Java code for dual_synteny_plot from MCscanx generating error

Question

[MAPK]

I am running the program called dual_synteny_plotter from MCScanx (https://github.com/wyp1125/MCScanX/blob/master/downstream_analyses/dual_synteny_plotter.java) like this: dual_synteny_plotter.java -g xyz.gff -s xyz.collinearity -c at_vv_dual_syn.ctl -o output_png.png. This generates error message below. Can someone please explain me why is this error? Thanks for your help in advance.

% dual_synteny_plotter.java -g xyz.gff -s xyz.collinearity -c at_vv_dual_syn.ctl -o output_png.png
import: no encode delegate for this image format `*' @ warning/constitute.c/WriteImage/1171.
/media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plotter.java: 1: /media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plo: not found
import: no encode delegate for this image format `*' @ warning/constitute.c/WriteImage/1171.
/media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plotter.java: 2: /media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plo: not found
import: no encode delegate for this image format `*' @ warning/constitute.c/WriteImage/1171.
/media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plotter.java: 3: /media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plo: not found
import: no encode delegate for this image format `*' @ warning/constitute.c/WriteImage/1171.
/media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plotter.java: 4: /media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plo: not found
/media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plotter.java: 5: /media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plo: not found
/media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plotter.java: 6: /media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plo: not found
/media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plotter.java: 7: /media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plo: not found
/media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plotter.java: 8: /media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plotter.java: public: not found
/media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plotter.java: 9: /media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plotter.java: cannot open String,: No such file
/media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plotter.java: 9: /media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plotter.java: Hashtable: not found
/media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plotter.java: 9: /media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plo: not found
/media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plotter.java: 10: /media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plotter.java: cannot open String,: No such file
/media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plotter.java: 10: /media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plotter.java: Hashtable: not found
/media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plotter.java: 10: /media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_pl: not found 
/media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plotter.java: 11: /media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plotter.java: cannot open Integer: No such file
/media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plotter.java: 11: /media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plotter.java: Vector: not found
/media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plotter.java: 11: /media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_pl: not found 
/media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plotter.java: 12: /media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plotter.java: cannot open String: No such file
/media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plotter.java: 12: /media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plotter.java: Vector: not found
/media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plotter.java: 12: /media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_pl: not found 
/media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plotter.java: 13: /media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plotter.java: cannot open String: No such file
/media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plotter.java: 13: /media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plotter.java: Vector: not found
/media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plotter.java: 13: /media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_pl: not found 
/media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plotter.java: 14: /media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plotter.java: cannot open Float: No such file
/media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plotter.java: 14: /media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plotter.java: Vector: not found
/media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plotter.java: 14: /media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_pl: not found 
/media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plotter.java: 15: /media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plotter.java: int: not found
/media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plotter.java: 15: /media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_pl: not found 
/media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plotter.java: 16: /media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plotter.java: cannot open String: No such file
/media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plotter.java: 16: /media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plotter.java: Vector: not found
/media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plotter.java: 16: /media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_pl: not found 
/media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plotter.java: 17: /media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plotter.java: cannot open String: No such file
/media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plotter.java: 17: /media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plotter.java: Vector: not found
/media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plotter.java: 17: /media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_pl: not found 
/media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plotter.java: 18: /media/owner/c92ed9e9-3d94-497c-bb2e-514a4806bbcd/mydir/NS/Sunflower/MCScanX/downstream_analyses/dual_synteny_plotter.java: Syntax error: "(" unexpected

Answer 1

[Pierre Lindenbaum]

you 're trying to execute a java source code. Just like 'c' or 'c++', java must be compiled. https://askubuntu.com/questions/145748/how-to-compile-a-java-file-on-ubuntu

try

javac  dual_synteny_plotter.java

and then

java  dual_synteny_plotter -g xyz.gff -s xyz.collinearity -c at_vv_dual_syn.ctl -o output_png.png

[MAPK]

Thank you for your answer. Now I am getting this error:

java  dual_synteny_plotter -g xyz.gff -s xyz.collinearity -c at_vv_dual_syn.ctl -o output_png.png
Reading control file error: For input string: "200 //plot width (in pixels)"
Exception in thread "main" java.lang.IllegalArgumentException: Width (0) and height (0) cannot be <= 0
    at java.awt.image.DirectColorModel.createCompatibleWritableRaster(DirectColorModel.java:1016)
    at java.awt.image.BufferedImage.<init>(BufferedImage.java:333)
    at dual_synteny_plotter.main(dual_synteny_plotter.java:263)