Re: [MUMmer-help] Problem with mummerplot

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

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
>>
>>
>