.gz,Th2_WCE_Control,peaks/GATA3_Ab_peaks.bed,macs,raw
>control_Ab,control_Ab,Th2,Resistant,Full_Media,1,databed/Th2_control_Ab.
>bed.gz,databed/Th2_WCE.bed.gz,Th2_WCE_Control,peaks/control_Ab_peaks.bed,
>macs,raw
>H3K27me3,H3K27me3,Th2,Responsive,Full_Media,1,databed/Th2_WT_anti_
>H3K27me3.bed.gz,databed/Th2_WT_input.bed.gz,Th2_WT_Control,peaks/
>H3K27me3_peaks.bed,macs,raw
>H3K4me3,H3K4me3,Th2,Responsive,Full_Media,1,databed/Th2_WT_anti_H3K4me3.
>bed.gz,databed/Th2_WT_input.bed.gz,Th2_WT_Control,peaks/H3K4me3_peaks.
>bed,macs,raw
>H3K9Ac,H3K9Ac,Th2,Responsive,Full_Media,1,databed/Th2_WT_anti_H3K9Ac.bed.
>gz,databed/Th2_WT_input.bed.gz,Th2_WT_Control,peaks/H3K9Ac_peaks.bed,
>macs,raw
>
>
>
>
>> th2 = dba(sampleSheet="th2diffbind.csv")
>GATA3_Ab GATA3_Ab Th2 Resistant Full_Media 1 macs
>control_Ab control_Ab Th2 Resistant Full_Media 1 macs
>H3K27me3 H3K27me3 Th2 Responsive Full_Media 1 macs
>H3K4me3 H3K4me3 Th2 Responsive Full_Media 1 macs
>H3K9Ac H3K9Ac Th2 Responsive Full_Media 1 macs
>> 
>> #th2
>> #str(th2)
>> #plot(th2)
>> 
>> # peaks counting reads
>> #th2 = dba.count(th2, bParallel=F)
>> th2 = dba.count(th2,minOverlap=3, bParallel=F)
>Sample: databed/Th2_GATA3_Ab.bed.gz
>
> *** caught segfault ***
>address 0x10, cause 'memory not mapped'
>
>Traceback:
> 1: .Call("croi_load_reads", as.character(bamfile), as.integer(
>insertLength))
> 2: pv.getCounts(job, bed, insertLength, bWithoutDupes = bWithoutDupes)
> 3: pv.listadd(results, pv.getCounts(job, bed, insertLength,
>bWithoutDupes = bWithoutDupes))
> 4: pv.counts(DBA, peaks = peaks, minOverlap = minOverlap, defaultScore
>= score,     bLog = bLog, insertLength = insertLength, bOnlyCounts = T,
>   bCalledMasks = bCalledMasks, minMaxval = maxFilter, bParallel =
>bParallel,     bUseLast = bUseLast, bWithoutDupes = bRemoveDuplicates,
>bScaleControl = bScaleControl)
> 5: dba.count(th2, minOverlap = 3, bParallel = F)
>
>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: 1
>
>
>
>> sessionInfo()
>R version 2.15.2 (2012-10-26)
>Platform: x86_64-suse-linux-gnu (64-bit)
>
>locale:
> [1] LC_CTYPE=ja_JP.UTF-8       LC_NUMERIC=C
> [3] LC_TIME=ja_JP.UTF-8        LC_COLLATE=ja_JP.UTF-8
> [5] LC_MONETARY=ja_JP.UTF-8    LC_MESSAGES=ja_JP.UTF-8
> [7] LC_PAPER=C                 LC_NAME=C
> [9] LC_ADDRESS=C               LC_TELEPHONE=C
>[11] LC_MEASUREMENT=ja_JP.UTF-8 LC_IDENTIFICATION=C
>
>attached base packages:
>[1] stats     graphics  grDevices utils     datasets  methods   base
>
>other attached packages:
>[1] DiffBind_1.4.2       Biobase_2.18.0       GenomicRanges_1.10.7
>[4] IRanges_1.16.6       BiocGenerics_0.4.0
>
>loaded via a namespace (and not attached):
> [1] RColorBrewer_1.0-5 amap_0.8-7         edgeR_3.0.8        gdata_2.12.
>0      
> [5] gplots_2.11.0      gtools_2.7.0       limma_3.14.4       parallel_2.
>15.2   
> [9] stats4_2.15.2      zlibbioc_1.4.0
>> 
>------------------------------------------------------------------------
>---------
>
>--------------------------------------
>Ken Tanaka
>MD-PhD Candidate
>Chiba University Medical School
>
>
>
>------------------------------
>
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>End of Bioconductor Digest, Vol 123, Issue 26
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