"Snepff problem because of java version"
carlosfreytas opened this issue · 0 comments
Hello, just trying to install snippy, but there is a problem. When I check snps.log, told me this:
echo snippy 4.5.0
cd /home/carlosfreytas
/home/carlosfreytas/miniconda3/envs/snippy_env/bin/snippy --cpus 8 --outdir variants --ref Agyy99.gb --R1 trimmed_R1.fastq.gz --R2 trimmed_R2.fastq.gz
samtools faidx reference/ref.fa
bwa index reference/ref.fa
[bwa_index] Pack FASTA... 0.03 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 1.11 seconds elapse.
[bwa_index] Update BWT... 0.02 sec
[bwa_index] Pack forward-only FASTA... 0.01 sec
[bwa_index] Construct SA from BWT and Occ... 0.27 sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa index reference/ref.fa
[main] Real time: 1.472 sec; CPU: 1.440 sec
mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa
ln -sf reference/ref.fa .
ln -sf reference/ref.fa.fai .
mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.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)
FIRST I WAS THINKING THAT I NEED A CURRENT VERSION OF JAVA, But reading another issues, I see that maybe is totally the opposite, i need java version <1.8, can you told me if I am right?