Mauve Contig Mover Command Line Error

Question

[jlc232]

Hello,

I'm encountering the following error when trying to run Mauve Contig Mover to reorder the contigs in a draft genome from the Command line.

$ java -Xmx500m -cp /Applications/Mauve.app/Contents/Java/Mauve.jar org.gel.mauve.contigs.ContigOrderer -output mA17 -ref EGDe.gbk -draft mA17.fasta
Error: A JNI error has occurred, please check your installation and try again
Exception in thread "main" java.lang.NoClassDefFoundError: org/biojava/bio/seq/OptimizableFilter
    at java.lang.Class.getDeclaredMethods0(Native Method)
    at java.lang.Class.privateGetDeclaredMethods(Class.java:2701)
    at java.lang.Class.privateGetMethodRecursive(Class.java:3048)
    at java.lang.Class.getMethod0(Class.java:3018)
    at java.lang.Class.getMethod(Class.java:1784)
    at sun.launcher.LauncherHelper.validateMainClass(LauncherHelper.java:544)
    at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:526)
Caused by: java.lang.ClassNotFoundException: org.biojava.bio.seq.OptimizableFilter
    at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
    at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
    ... 7 more

I'm running Mac OSX 10.9.5, with JDK v. 8, and Mauve-2.4.0, though I've tried other versions of Mauve and have gotten the same error.

Any thoughts on this would be greatly appreciated!

[h.mon]

Are you able to run Mauve with some small toy datasets, using the same command-line?

Answer 1

[alexander.d.esin]

I had an exactly identical problem trying to run the Contig Mover from the command line, and stumbled across your question. In case you still need it, or someone else stumbles across this - this is how I fixed it. My error message was identical to the one above. I am also running Mac OSX 10.9.5 with JDK 8, and the latest snapshot of Mauve.

UPDATE

The older method is still workable, but I went back to it and simply solved it by running the command line as such:

java -Xmx4096m -cp "/Applications/Mauve.app/Contents/Java/*" org.gel.mauve.contigs.ContigOrderer (etc)

This way the java classpath (-cp) will pick up all the Jars in the Mauve.app directory, including the essential biojava .jars.

OLD

I downloaded the following .jar binaries from http://biojava.org/wiki/BioJava:Download_1.7.1:

• biojava.jar
• bytecode.jar
• commons-cli.jar

I placed these in my $JAVA_HOME/jre/lib/ext directory

$JAVA_HOME can be found by running from terminal shell:

/usr/libexec/java_home

In my case tthe full path was: /Library/Java/JavaVirtualMachines/jdk1.8.0_60.jdk/Contents/Home/jre/lib/ext

After transferring the .jar files my Contig Mover ran without problems with the same arguments and setup as your initial command line!

Hope this works for you.

-S

[rrcutler]

I was trying your updated terminal command but got this error: ref file: org.gel.mauve.contigs.ContigMauveAlignFrame[panel0,0,0,400x383,invalid] Directory already contains reorder

Any help with this?

[jessica]

You've probably figured this out or given up, but for anyone who happens upon this question: you just need to first delete the directory that Mauve created the first time you tried to run it (should be called alignment1).

[jessica]

This answer did it for me, except for one thing: The Contig Mover uses the progressiveMauve script and (unless I've missed something) assumes it will be on the system PATH. So first, I created a symbolic link to that in /usr/local/bin:

ln -s /Applications/Mauve.app/Contents/MacOS/progressiveMauve /usr/local/bin/