snippy error

[sekhwal]

I am running snippy using following command. However, it shows the following error..

snippy --cpus 8 --outdir variants --ref reference.gbk --R1 trimmed_S_010_R1.fastq.gz --R2 trimmed_S_010_R2.fastq.gz

snpEff build -c reference/snpeff.config -dataDir . -gff3 ref

Error: A JNI error has occurred, please check your installation and try again Exception in thread "main" java.lang.UnsupportedClassVersionError: org/snpeff/SnpEff 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: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)

[sekhwal]

Next, it shows "Need bcftools --version >= 1.7 but you have 0 - please upgrade it." However, I have bcftools1.15 in my conda environment.

[apetkau]

See https://github.com/tseemann/snippy/issues/501#issuecomment-1083236553