Question: Error running Realigner Target Creator on Cloudman
gravatar for braveen.joseph
14 days ago by
braveen.joseph20 wrote:


While running the tool "Realigner Target Creator" on cloudman I encounter the following error. I TRIED running using on a node with high memory. It gave me the same error. Can anyone help me to rectify this?

Thank You!

java.lang.ExceptionInInitializerError at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.<init>( at org.broadinstitute.sting.gatk.CommandLineExecutable.<init>( at org.broadinstitute.sting.gatk.CommandLineGATK.<init>( at org.broadinstitute.sting.gatk.CommandLineGATK.main( Caused by: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: could not create class file from Accessible.class at org.reflections.Reflections.scan( at org.reflections.Reflections.<init>( at org.broadinstitute.sting.utils.classloader.PluginManager.<clinit>( ... 4 more Caused by: java.util.concurrent.ExecutionException: java.lang.RuntimeException: could not create class file from Accessible.class at at java.util.concurrent.FutureTask.get( at org.reflections.Reflections.scan( ... 6 more Caused by: java.lang.RuntimeException: could not create class file from Accessible.class at org.reflections.scanners.AbstractScanner.scan( at org.reflections.Reflections$ at java.util.concurrent.Executors$ at at java.util.concurrent.ThreadPoolExecutor.runWorker( at java.util.concurrent.ThreadPoolExecutor$ at Caused by: invalid constant type: 18 at javassist.bytecode.ConstPool.readOne( at at javassist.bytecode.ConstPool.<init>( at at javassist.bytecode.ClassFile.<init>( at org.reflections.adapters.JavassistAdapter.createClassObject( at org.reflections.adapters.JavassistAdapter.createClassObject( at org.reflections.scanners.AbstractScanner.scan( ... 6 more

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version exported):
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
ERROR Visit our forum to view answers to commonly asked questions
ERROR MESSAGE: Code exception (see stack trace for error itself)
ERROR ------------------------------------------------------------------------------------------
ADD COMMENTlink modified 9 days ago by Jennifer Hillman Jackson23k • written 14 days ago by braveen.joseph20
gravatar for Jennifer Hillman Jackson
9 days ago by
United States
Jennifer Hillman Jackson23k wrote:


All wrapped GATK tools are considered deprecated and may fail for code/dependency issues. No firm plans to update these have been made (yet) as far as I know.

That said, if you really want to use GATK tools right now, some might work, but you'll need to double check your inputs carefully against the Broad's requirements based on the version of the wrappers/underlying tools on your instance. Then, if the tool/tools fail even when given proper inputs, consider using alternative methods.

Galaxy tutorials, including those for Variant discovery:

Thanks! Jen, Galaxy team

ADD COMMENTlink written 9 days ago by Jennifer Hillman Jackson23k
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