Hi Gordon, I tried test=dba.count(test,bParallel=F) but still facing the same problem, it seems that 6 Gb of RAM are not enough to load 2 GB of bed file, is it possibile? I suggest I should switch to a bigger machine.. paolo 2012/7/31 Gordon Brown <gordon.brown at="" cancer.org.uk="">: > Hi, Paolo, > > DiffBind uses quite a lot of memory for the dba.count step, because it loads > the whole data file into memory. (In hindsight, not the best design > choice...) Try running with parallelization turned off: > >> test=dba.count(test,bParallel=F) > > so that it only loads one file at a time, to reduce the memory footprint. > For the upcoming release, we'll probably fix this, at the cost of somewhat > slower counting. > > How much RAM does your machine have? > > Cheers, > > - Gord > > > On 2012/07/30 11:00, "Paolo Kunderfranco" <paolo.kunderfranco at="" gmail.com=""> > wrote: > >> Dear All, >> I am facing some problems with RGUI loading dba.count with my dataset, >> >>> setwd("C:/Documents and Settings/pkunderfranco/Documenti/Data /ChIP-seq >>> Roberto/Analisi_PK/DiffBind/H3K27me3/") >> >>> library("DiffBind") >> >>> test= dba(sampleSheet='database.csv') >> ES_H3K27 ES H3K27 1 1 raw >> CMN_H3K27 CMN H3K27 1 1 raw >> CMA_H3K27 CMA H3K27 1 1 raw >> >>> test=dba.count(test) >> AppName: rgui.exe AppVer: 2.150.58871.0 ModName: diffbind.dll >> ModVer: 0.0.0.0 Offset: 00003be1 >> >> Did anyone faced the same problem? which are the memory requirements >> to run DiffBind? >> Thanks, >> Paolo >> >> > > > NOTICE AND DISCLAIMER > This e-mail (including any attachments) is intended fo...{{dropped:16}}

Hi, Paolo, 6Gb ought to be enough. I suspect there's something else wrong. Unfortunately, I don't have a Windows machine available to test on. Can you provide any other information about the error? Does it run for a long time, then fail, or does it fail quickly? Is there any other diagnostic message? Does Rgui crash completely, or can you run "traceback()" to see where the error is? Also, can you provide the output of "sessionInfo()" so I can see what version you're running? Thanks, - Gord On 01/08/2012 10:34, "Paolo Kunderfranco" <paolo.kunderfranco at="" gmail.com=""> wrote: >Hi Gordon, >I tried test=dba.count(test,bParallel=F) but still facing the same >problem, it seems that 6 Gb of RAM are not enough to load >2 GB of bed file, is it possibile? >I suggest I should switch to a bigger machine.. >paolo > > > >2012/7/31 Gordon Brown <gordon.brown at="" cancer.org.uk="">: >> Hi, Paolo, >> >> DiffBind uses quite a lot of memory for the dba.count step, because it >>loads >> the whole data file into memory. (In hindsight, not the best design >> choice...) Try running with parallelization turned off: >> >>> test=dba.count(test,bParallel=F) >> >> so that it only loads one file at a time, to reduce the memory >>footprint. >> For the upcoming release, we'll probably fix this, at the cost of >>somewhat >> slower counting. >> >> How much RAM does your machine have? >> >> Cheers, >> >> - Gord >> >> >> On 2012/07/30 11:00, "Paolo Kunderfranco" <paolo.kunderfranco at="" gmail.com=""> >> wrote: >> >>> Dear All, >>> I am facing some problems with RGUI loading dba.count with my dataset, >>> >>>> setwd("C:/Documents and Settings/pkunderfranco/Documenti/Data /ChIP-seq >>>> Roberto/Analisi_PK/DiffBind/H3K27me3/") >>> >>>> library("DiffBind") >>> >>>> test= dba(sampleSheet='database.csv') >>> ES_H3K27 ES H3K27 1 1 raw >>> CMN_H3K27 CMN H3K27 1 1 raw >>> CMA_H3K27 CMA H3K27 1 1 raw >>> >>>> test=dba.count(test) >>> AppName: rgui.exe AppVer: 2.150.58871.0 ModName: diffbind.dll >>> ModVer: 0.0.0.0 Offset: 00003be1 >>> >>> Did anyone faced the same problem? which are the memory requirements >>> to run DiffBind? >>> Thanks, >>> Paolo >>> >>> >> >> >> NOTICE AND DISCLAIMER >> This e-mail (including any attachments) is intended for the above- named >>person(s). If you are not the intended recipient, notify the sender >>immediately, delete this email from your system and do not disclose or >>use for any purpose. >> >> We may monitor all incoming and outgoing emails in line with current >>legislation. We have taken steps to ensure that this email and >>attachments are free from any virus, but it remains your responsibility >>to ensure that viruses do not adversely affect you. >> Cancer Research UK >> Registered in England and Wales >> Company Registered Number: 4325234. >> Registered Charity Number: 1089464 and Scotland SC041666 >> Registered Office Address: Angel Building, 407 St John Street, London >>EC1V 4AD. NOTICE AND DISCLAIMER This e-mail (including any attachments) is intended for ...{{dropped:16}}