Hello!
I have been having difficulty using Mauve tool to reorder contigs from a genome
assembly.
I have installed Mauve2.3.1 as well as snapshot_2012-06-07 on linux but
couldn’t get either working for the desired task. I am interested in running it
for several assemblies on the command line but its not just working...
Below is a message I got:
akinrina@hippu4:/fs/lustre/appl/rhel6/users/akinrina/mauve_snapshot_2012-06-07>
java -cp Mauve.jar org.gel.mauve.contigs.ContigOrderer -output RESULTS -ref
$WRKDIR/REFERENCE_GENOME/CAMPY_REF/NCTC11168.gbk -draft
$WRKDIR/CAMPY/FASTQ_TRIMMED/PAIRED_FASTQ/mygenome_75.final.scaffolds.fasta
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 would appreciate any help from you.
Looking forward to hearing from you.
BR,
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