Thanks Martin. I agree this sounds like something we should fix. 
--
Raphael Gottardo, Associate Member
http://www.rglab.org
Fred Hutchinson Cancer Research Center
Vaccine and Infectious Disease Division
Public Health Sciences Division



On May 22, 2012, at 5:48 AM, Martin Morgan wrote:

> On 05/21/2012 10:09 AM, Xuekui Zhang wrote:
>> Hi Lars,
>> 
>>   Thanks for your feed back!
>>   Yes, cutting chromosome before segmentation is not preferred, since the cutting points might be where the peaks/nucleosomes are.
>>   To avoid this problem, you could run a sliding window (e.g. window size 300bp, step size 10 bp) on a chromosome, count reads count in each window to find valley of reads counts curve and good cutting there.
>>   When we make the next version of PING, we could integrate cutting into segmentation step to avoid cutting chromosome on wrong place.
> 
> The original problem sounded like an integer overflow in the underlying C code in PING. Can that be fixed? If there is a simple reproducible example (e.g., using R's random number generators to simulate large enough data) I can perhaps help to identify this.
> 
> Martin
> 
>> Xuekui
>> 
>> On May 20, 2012, at 3:25 AM, Lars Hennig wrote:
>> 
>>> Yes, I tried. Restricting to single chromosomes of ~ 20MB did not help but going to much smaller subchromosomal domains did eventually solve the problem. Still, this is not a preferred option to slice the genome into many small sectons.
>>> 
>>> Lars
>>> 
>>> -----Original Message-----
>>> From: Dan Tenenbaum [mailto:dtenenba@fhcrc.org]
>>> Sent: Sunday, May 20, 2012 12:30 AM
>>> To: Xuekui Zhang
>>> Cc: Raphael Gottardo; Lars Hennig; Renan Sauteraud; bioconductor@r-project.org
>>> Subject: Re: [BioC] Excessive memory requirements of PING or bug?
>>> 
>>> [cc'ing Bioconductor list so others can benefit...]
>>> 
>>> On Sat, May 19, 2012 at 3:28 PM, Xuekui Zhang<ubcxzhang@gmail.com>  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@slu.se>  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:
>>>> 
>>>> [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>>>> 
>>>> [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>>>> 
>>>> [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>>>> 
>>>> [7] LC_PAPER=C                 LC_NAME=C
>>>> 
>>>> [9] LC_ADDRESS=C               LC_TELEPHONE=C
>>>> 
>>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>>> 
>>>> 
>>>> attached base packages:
>>>> 
>>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>> 
>>>> 
>>>> other attached packages:
>>>> 
>>>> [1] snowfall_1.84       snow_0.3-9          PING_1.0.0
>>>> 
>>>> [4] chipseq_1.6.0       ShortRead_1.14.3    latticeExtra_0.6-19
>>>> 
>>>> [7] RColorBrewer_1.0-5  Rsamtools_1.8.4     lattice_0.20-6
>>>> 
>>>> [10] BSgenome_1.24.0     Biostrings_2.24.1   GenomicRanges_1.8.6
>>>> 
>>>> [13] IRanges_1.14.3      BiocGenerics_0.2.0
>>>> 
>>>> 
>>>> loaded via a namespace (and not attached):
>>>> 
>>>> [1] Biobase_2.16.0      biomaRt_2.12.0      bitops_1.0-4.1
>>>> 
>>>> [4] GenomeGraphs_1.16.0 grid_2.15.0         hwriter_1.3
>>>> 
>>>> [7] RCurl_1.91-1        stats4_2.15.0       tools_2.15.0
>>>> 
>>>> [10] 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@vbsg.slu.se
>>>> 
>>>> 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@r-project.org
>>>> 
>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>> 
>>>> Search the archives:
>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>> 
>>>> 
>>>> 
>> 
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor@r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
> 
> 
> -- 
> Computational Biology
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
> 
> Location: M1-B861
> Telephone: 206 667-2793


	[[alternative HTML version deleted]]

