About the DiffBind dba.count() crash problems
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@kentanakachiba-ujp-5955
Last seen 9.6 years ago
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,bamContr ol, 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,r aw control_Ab,control_Ab,Th2,Resistant,Full_Media,1,databed/Th2_control_A b. bed.gz,databed/Th2_WCE.bed.gz,Th2_WCE_Control,peaks/control_Ab_peaks.b ed, 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_H3K4me 3. 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.b ed. 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
DiffBind DiffBind • 1.7k views
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Gord Brown ▴ 650
@gord-brown-5664
Last seen 3.2 years ago
United Kingdom
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,bamCont rol, >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_H3K4m e3. >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 > > > >------------------------------ > >_______________________________________________ >Bioconductor mailing list >Bioconductor at r-project.org >https://stat.ethz.ch/mailman/listinfo/bioconductor > > >End of Bioconductor Digest, Vol 123, Issue 26 >*********************************************
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Dear Dr. Brown, Thank you very much for your kind prompt reply. I think it might take a few days but, I'm going to version up to the Bioconductor 2.12 and see how DiffBind works. Thank you very much for your instructions. I really appreciate for your cordial reply. My Best Regards, Ken Tanaka ----- Original Message ----- > 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.b ed. 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_pea ks. > >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 > > > > > > > >------------------------------ > > > >_______________________________________________ > >Bioconductor mailing list > >Bioconductor at r-project.org > >https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > > >End of Bioconductor Digest, Vol 123, Issue 26 > >********************************************* > >
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