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  • 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!

  • #2
    Looks like this issue?
    Hi, I am trying to align contigs from a de-novo assembly against a reference strain sequence. When running mummerplot with the delta file following error is thrown: mummerplot -p all all.delta gnup...


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

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