mummer: mummerplot error message: "Inappropriate ioctl for device"

After a few hours test, I solved this issue. I think the people who got WARNING: Unable to run 'false out.gp', Inappropriate ioctl for device is that when they installed mummer, the gnuplot was NOT in the environment path. The solution is simply, change the line 27 in mummerplot

my $GNUPLOT_EXE = "false";

to

my $GNUPLOT_EXE = "gnuplot";

If your gnuplot is in your environment path, just set “gnuplot”, if not, put the path there, like what “$LIB_DIR” and “$BIN_DIR” did.

The point why mummer 3x worked but not mummer 4x is that in mummer 3x, they did not have the “$GNUPLOT_EXE” variable, they directly used “gnuplot”. But in mummer 4x, they use “$GNUPLOT_EXE” to try to hardcode the path of gnuplot (I guess).

I also had this error. I strongly recommend people don’t bother to troubleshoot this. I wasted 1.5 days on this. Get the matching coordinates and use this R package (https://github.com/tpoorten/dotPlotly) to plot. It is so much better with both the static and interactive plots!!!

I followed asdcid’s instruction above. The “false xxx.gp” clearly should be “gnuplot xxx.gp”. It took me a whole day to solve this. Another thing to realize is the mummer4 only works with gnuplot 4.6, NOT 5.0 or higher. Here is what I did from the beginning:

1. Install Anaconda3 sudo wget https://repo.anaconda.com/archive/Anaconda3-2019.07-Linux-x86_64.sh Anaconda3-2019.07-Linux-x86_64.sh conda init
   source ~/.bashrc conda config --add channels bioconda # add channel unset PYTHONPATH # this solve an error: AttributeError: module ‘enum’ has no attribute ‘IntFlag’

2. Install Gnuplot 4.6, I had error with the most recent version of gnuplot sudo conda install -c bioconda gnuplot=4.6.0

3. Install mummer4 sudo ./conda install -c bioconda mummer4

4. Solve an error: “Can’t find PostScript prologue file prologue.ps” export GNUPLOT_PS_DIR=/home/YOURNAME/anaconda3/share/gnuplot/4.6/

This works for me. But I hope the developer or someone else could define a Docker container or Anaconda environment that solves this issue by including both Gnuplot and Mummer4 in the same environment.

Update: if you are struggling with gnuplot, there are ways to go around it completely by using R based plotting scripts like: https://jmonlong.github.io/Hippocamplus/2017/09/19/mummerplots-with-ggplot2/ https://github.com/tpoorten/dotPlotly

Install the dependencies first: conda install -c conda-forge fig2dev xfig gnuplot -y Then install mummer4 from bioconda: conda install -c bioconda mummer4 Finally, editing the mummerplot script as suggested above, form my $GNUPLOT_EXE = "false" to my $GNUPLOT_EXE = "gnuplot"

These works for me.

In my case commenting out the single line of the code mentioned by girum89 was not enough. I had to comment out the 3 lines of “$P_FORMAT” (lines 1153, 1154, 1155 of mummerplot file). In the last version of mummer the problem persists:

mummer, 4.0.0rc1 GnuPlot, gnuplot 5.2 patchlevel 8

I had this problem**** gnuplot 5.2 patchlevel 2 Reading mummer file mummer.mums (use mummer -c) Writing plot files mummer.fplot, mummer.rplot Writing gnuplot script mummer.gp Rendering plot mummer.ps

set mouse clipboardformat “[%.0f, %.0f]” ^ “mummer.gp”, line 18: wrong option

WARNING: Unable to run ‘gnuplot mummer.gp’, Inappropriate ioctl for device

Problem gone after removing the “$P_FORMAT .= “\nset mouse clipboardformat "$MFORMAT"”;” in line 1154 of mummerplot

I had the similar problem I realized that i had installed gnuplot (using sudo apt-get install gnuplot) after mummer installation. So i uninstalled mummer and re-installed it. and it worked perfectly for me

Installing the previous version of mummer, 3.9.4alpha worked!

[ljcohen@dev-intel14 mummer]$ mummerplot --fat --filter --png --large -p F_olivaceus F_oli_ONT_Fhet.delta
gnuplot 5.2 patchlevel 0
Writing filtered delta file F_olivaceus.filter
Reading delta file F_olivaceus.filter
Writing plot files F_olivaceus.fplot, F_olivaceus.rplot
Writing gnuplot script F_olivaceus.gp
Rendering plot F_olivaceus.png

Although, it does say that the mummerplot version is the same as before, which is odd:

[ljcohen@dev-intel14 mummer]$ mummerplot --version
mummerplot 3.5