Hi Yealing It sounds like it may be the user plots or you are zooming out to far to display too many reads. I would make sure you have the latest Java version.
As a check you could run the BamView on its own from : http://bamview.sourceforge.net/ I should have also mentioned to try filtering out low quality reads (when you right click on the BamView window there is a Filter By Flag...¹ option which lets you set a mapping quality cut-off). Additionally as it only loads into memory the reads from the BAM in the region that is being displayed, it will be slower the more you zoom out. The different user plot formats are described in the manual. Below is an example of the format where you specifying the base number and the values: # BASE VAL1 VAL2 VAL3 VAL4 VAL5 VAL6 # colour 5:150:55 255:0:0 0:255:0 0:0:255 100:100:100 50:150:50 176 2204.8 848.23 0 0 0 536.04 278 804.99 0 837.2 0 681.63 0 452 0 699.98 0 0 0 251.18 553 0 0 0 0 0 52.4 654 0 0 0 0 334.2 0 686 0 0 652.78 0 0 0 831 0 0 0 0 0 67.97 ... I hope this helps. Regards Tim On 3/17/10 4:53 AM, "Yealing" <yealingt+arte...@gmail.com> wrote: > 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 >> <mailto: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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