About the DiffBind dba.count() crash problems
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@kentanakachiba-ujp-5955
Last seen 7.1 years ago
Dear Dr. Brown, I asked the questions earlier regarding the DiffBind last week. I have versioned up to R3.0.1 and Bioconductor 2.12, and I checked to see how DiffBind 1.6.2 works. But the dba.count() still crashes in the bed data and I attached the logs of the bed data below. Since the versioned up DiffBind 1.6.2 output the GEO DATA as an Alignment Data Sample, I downloaded the data and I checked to see what that is. And I found that the BWA bam files were created. I converted the fastq data on Th2 immune cells to bam files and I checked to see how it works. And finally, I could obtain the dba.report (). Thank you very much for all your advice and I really appreciate for your kindness. My Best Regards, Ken Tanaka ---------------------------------------------------------------------- -- ------------------------ > sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-suse-linux-gnu (64-bit) locale: [1] C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] DiffBind_1.6.2 Biobase_2.20.0 GenomicRanges_1.12.4 [4] IRanges_1.18.1 BiocGenerics_0.6.0 loaded via a namespace (and not attached): [1] RColorBrewer_1.0-5 amap_0.8-7 edgeR_3.2.3 gdata_2.12. 0.2 [5] gplots_2.11.0.1 gtools_2.7.1 limma_3.16.5 stats4_3.0. 1 [9] zlibbioc_1.6.0 > th2 = dba(sampleSheet="th2diffbind.csv") GATA3_Ab GATA3_Ab Th2 Resistant Full_Media 1 macs H3K4me3 H3K4me3 Th2 Responsive Full_Media 1 macs H3K9Ac H3K9Ac Th2 Responsive Full_Media 1 macs > th2 3 Samples, 16806 sites in matrix (35676 total): ID Tissue Factor Condition Treatment Replicate Peak.caller 1 GATA3_Ab GATA3_Ab Th2 Resistant Full_Media 1 macs 2 H3K4me3 H3K4me3 Th2 Responsive Full_Media 1 macs 3 H3K9Ac H3K9Ac Th2 Responsive Full_Media 1 macs Intervals 1 464 2 25875 3 32569 > th2 = dba.count(th2,minOverlap=3, bParallel=F) Sample: databed/Th2_GATA3_Ab.bed.gz *** caught segfault *** address (nil), cause 'memory not mapped' Traceback: 1: .Call("croi_load_reads", as.character(bamfile), as.integer( insertLength)) 2: pv.getCounts(job, bed, insertLength, bWithoutDupes = bWithoutDupes, bLowMem, yieldSize, mode, singleEnd, scanbamparam) 3: pv.listadd(results, pv.getCounts(job, bed, insertLength, bWithoutDupes = bWithoutDupes, bLowMem, yieldSize, mode, singleEnd, scanbamparam)) 4: 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) 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: ---------------------------------------------------------------------- -- ------------------------ # 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.xls,macs, macs 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. xls,macs,macs 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.xls, macs,macs #zmore Th2_GATA3_Ab.bed.gz |head ------> Th2_GATA3_Ab.bed.gz <------ chrY 28285 28404 Th2_GATA3_Ab 1 chrY 28363 28482 Th2_GATA3_Ab 1 chrY 28466 28585 Th2_GATA3_Ab 1 chrY 30469 30588 Th2_GATA3_Ab 1 chrY 99937 100056 Th2_GATA3_Ab 1 chrY 114597 114716 Th2_GATA3_Ab 1 chrY 269098 269217 Th2_GATA3_Ab 1 chrY 269773 269892 Th2_GATA3_Ab 1 chrY 410005 410124 Th2_GATA3_Ab 1 # head -30 GATA3_Ab_peaks.xls # This file is generated by MACS version 1.4.2 20120305 # ARGUMENTS LIST: # name = GATA3_Ab # format = BED # ChIP-seq file = ../databed/Tst_GATA3_Ab.bed # control file = ../databed/Tst_WCE.bed # effective genome size = 1.87e+09 # band width = 300 # model fold = 10,30 # pvalue cutoff = 1.00e-05 # Large dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 1000 bps and 10000 bps # tag size is determined as 119 bps # total tags in treatment: 353649 # tags after filtering in treatment: 353649 # maximum duplicate tags at the same position in treatment = 1 # Redundant rate in treatment: 0.00 # total tags in control: 481971 # tags after filtering in control: 481971 # maximum duplicate tags at the same position in control = 1 # Redundant rate in control: 0.00 # d = 200 chr start end length summit tags -10*log10(pvalue) fold_enrichment FDR(%) chr1 3704028 3704311 284 142 4 53.27 19.47 13.74 chr1 3787290 3787781 492 299 4 69.45 68.14 10.89 chr1 5694647 5695942 1296 189 11 104.10 25.55 8.33 chr1 5794055 5794296 242 121 4 85.91 38.94 4.17 chr1 6125574 6126093 520 337 7 56.83 16.22 13.71 chr1 6444066 6445227 1162 558 19 63.10 10.22 14.29 ------------------------------ ------------------------------------------------------------------ ----- 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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Gord Brown ▴ 640
@gord-brown-5664
Last seen 9 months ago
United Kingdom
