Dear all,
I have a problem when trying to run ContigOrderer from command line. It works
fine from the GUI but I get some errors in the shell.
java -Xmx500m -cp /home/jlr/Build/mauve_snapshot_2012-06-07/Mauve.jar
org.gel.mauve.contigs.ContigOrderer -output test -ref NC_003210.fna -draft
42-40_20071307_clc.fa
Exception in thread "main" java.lang.NullPointerException
at javax.swing.JFileChooser.isTraversable(JFileChooser.java:1596)
at javax.swing.JFileChooser.setCurrentDirectory(JFileChooser.java:575)
at javax.swing.JFileChooser.<init>(JFileChooser.java:344)
at javax.swing.JFileChooser.<init>(JFileChooser.java:296)
at org.gel.mauve.gui.AlignFrame$1.<init>(Unknown Source)
at org.gel.mauve.gui.AlignFrame.<init>(Unknown Source)
at org.gel.mauve.gui.ProgressiveMauveAlignFrame.<init>(Unknown Source)
at org.gel.mauve.contigs.ContigMauveAlignFrame.<init>(Unknown Source)
at org.gel.mauve.contigs.ContigOrderer.init(Unknown Source)
at org.gel.mauve.contigs.ContigOrderer.<init>(Unknown Source)
at org.gel.mauve.contigs.ContigOrderer.main(Unknown Source)
I have tried it with absolute paths as well, but the same error comes up. I
have tried adding /home/jlr/Build/mauve_snapshot_2012-06-07/ to my PATH. The
error have been up in the list previously but then I never saw the final
solution. It just looks like the paths to my files and/or directories are
wrong, but I have no real idea how to fix it.
Best wishes, Jonas
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