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Old 09-19-2013, 08:04 PM   #1
szimmerman
Junior Member
 
Location: United States

Join Date: Jul 2013
Posts: 7
Default mummerplot unable to generate graphic

Hi everyone,

So I used nucmer and successfully generated a .delta file. Then, I tried to run mummerplot using the command

mummerplot ref_qry.delta -R ham_pb4_shred_2k.utg.fasta -Q G5_long_contig --filter --layout

where ref_qry.delta is my .delta file, ham_pbu_shred_2k.utg.fast is my reference file. This is an entire genome with many contigs. And G5_long_contig is a single contig from a related genome.

When I run mummerplot I get this output.

gnuplot 4.2 patchlevel 6
Writing filtered delta file out.filter
Reading delta file out.filter
Writing plot files out.fplot, out.rplot
Writing gnuplot script out.gp
Forking mouse listener
Rendering plot to screen

gnuplot: unable to open display ''
gnuplot: X11 aborted.
WARNING: Unable to query clipboard with xclip

And no plot is made. Does anyone know why this is happening? Any help would be appreciated. Thank you very much!
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Old 09-20-2013, 08:02 AM   #2
SES
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Location: Vancouver, BC

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Posts: 275
Default

What OS are you using? The problem is that the default device for plotting is X11, which can't be found on your system. Trying setting the terminal to something else, like png, to see if you can at least save an image. That will tell you mummerplot is working and this is just an issue with X11. For example, try adding "-t png" or "-t postscript" to your command and see what happens.
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Old 10-03-2013, 11:20 AM   #3
szimmerman
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Location: United States

Join Date: Jul 2013
Posts: 7
Default Thank you and follow up question about coverage plot

Thanks a lot for the response. I got it to work doing what you said. However, I figured that the dot plot is not actually what I want, since I am comparing many query contig sequences that map to a single reference scaffold sequence. Instead I think I should use a coverage plot. Any idea on how to make a coverage plot instead of the dot plot? In the MuMer manual, it explains the different plots, but does not give instructions on how to make them.

Again, Thanks a lot for the fast response. Sorry for the slow reply.
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