20 May 2012 00:29
Re: Excessive memory requirements of PING or bug?
Dan Tenenbaum <dtenenba@...>
2012-05-19 22:29:53 GMT
2012-05-19 22:29:53 GMT
[cc'ing Bioconductor list so others can benefit...] On Sat, May 19, 2012 at 3:28 PM, Xuekui Zhang <ubcxzhang@...> wrote: > Hi Lars, > > Did you try to analyze each chromosome separately? > Please let me know if that still can not solve the problem. > > Xuekui > > On May 19, 2012, at 5:35 PM, Raphael Gottardo wrote: > > Hi Lars, > > Xuekui ccied here will look into it. > > Raphael > > -- > Raphael Gottardo, Associate Member > http://www.rglab.org > Fred Hutchinson Cancer Research Center > Vaccine and Infectious Disease Division > Public Health Sciences Division > > > > On May 18, 2012, at 11:56 AM, Dan Tenenbaum wrote: > > I'm cc'ing one of the PING maintainers who can perhaps shed more light on > this. > Dan > > > On Thu, May 17, 2012 at 2:55 PM, Lars Hennig <Lars.Hennig@...> wrote: > > Dear PING maintainers, > > > Running PING with the example from the vignette works fine, but segmentReads > causes a "cannot allocate memory block of size 68719476735.9 Gb" error when > using my own ChIP-seq sample data. (16Mio paired end reads mapped with > bowtie). This is an Arabidopsis sample (genome size = 130MB). > > Using a sample of 100000 of our own reads runs smoothly again, 2.5 Mio crash > with a similarly high memory request as mentioned above. Including snowfall > or not has no effect. > > > Is there a way to trick PING into processing more than some few 100000 reads > with "normal" memory (I have 48 Gb available). If PING really has a very > high memory need, this could be mentioned in the documentation. > > > Thank you very much, > > > Lars > > > Script: > > > library(ShortRead) > > > reads <- readAligned("reads_sorted.bam", type="BAM") > > reads <- reads[!is.na(position(reads))] > > reads <- reads[chromosome(reads) %in% c("Chr4")] > > > #reads <- reads[1:100000] > > > library(PING) > > library(snowfall) > > sfInit(parallel=TRUE,cpus=4) > > sfLibrary(PING) > > > > reads <- as(reads,"RangesList") > > reads <- as(reads,"RangedData") > > reads <- as(reads,"GenomeData") > > > seg <-segmentReads(reads, minReads=5, maxLregion=1200,minLregion=80, > jitter=T) > > > > > > traceback() > > 2: .Call("segReadsAll", data, dataC, start, end, as.integer(jitter), > > paraSW, as.integer(maxStep), as.integer(minLregion), PACKAGE = "PING") > > 1: segmentReads(reads_gd, minReads = 5, maxLregion = 1200, minLregion = 80, > > jitter = T) > > > > sessionInfo() > > R version 2.15.0 (2012-03-30) > > Platform: x86_64-pc-linux-gnu (64-bit) > > > locale: > >  LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > >  LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > >  LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > >  LC_PAPER=C LC_NAME=C > >  LC_ADDRESS=C LC_TELEPHONE=C > >  LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > > attached base packages: > >  stats graphics grDevices utils datasets methods base > > > other attached packages: > >  snowfall_1.84 snow_0.3-9 PING_1.0.0 > >  chipseq_1.6.0 ShortRead_1.14.3 latticeExtra_0.6-19 > >  RColorBrewer_1.0-5 Rsamtools_1.8.4 lattice_0.20-6 > >  BSgenome_1.24.0 Biostrings_2.24.1 GenomicRanges_1.8.6 > >  IRanges_1.14.3 BiocGenerics_0.2.0 > > > loaded via a namespace (and not attached): > >  Biobase_2.16.0 biomaRt_2.12.0 bitops_1.0-4.1 > >  GenomeGraphs_1.16.0 grid_2.15.0 hwriter_1.3 > >  RCurl_1.91-1 stats4_2.15.0 tools_2.15.0 > >  XML_3.9-4 zlibbioc_1.2.0 > > > > Dr. Lars Hennig > > Professor of Genetics > > Swedish University of Agricultural Sciences > > Uppsala BioCenter > > Department of Plant Biology and Forest Genetics > > PO-Box 7080 > > SE-75007 Uppsala, Sweden > > Lars.Hennig@... > > Tel. +46 18 67 3326 > > Fax +46 18 67 3389 > > > Visiting address: > > Uppsala BioCenter > > Almas Allé 5 > > SE-75651 Uppsala, Sweden > > Room A-489 > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@... > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > _______________________________________________ Bioconductor mailing list Bioconductor@... https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor