When I used SnpEff in local galaxy instance, I got an error: Exception in thread "main" java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.j
Which Java version do you use. Please make sure you are running Java 1.7.
Yes, it is figured, when I changed the java version to 1.7. Thank you so much!
But, I got another error for snpEff.
java.lang.RuntimeException: Property: 'dm5.30.genome' not found at ca.mcgill.mcb.pcingola.interval.Genome.<init>(Genome.java:92) at ca.mcgill.mcb.pcingola.snpEffect.Config.readGenomeConfig(Config.java:481) at ca.mcgill.mcb.pcingola.snpEffect.Config.readConfig(Config.java:444) at ca.mcgill.mcb.pcingola.snpEffect.Config.init(Config.java:345) at ca.mcgill.mcb.pcingola.snpEffect.Config.<init>(Config.java:96) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.readConfig(SnpEff.java:245) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:981) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:963) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:352) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:320) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:83)
What does this mean? I found the similar error on this thead http://dev.list.galaxyproject.org/snpEff-on-Galaxy-td4659332.html, but there is no reply.
Does this mean I need to add genome to Galaxy? Following this webpage: http://snpeff.sourceforge.net/SnpEff_manual.html? If yes, could you give me an example how to edit the snpEffect.xml file in dm (Drosophila) case as below? (In fact, on the drap-down menu of Genome in snpEff, there is different options for genome. Why the error shows '*.genome' not found? )
<param name="genomeVersion" type="select" label="Genome"> <option value="hg37">Human (hg37)<option> <option value="mm37.61">Mouse (mm37.61)<option> <param>
________________________________________ From: Björn Grüning [bjoern.gruening@gmail.com] Sent: Wednesday, April 02, 2014 10:35 AM To: Wang, Xiaofei; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
Hi Xiaofei,
Dear there,
When I used SnpEff in local galaxy instance, I got an error: Exception in thread "main" java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.j
Which Java version do you use. Please make sure you are running Java 1.7.
Also, when I used the FASTQ Summary Statistics, I got an error like this: Traceback (most recent call last): File "/Users/...../softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py", line 48, in if __name__ == "__main__": main() File "/Users/...
Can you give us the complete error message. The important part is missing.
Ciao, Bjoern
I tried to google and solve them by myself. But I really do not know how to do that. Could anybody give me some clue? Thanks a lot for your help!
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