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Old 11-11-2015, 07:25 AM   #1
kramergj
Junior Member
 
Location: Toronto

Join Date: Nov 2015
Posts: 3
Default Mummerplot Error

Hello everyone,

I am hoping that you may have some insight into a mummerplot error that I am encountering.

I have been able to generate a .delta files using nucmer and have attempted to run mummerplot using the command:

mummerplot Ref_Query.delta -R Ref.fasta -Q Query.fasta --filter --layout

The command is returning this error:

defined(%hash) is deprecated at /home/nodwell/MUMmer3.23/mummerplot line 884.
(Maybe you should just omit the defined()?)
defined(%hash) is deprecated at /home/nodwell/MUMmer3.23/mummerplot line 894.
(Maybe you should just omit the defined()?)
defined(%hash) is deprecated at /home/nodwell/MUMmer3.23/mummerplot line 981.
(Maybe you should just omit the defined()?)
defined(%hash) is deprecated at /home/nodwell/MUMmer3.23/mummerplot line 991.
(Maybe you should just omit the defined()?)
defined(%hash) is deprecated at /home/nodwell/MUMmer3.23/mummerplot line 1034.
(Maybe you should just omit the defined()?)
defined(%hash) is deprecated at /home/nodwell/MUMmer3.23/mummerplot line 1044.
(Maybe you should just omit the defined()?)
gnuplot 5.0 patchlevel 1
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

set mouse clipboardformat "[%.0f, %.0f]"
^
"out.gp", line 668: wrong option

WARNING: Unable to run 'gnuplot -geometry 500x500+0+0 -title mummerplot out.gp', Inappropriate ioctl for device

It seems like something is going off with gnuplot, but I am at a loss for what it is. Maybe my install/configuration of gnuplot? Any ideas are much appreciated!

Thank you!
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Old 05-22-2018, 07:35 AM   #2
maubp
Peter (Biopython etc)
 
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,543
Default

Looks like this issue?
https://github.com/mummer4/mummer/issues/9

(I just ran into this error with mummer v3.23 and "gnuplot 5.0 patchlevel 5")
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