Hello Tim, First, thanks for your reply.
It makes me wonder why a -mx9000m will still run out of memory. I'm using version 12.0 now, (and just by chance I was using stacked view also) but BamView didn't warn me I was running out. I only knew it was running out when the windows was lagging very heavily and the BAM window keeps saying "waiting" and I checked with "top" to find that java process for artemis is using about 10G of memory. Could there be any other reason for the artemis to lag? Oh? By "specifying the base number and the values" do you mean instead of making a file that has values in each line for each base, we make a file that has the base number in one column and the plot value in another column? In this case, what about multiple plots in one file? can we get this from the manual? sorry for asking before I check. -- yealing -- On Tue, Mar 16, 2010 at 8:33 PM, Tim Carver <t...@sanger.ac.uk> wrote: > > There is no straightforward way as it it depends on the number of features > and annotation as well. It usually is a matter of trial and error. The > maximum used here would be –mx2500m which is usually more than sufficient. > > The BamView window only reads in what it is displaying. It will warn you > when it is running out of memory. You may find that it is best to use the > stack view as this is quicker to compute and uses less memory. > > The user plot does load all the data values in and there are more format > options now (in Artemis v12) for the userplots which you may find speed > things up. For example, you may find that specifying the base number and the > values reduces the file size and helps. > > Regards > Tim > > > On 3/16/10 11:47 AM, "Yealing" > <yealingt+arte...@gmail.com<yealingt%2barte...@gmail.com>> > wrote: > > Dear all, > > is there a way to estimate how much memory is needed by artemis? So we can > change the -mx flag in the art script? > I am working on an approximately 60Mb genome, I need to load a user plot of > about 40Mb, and I have 4 BAM files of about 2Gb each. > While I set the artemis to have a -mx of 9000m, it still lags after an hour > or so with the user plot and one of the BAM files loaded. > Any ideas? > > Cheers, > -- yealing -- > > ------------------------------ > _______________________________________________ > Artemis-users mailing list > Artemis-users@sanger.ac.uk > http://lists.sanger.ac.uk/mailman/listinfo/artemis-users > > > > -- The Wellcome Trust Sanger Institute is operated by Genome Research > Limited, a charity registered in England with number 1021457 and a company > registered in England with number 2742969, whose registered office is 215 > Euston Road, London, NW1 2BE. >
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