snpEFF Database building error

[parimaladevi]

I am using snpEFF for SNP annotation. I am building my own database. I added genome entry to snpEff's configuration. I'm building the database from a GFF file.

When I wrote out this command :

$ java -jar snpEff.jar build -gff -v Y55

I got this error:

Exception in thread "main" java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpEffect/commandLine/SnpEff : Unsupported major.minor version 51.0
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClass(ClassLoader.java:643)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:277)
at java.net.URLClassLoader.access$000(URLClassLoader.java:73)
at java.net.URLClassLoader$1.run(URLClassLoader.java:212)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:205)
at java.lang.ClassLoader.loadClass(ClassLoader.java:323)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294)
at java.lang.ClassLoader.loadClass(ClassLoader.java:268)
Could not find the main class: ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff. Program will exit.

How do I fix this?

Thanks in advance!

[ebioman]

Hi
It looks to me as if your java version is old - I had the same issue and updating it fixed it.
Cheers

[loyaltman]

error in building annotation database by SnpEff

Hello!
I am building an annotation database according to the manual of SnpEff.
I got the error warning as following:

00:00:00 SnpEff version SnpEff 4.2 (build 2015-12-05), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'IRGSP1'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'IRGSP1'
00:00:00 Reading config file: /.../snpEff/snpEff.config
java.lang.RuntimeException: Property: 'IRGSP1.genome' not found
at ca.mcgill.mcb.pcingola.interval.Genome.<init>(Genome.java:106)
at ca.mcgill.mcb.pcingola.snpEffect.Config.readGenomeConfig(Config.java:619)
at ca.mcgill.mcb.pcingola.snpEffect.Config.readConfig(Config.java:587)
at ca.mcgill.mcb.pcingola.snpEffect.Config.init(Config.java:434)
at ca.mcgill.mcb.pcingola.snpEffect.Config.<init>(Config.java:110)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.loadConfig(SnpEff.java:273)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdBuild.run(SnpEffCmdBuild.java:340)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:978)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:136)
00:00:00 Logging

Does someone know how to fix it?
Thank you very much