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From: Adam P. <aph...@gm...> - 2015-05-28 20:34:27
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Hm, yes, that could be because delta-filter is using too much memory. I'd suggest monitoring the memory usage. Also, some managed servers might be configured to kill a process using more than some pre allocated amount of memory. Best, -Adam On Thu, May 28, 2015 at 3:07 PM, Guannan <wan...@gm...> wrote: > Thanks, Adam. That does make sense. I am ssh'ing to a server where > graphical interface is not allowed. I am now running mummerplot with '-t > png' to see whether it is working or not. Another problem I have here is > that even when I tried delta-filter which doesn't require X, I still ended > up with "killed" without any error message. So I even don't know what is > the problem here. Do you have any idea about it? Is it because the > generated 71GB delta file is too big? > Thanks > > Nan > > On Thu, May 28, 2015 at 10:16 AM, Adam Phillippy <aph...@gm...> > wrote: > >> This is probably because you don't have a running X server. Mummerplot, >> by default, will try and launch an interactive gnuplot window which >> requires X. If you don't have X, you can generate a static plot with >> mummerplot '-t png' which will generate a png image. (If you are ssh'ing to >> a server, and that's what is confusing things, make sure to ssh with the -X >> option to forward X) >> >> Best, >> -Adam >> >> >> On Tue, May 26, 2015 at 7:57 PM, Guannan <wan...@gm...> >> wrote: >> >>> Hello, >>> >>> I have been using Amoscmp-shortreads for a reference-guided assembly, in >>> which nucmer is used. >>> The command in that pipeline is : /usr/local/bin/nucmer --maxmatch >>> --prefix=my_file -l 20 -c 20 my_file.1con my_file.seq.After this, a 71G >>> delta file is generated. >>> But when I wanted to visualize this delta file with mummerplot, it shown >>> 'killed' without any error message. Here is the command I used: mummerplot >>> my_file.delta. >>> What is the problem here and how should I solve it? >>> Thank you. >>> >>> Nan >>> >>> >>> ------------------------------------------------------------------------------ >>> >>> _______________________________________________ >>> MUMmer-help mailing list >>> MUM...@li... >>> https://lists.sourceforge.net/lists/listinfo/mummer-help >>> >>> >> > |