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wyp1125 / MCScanX

MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!
http://chibba.pgml.uga.edu/mcscan2/
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Error in family_tree_plotter #23

Closed ashish674675 closed 4 years ago

ashish674675 commented 4 years ago

Hi I want to display segmental and tandem duplications in a gene family tree. I ran the following commands :

javac family_tree_plotter.java
java family_tree_plotter -t ../../mcscanx_input/tree.nwk -s ../../mcscanx_input/rice.collinearity  –d ../../mcscanx_input/rice.tandem -o tandem_segmental_genes_tree.png

I get this error:

Exception in thread "main" java.lang.NullPointerException
        at family_tree_plotter.compute(family_tree_plotter.java:263)
        at family_tree_plotter.paint(family_tree_plotter.java:299)
        at family_tree_plotter.main(family_tree_plotter.java:397)

Please help me resolve this error. I am doing it on ubuntu in WSL. All other MCScanX commands I ran were successfull except this one.

Thank You

ashish674675 commented 4 years ago

I found the problem. The tree file had bootstrap values instead of branch lengths which was causing a format problem between ":" and ",".