Hi trying to set up a pipeline for an inexperienced student on a Galaxy server , this includes using PROKKA to annotate a SPADES assembly if I run PROKKA I obtain a fatal error.
Fatal error: Exit code 2 ()
Error: A JNI error has occurred, please check your installation and try again
Exception in thread “main” java.lang.UnsupportedClassVersionError: minced has been compiled by a more recent version of the Java Runtime (class file
The VM I’m running is a GVL instance MSC14 at Warwick
Any suggestions on what the problem is or how to resolve this
Looks like this is an issue with minced. Others seem to have encountered a similar issue with the conda installation (https://github.com/bioconda/bioconda-recipes/issues/14975). A starting point would be to manually upgrade minced and see if it works outside of the prokka pipeline.
You could download the binary from here - https://github.com/ctSkennerton/minced. See if it works and replace the binary that galaxy is using with the working one.
Fatal error: Exit code 2 ()
Error: A JNI error has occurred, please check your installation and try again
Exception in thread “main” java.lang.UnsupportedClassVersionError: minced has been compiled by a more recent version of the Java Runtime (class file version 55.0), this version of the Java Runtime only recognizes class file versions up to 52.0
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClass(ClassLoader.java:763)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:467)
at java.net.URLClassLoader.access$100(URLClassLoader.java:73)
at java.net.URLClassLoader$1.run(URLClassLoader.java:368)
at java.net.URLClassLoader$1.run(URLClassLoader.java:362)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:361)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:495)
[13:46:30] Could not determine version of minced - please install version 2.0 or higher
doesnt this mean the the binary was compiled with a higher version of Java (11) than Galaxy is trying to run it with (java 8)?
I would suggest testing a newer version of minced. If it works then replace the appropriate directory in /home/linuxbrew/.linuxbrew/Cellar/prokka/HEAD-f7f819b/binaries/common/ with the functioning version.
I replaced the binaries in the Prokka subdir directory, checked they work by running the jar file with --help which worked fine. running Prokka in galaxy still get the same error message. Not sure what I can do
Ok the former is just a directory that contains the minced.jar file and the doesn’t include executable attributes, but Ive substituted it and change the attributes check it works but same outcome in Galaxy
done the same in /home/linuxbrew/.linuxbrew/Cellar/minced/0.2.0/share/minced/
same outcome
Hi Sion,
ran brew upgrade
brew update prokka gave the error message
ubuntu@msc14:~$ brew update prokka
Error: This command updates brew itself, and does not take formula names.
Use ‘brew upgrade prokka’ instead.
but ran brew upgrade prokka with the following message