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deepSNV Question

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Asma rabe ▴ 290

@asma-rabe-4697

Last seen 6.9 years ago

Japan

Hi All, I appreciate if anyone can provide an example to use DeepSNV where the reference genome is used. I have used BSgenpme and tried sq<-as(seqinfo(Hsapiens), "GRanges") counts<- loadAllData(files, sq, q = 10) but I got memory allocation error Warning messages: 1: In structure(y, class = class(x), levels = levels(x)) : Reached total allocation of 3958Mb: see help(memory.size) 2: In structure(y, class = class(x), levels = levels(x)) : Reached total allocation of 3958Mb: see help(memory.size) 3: In structure(y, class = class(x), levels = levels(x)) : Reached total allocation of 3958Mb: see help(memory.size) 4: In structure(y, class = class(x), levels = levels(x)) : Reached total allocation of 3958Mb: see help(memory.size) Error in unlist(sapply(1:nrow(regions), function(i) rep(regions$chr[i], : error in evaluating the argument 'x' in selecting a method for function 'unlist': Error: cannot allocate vector of size 927.7 Mb ----------------------------------------------------------- Shall i use the exome sequence only ?? Any help is highly appreciated ---------------------------------- In deepSNV example library(deepSNV) regions <- data.frame(chr="B.FR.83.HXB2_LAI_IIIB_BRU_K034", start = 2074, stop=3585) ## ------------------------------------------------------------------- ----- # HIVmix <- deepSNV(test = " http://www.bsse.ethz.ch/cbg/software/deepSNV/data/test.bam", # control = " http://www.bsse.ethz.ch/cbg/software/deepSNV/data/control.bam", # regions=regions, q=10) ------------------------------------------------- [[alternative HTML version deleted]]

deepSNV deepSNV • 1.9k views

ADD COMMENT • link updated 10.4 years ago by Dario Strbenac ★ 1.5k • written 10.4 years ago by Asma rabe ▴ 290

score 0 · Answer 1 · 2014-07-14

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Dario Strbenac ★ 1.5k

@dario-strbenac-5916

Last seen 2 days ago

Australia

Hello, You will need more than 4 GB RAM to do the analysis. Can you find another computer with more memory ? Also, make sure you are not using 32-bit R. You need 64-bit R and an operating system which is 64-bit to be able to access more RAM. -------------------------------------- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia

ADD COMMENT • link 10.4 years ago Dario Strbenac ★ 1.5k

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Hello Dario, Thank you for help. I have tried looping on chromosomes one by one (tried 3 chromosomes for testing) but I got no result as followsâ¦. seq<-as(seqinfo(Hsapiens), "GRanges") seq GRanges with 93 ranges and 0 metadata columns: seqnames ranges strand <rle> <iranges> <rle> chr1 chr1 [1, 249250621] * chr2 chr2 [1, 243199373] * chr3 chr3 [1, 198022430] * chr4 chr4 [1, 191154276] * chr5 chr5 [1, 180915260] * ... ... ... ... chrUn_gl000245 chrUn_gl000245 [1, 36651] * chrUn_gl000246 chrUn_gl000246 [1, 38154] * chrUn_gl000247 chrUn_gl000247 [1, 36422] * chrUn_gl000248 chrUn_gl000248 [1, 39786] * chrUn_gl000249 chrUn_gl000249 [1, 38502] * --- seqlengths: chr1 chr2 ... chrUn_gl000249 249250621 243199373 ... 38502 for (i in 16:18){assign(paste("count",i,sep=""),loadAllData(files,seq[i]))} count16 [ reached getOption("max.print") -- omitted 10 matrix slice(s) ] Any help is appreciated On Tue, Jul 15, 2014 at 11:00 AM, Dario Strbenac <dstr7320@uni.sydney.edu.au> wrote: > Hello, > > You will need more than 4 GB RAM to do the analysis. Can you find another > computer with more memory ? Also, make sure you are not using 32-bit R. You > need 64-bit R and an operating system which is 64-bit to be able to access > more RAM. > > -------------------------------------- > Dario Strbenac > PhD Student > University of Sydney > Camperdown NSW 2050 > Australia [[alternative HTML version deleted]]

ADD REPLY • link 10.4 years ago Asma rabe ▴ 290

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I'm sure you did get a result. What happens if you type count16 and press Enter ? Also, you can write your code better. dataList <- lapply(seqnames(Hsapiens)[16:18], function(chrName) loadAllData(files, chrName)) # Read in data for 3 chromosomes dataList[[1]] # Look at data for the first chromosome that was used. dataList[[3]] # Look at data for the last chromosome that was used. -------------------------------------- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia ________________________________ From: Asma rabe <asma.rabe@gmail.com> Sent: Tuesday, 15 July 2014 9:03 PM To: Dario Strbenac Cc: Bioconductor@r-project.org Subject: Re: [BioC] deepSNV Question Hello Dario, Thank you for help. I have tried looping on chromosomes one by one (tried 3 chromosomes for testing) but I got no result as follows.... seq<-as(seqinfo(Hsapiens), "GRanges") seq GRanges with 93 ranges and 0 metadata columns: seqnames ranges strand <rle> <iranges> <rle> chr1 chr1 [1, 249250621] * chr2 chr2 [1, 243199373] * chr3 chr3 [1, 198022430] * chr4 chr4 [1, 191154276] * chr5 chr5 [1, 180915260] * ... ... ... ... chrUn_gl000245 chrUn_gl000245 [1, 36651] * chrUn_gl000246 chrUn_gl000246 [1, 38154] * chrUn_gl000247 chrUn_gl000247 [1, 36422] * chrUn_gl000248 chrUn_gl000248 [1, 39786] * chrUn_gl000249 chrUn_gl000249 [1, 38502] * --- seqlengths: chr1 chr2 ... chrUn_gl000249 249250621 243199373 ... 38502 for (i in 16:18){assign(paste("count",i,sep=""),loadAllData(files,seq[i]))} count16 [ reached getOption("max.print") -- omitted 10 matrix slice(s) ] Any help is appreciated On Tue, Jul 15, 2014 at 11:00 AM, Dario Strbenac <dstr7320@uni.sydney.edu.au<mailto:dstr7320@uni.sydney.edu.au>> wrote: Hello, You will need more than 4 GB RAM to do the analysis. Can you find another computer with more memory ? Also, make sure you are not using 32-bit R. You need 64-bit R and an operating system which is 64-bit to be able to access more RAM. -------------------------------------- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia [[alternative HTML version deleted]]

ADD REPLY • link 10.4 years ago Dario Strbenac ★ 1.5k

score 0 · Answer 2 · 2014-07-15

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Dario Strbenac ★ 1.5k

@dario-strbenac-5916

Last seen 2 days ago

Australia

> I got > count16 > [ reached getOption("max.print") -- omitted 10 matrix slice(s) ] > Any idea? It must be a big data object. Use head(count16) or str(count16) to see the beginning of it.

ADD COMMENT • link 10.4 years ago Dario Strbenac ★ 1.5k