Hello,
I seem to have the same error as the one posted 14 days ago on BioStar (https://www.biostars.org/p/208982/).
Had successfully run this command in June: java -jar RNA-SeQC_v1.1.8.jar -o rnaSeQC -r Homo_sapiens_assembly19.fasta -t gencode.v19.gtf -s sample.info.file -n 1.
Tried to poke around, however without any success. Could you please help figure out how to get it to run?
Thank you!
Output + error stack trace:
Creating rRNA Interval List based on given GTF annotations
Retriving contig names from reference
contig names in reference: 85
Loading GTF for Read Counting
Converting to refGene
Transcript objects to RefGen format: 1 s
Running IntronicExpressionReadBlock Walker ....
Exception in thread "main" java.lang.ExceptionInInitializerError
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.(GenomeAnalysisEngine.java:146)
at org.broadinstitute.sting.gatk.CommandLineExecutable.(CommandLineExecutable.java:53)
at org.broadinstitute.sting.gatk.CommandLineGATK.(CommandLineGATK.java:55)
at org.broadinstitute.cga.rnaseq.gatk.GATKTools.runIntronReadCount(GATKTools.java:216)
at org.broadinstitute.cga.rnaseq.ReadCountMetrics.runRegionCounting(ReadCountMetrics.java:244)
at org.broadinstitute.cga.rnaseq.ReadCountMetrics.runReadCountMetrics(ReadCountMetrics.java:59)
at org.broadinstitute.cga.rnaseq.RNASeqMetrics.runMetrics(RNASeqMetrics.java:225)
at org.broadinstitute.cga.rnaseq.RNASeqMetrics.execute(RNASeqMetrics.java:171)
at org.broadinstitute.cga.rnaseq.RNASeqMetrics.main(RNASeqMetrics.java:139)
Caused by: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: could not create class file from NativeString.class
at org.reflections.Reflections.scan(Reflections.java:166)
at org.reflections.Reflections.(Reflections.java:91)
at org.broadinstitute.sting.utils.classloader.PluginManager.(PluginManager.java:79)
... 9 more
Caused by: java.util.concurrent.ExecutionException: java.lang.RuntimeException: could not create class file from NativeString.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)
... 11 more
Caused by: java.lang.RuntimeException: could not create class file from NativeString.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:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
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.(ConstPool.java:127)
at javassist.bytecode.ClassFile.read(ClassFile.java:693)
at javassist.bytecode.ClassFile.(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``