Question: (Closed) Realigner Target Creator Error
0
gravatar for m.v.garciacastiglioni
8 weeks ago by
m.v.garciacastiglioni0 wrote:

Hi, I keep running into this problem and can't seem to figure out how to solve it...

I'm using Realigner Target Creator (version 0.0.4), files coming from Map with BWA for Illumina -> Filter SAM -> Add or replace groups.

Does anyone have any idea?

OpenJDK 64-Bit Server VM warning: DefaultMaxRAMFraction is deprecated and will likely be removed in a future release. Use MaxRAMFraction instead.

<h5>ERROR ------------------------------------------------------------------------------------------</h5> <h5>ERROR stack trace</h5>

java.lang.ExceptionInInitializerError at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.<init>(GenomeAnalysisEngine.java:143) at org.broadinstitute.sting.gatk.CommandLineExecutable.<init>(CommandLineExecutable.java:50) at org.broadinstitute.sting.gatk.CommandLineGATK.<init>(CommandLineGATK.java:53) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:89) Caused by: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: could not create class file from NativeFunction$Constructor.class at org.reflections.Reflections.scan(Reflections.java:166) at org.reflections.Reflections.<init>(Reflections.java:91) at org.broadinstitute.sting.utils.classloader.PluginManager.<clinit>(PluginManager.java:79) ... 4 more Caused by: java.util.concurrent.ExecutionException: java.lang.RuntimeException: could not create class file from NativeFunction$Constructor.class at java.util.concurrent.FutureTask.report(FutureTask.java:122) at java.util.concurrent.FutureTask.get(FutureTask.java:192) at org.reflections.Reflections.scan(Reflections.java:162) ... 6 more Caused by: java.lang.RuntimeException: could not create class file from NativeFunction$Constructor.class at org.reflections.scanners.AbstractScanner.scan(AbstractScanner.java:41) at org.reflections.Reflections$2.run(Reflections.java:149) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748) Caused by: java.io.IOException: invalid constant type: 15 at javassist.bytecode.ConstPool.readOne(ConstPool.java:1023) at javassist.bytecode.ConstPool.read(ConstPool.java:966) at javassist.bytecode.ConstPool.<init>(ConstPool.java:127) at javassist.bytecode.ClassFile.read(ClassFile.java:693) at javassist.bytecode.ClassFile.<init>(ClassFile.java:85) at org.reflections.adapters.JavassistAdapter.createClassObject(JavassistAdapter.java:86) at org.reflections.adapters.JavassistAdapter.createClassObject(JavassistAdapter.java:22) at org.reflections.scanners.AbstractScanner.scan(AbstractScanner.java:38) ... 6 more

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version exported):
ERROR
ERROR Please visit the wiki to see if this is a known problem
ERROR If not, please post the error, with stack trace, to the GATK forum
ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki
ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa
ERROR
ERROR MESSAGE: Code exception (see stack trace for error itself)
ERROR ------------------------------------------------------------------------------------------

When I download the newer version of Realigner Target Creator tool (version 2.8.0) the error says:

Error: Unable to access jarfile /GenomeAnalysisTK.jar

Thank you in advance!

galaxy gatk • 84 views
ADD COMMENTlink modified 8 weeks ago by Jennifer Hillman Jackson23k • written 8 weeks ago by m.v.garciacastiglioni0

Hello m.v.garciacastiglioni!

Questions similar to yours can already be found at:

We have closed your question to allow us to keep similar content in the same thread.

If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.

Cheers!

PS: All GATK tools are deprecated. Please see alternative tool options in our tutorials: https://galaxyproject.org/learn/
ADD REPLYlink written 8 weeks ago by Jennifer Hillman Jackson23k
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