Re: [MUMmer-help] Problem with mummerplot

[Guannan <wan...@gm...>]

Thanks, Adam. I am just not sure whether a 71 GB delta is normal or
not.Most the delta files generated from others in my lab are just in MB
even the alignment between two entire genomes. I will try this again and
monitor the memory usage this time.
Thank you.

Guannan

On Thu, May 28, 2015 at 3:34 PM, Adam Phillippy <aph...@gm...>
wrote:

> 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
>>>>
>>>>
>>>
>>
>