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ctSkennerton / minced

Mining CRISPRs in Environmental Datasets
GNU General Public License v3.0
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Exception in thread "main" java.lang.NoClassDefFoundError: IntervalSearchTree$IntervalNode #19

Closed tseemann closed 6 years ago

tseemann commented 6 years ago

This is happening randomly - any ideas?

Exception in thread "main" java.lang.NoClassDefFoundError: IntervalSearchTree$IntervalNode
        at IntervalSearchTree.add(IntervalSearchTree.java:47)
        at DNASequence.mask(DNASequence.java:363)
        at CRISPRFinder.goCRISPRFinder(CRISPRFinder.java:131)
        at minced.main(minced.java:246)
Caused by: java.lang.ClassNotFoundException: IntervalSearchTree$IntervalNode
        at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:582)
        at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:185)
        at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:496)
        ... 4 more
ctSkennerton commented 6 years ago

By randomly you mean on different machines or randomly on the same machine?

ctSkennerton commented 6 years ago

Try downloading version 0.3.0 - should have the error fixed and has improved GFF output as a bonus (should also work on older JVM versions too)

tseemann commented 6 years ago

Randomly on the same machine. I'm running Prokka on ~20,000 genomes and it happens a lot.

I'll upgrade and start over :)

tseemann commented 6 years ago

Made a new brew package - probably need to tell the Conda guys. @slugger70 can you please fix minced to 0.3.0 ?

Slugger70 commented 6 years ago

In Prokka?

tseemann commented 6 years ago

@Slugger70 upgrade the whole minced package.

ctSkennerton commented 6 years ago

@tseemann did this fix your issue? Is it okay to close this now?