Dear Ken, Thanks for the bug report. Can you share your bed files with me (maybe just the first 100 lines or so of each) so I can try to reproduce this bug? It must be a different one from the previous bed reading bug. Thanks, - Gord On 2013-06-06 23:50, "kentanaka at chiba-u.jp" <kentanaka at="" chiba-u.jp=""> wrote: >Dear Dr. Brown, > >I asked the questions earlier regarding the DiffBind last week. > >I have versioned up to R3.0.1 and Bioconductor 2.12, and I checked to >see how DiffBind 1.6.2 works. But the dba.count() still crashes in the >bed data and I attached the logs of the bed data below. > >Since the versioned up DiffBind 1.6.2 output the GEO DATA as an >Alignment Data Sample, I downloaded the data and I checked to see what >that is. And I found that the BWA bam files were created. > >I converted the fastq data on Th2 immune cells to bam files and I >checked to see how it works. And finally, I could obtain the dba.report >(). > >Thank you very much for all your advice and I really appreciate for your >kindness. > >My Best Regards, >Ken Tanaka > >--------------------------------------------------------------------- --- >------------------------ >> sessionInfo() >R version 3.0.1 (2013-05-16) >Platform: x86_64-suse-linux-gnu (64-bit) > >locale: >[1] C > >attached base packages: >[1] parallel stats graphics grDevices utils datasets methods >[8] base > >other attached packages: >[1] DiffBind_1.6.2 Biobase_2.20.0 GenomicRanges_1.12.4 >[4] IRanges_1.18.1 BiocGenerics_0.6.0 > >loaded via a namespace (and not attached): >[1] RColorBrewer_1.0-5 amap_0.8-7 edgeR_3.2.3 gdata_2.12. >0.2 >[5] gplots_2.11.0.1 gtools_2.7.1 limma_3.16.5 stats4_3.0. >1 >[9] zlibbioc_1.6.0 > > >> th2 = dba(sampleSheet="th2diffbind.csv") >GATA3_Ab GATA3_Ab Th2 Resistant Full_Media 1 macs >H3K4me3 H3K4me3 Th2 Responsive Full_Media 1 macs >H3K9Ac H3K9Ac Th2 Responsive Full_Media 1 macs > > >> th2 >3 Samples, 16806 sites in matrix (35676 total): > ID Tissue Factor Condition Treatment Replicate Peak.caller >1 GATA3_Ab GATA3_Ab Th2 Resistant Full_Media 1 macs >2 H3K4me3 H3K4me3 Th2 Responsive Full_Media 1 macs >3 H3K9Ac H3K9Ac Th2 Responsive Full_Media 1 macs > Intervals >1 464 >2 25875 >3 32569 > > >> th2 = dba.count(th2,minOverlap=3, bParallel=F) >Sample: databed/Th2_GATA3_Ab.bed.gz > > *** caught segfault *** >address (nil), cause 'memory not mapped' > >Traceback: > 1: .Call("croi_load_reads", as.character(bamfile), as.integer( >insertLength)) > 2: pv.getCounts(job, bed, insertLength, bWithoutDupes = bWithoutDupes, > bLowMem, yieldSize, mode, singleEnd, scanbamparam) > 3: pv.listadd(results, pv.getCounts(job, bed, insertLength, >bWithoutDupes = bWithoutDupes, bLowMem, yieldSize, mode, singleEnd, >scanbamparam)) > 4: 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) > 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: > >--------------------------------------------------------------------- --- >------------------------ > ># 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.xls,macs, >macs >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 . >xls,macs,macs >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.xls, >macs,macs > > >#zmore Th2_GATA3_Ab.bed.gz |head >------> Th2_GATA3_Ab.bed.gz <------ >chrY 28285 28404 Th2_GATA3_Ab 1 >chrY 28363 28482 Th2_GATA3_Ab 1 >chrY 28466 28585 Th2_GATA3_Ab 1 >chrY 30469 30588 Th2_GATA3_Ab 1 >chrY 99937 100056 Th2_GATA3_Ab 1 >chrY 114597 114716 Th2_GATA3_Ab 1 >chrY 269098 269217 Th2_GATA3_Ab 1 >chrY 269773 269892 Th2_GATA3_Ab 1 >chrY 410005 410124 Th2_GATA3_Ab 1 > > ># head -30 GATA3_Ab_peaks.xls ># This file is generated by MACS version 1.4.2 20120305 ># ARGUMENTS LIST: ># name = GATA3_Ab ># format = BED ># ChIP-seq file = ../databed/Tst_GATA3_Ab.bed ># control file = ../databed/Tst_WCE.bed ># effective genome size = 1.87e+09 ># band width = 300 ># model fold = 10,30 ># pvalue cutoff = 1.00e-05 ># Large dataset will be scaled towards smaller dataset. ># Range for calculating regional lambda is: 1000 bps and 10000 bps ># tag size is determined as 119 bps ># total tags in treatment: 353649 ># tags after filtering in treatment: 353649 ># maximum duplicate tags at the same position in treatment = 1 ># Redundant rate in treatment: 0.00 ># total tags in control: 481971 ># tags after filtering in control: 481971 ># maximum duplicate tags at the same position in control = 1 ># Redundant rate in control: 0.00 ># d = 200 >chr start end length summit tags -10*log10(pvalue) >fold_enrichment FDR(%) >chr1 3704028 3704311 284 142 4 53.27 19.47 13.74 >chr1 3787290 3787781 492 299 4 69.45 68.14 10.89 >chr1 5694647 5695942 1296 189 11 104.10 25.55 8.33 >chr1 5794055 5794296 242 121 4 85.91 38.94 4.17 >chr1 6125574 6126093 520 337 7 56.83 16.22 13.71 >chr1 6444066 6445227 1162 558 19 63.10 10.22 14.29 > >------------------------------ >------------------------------------------------------------------ > >----- 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. 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_pe aks. >> >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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