Issue
I was trying to use fastqc
command for qualification of fastq files. it was working alright few weeks ago, but after i updated my ubuntu software, i get this error:
$ fastqc -f fastq chrX_data/samples/ERR188245_chrX_1.fastq
Error: A JNI error has occurred, please check your installation and try again
Exception in thread "main" java.lang.UnsupportedClassVersionError: uk/ac/babraham/FastQC/FastQCApplication has been compiled by a more recent version of the Java Runtime (class file version 53.0), 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:757)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:473)
at java.net.URLClassLoader.access$100(URLClassLoader.java:74)
at java.net.URLClassLoader$1.run(URLClassLoader.java:369)
at java.net.URLClassLoader$1.run(URLClassLoader.java:363)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:362)
at java.lang.ClassLoader.loadClass(ClassLoader.java:419)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:352)
at java.lang.ClassLoader.loadClass(ClassLoader.java:352)
at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:601)
I checked java
and javac
versions:
$ java -version
openjdk version "1.8.0_312"
OpenJDK Runtime Environment (Zulu 8.58.0.13-CA-linux64) (build 1.8.0_312-b07)
OpenJDK 64-Bit Server VM (Zulu 8.58.0.13-CA-linux64) (build 25.312-b07, mixed mode)
And
$ javac -version
javac 1.8.0_312
I tried to update my jdk to jdk-17. i downloaded jdk-17_linux-x64_bin.tar.gz file and locally copied to its path and installed it, but java version did not changed.
I used this instruction to installing jdk-17
https://www.javahelps.com/2021/09/install-oracle-jdk-17-on-linux.html
Solution
Please use a newer version of Java. Most likely you already have it. Just reconfigure to use Open JDK 11 or newer.
$ sudo update-alternatives --config java
There are 2 choices for the alternative java (providing /usr/bin/java).
Selection Path Priority Status
------------------------------------------------------------
0 /usr/lib/jvm/java-11-openjdk-amd64/bin/java 1111 auto mode
1 /usr/lib/jvm/java-11-openjdk-amd64/bin/java 1111 manual mode
* 2 /usr/lib/jvm/java-8-oracle/jre/bin/java 1081 manual mode
Press <enter> to keep the current choice[*], or type selection number: 0
update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode
Answered By - Mikhail Olferiev Answer Checked By - Dawn Plyler (WPSolving Volunteer)