PROKKA fatal error on Galaxy

#1

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

Ken

#2

Hi Ken,

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.

All the best,
Sion

#3

Sorry Siion,
can you give me some guidance on how to do this?

#4

Hi Ken,

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.

You can find the existing binary on the system using find - https://www.linode.com/docs/tools-reference/tools/find-files-in-linux-using-the-command-line/

All the best,
Sion

#5

Hi Sion,
should all of these be replaced or just those in the prokka sub directory substituting the files under prokka gives the same error message

/home/linuxbrew/.linuxbrew/Cellar/prokka/HEAD-f7f819b/binaries/common/minced
/home/linuxbrew/.linuxbrew/Cellar/prokka/HEAD-f7f819b/binaries/common/minced.jar
/home/linuxbrew/.linuxbrew/Cellar/minced
/home/linuxbrew/.linuxbrew/Cellar/minced/0.2.0/bin/minced
/home/linuxbrew/.linuxbrew/Cellar/minced/0.2.0/share/minced
/home/linuxbrew/.linuxbrew/Cellar/minced/0.2.0/share/minced/minced.jar
/home/linuxbrew/.linuxbrew/bin/minced
/home/linuxbrew/.linuxbrew/var/homebrew/linked/minced
/home/linuxbrew/.linuxbrew/opt/minced
/home/linuxbrew/.linuxbrew/Library/Taps/homebrew/homebrew-science/minced.rb
/home/linuxbrew/.linuxbrew/share/minced

#6

heres the full error message

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)?

#7

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.

#8

Hi Sion,

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

Ken

#9

Hi Ken,

Have you replaced the ones in the other locations as well?

/home/linuxbrew/.linuxbrew/Cellar/minced/0.2.0/share/minced
/home/linuxbrew/.linuxbrew/Cellar/minced/0.2.0/share/minced/minced.jar

Otherwise it might be that galaxy is calling a different version java than your home environment which could be a bit trickier to resolve.

All the best,
Sion

#10

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

#11

Hi Ken,

We can try update the prokka version using brew. The commands are:

brew upgrade 
brew update prokka

If this fails then we might want to regenerate your instance and see if that resolves the issues you have encountered.

S

#12

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

ubuntu@msc14:~$ brew upgrade prokka
==> Migrating from Linuxbrew/brew to Homebrew/brew
Linuxbrew/brew has been merged into Homebrew/brew!
Linuxbrew/brew will no longer be updated.
Your git remote has been changed from
https://github.com/Linuxbrew/brew.git
to https://github.com/Homebrew/brew
See the blog post at https://brew.sh/2019/02/02/homebrew-2.0.0/
Updating Homebrew…
Error: prokka HEAD-f7f819b already installed

checked if anything had change prokka still gave same error message

Ken

#13

Hi Ken,

I will see if we can make you a new instance in Warwick. Is your data on a volume or otherwise backed up?

All the best,
Sion

#14

Could you also send me your CLIMB group name please?
S

#15

yes the data is on a volume attached to this instance

the group name is nxgenomics

#16

Hi Ken,

You should be able to spawn an instance in Warwick now. I have opened the site for you.

All the best,
Sion

#17

Hi Ken,

I have closed Warwick for now. I will PM you about reopening it tomorrow to allow you to make a new instance.

All the best,
Sion

#18

I’m out of the office tomorrow so friday would be better

closed #19

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