Re: [MUMmer-help] Problem with mummerplot

[Adam P. <aph...@gm...>]

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
>>>
>>>
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>>
>