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RNA-SeQC/GATK: IntronicExpressionReadBlock error

IrinaMAIrinaMA Member, Broadie
edited September 2016 in Ask the GATK team


I seem to have the same error as the one posted 14 days ago on BioStar (

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 -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.(
at org.broadinstitute.sting.gatk.CommandLineExecutable.(
at org.broadinstitute.sting.gatk.CommandLineGATK.(
at org.broadinstitute.cga.rnaseq.gatk.GATKTools.runIntronReadCount(
at org.broadinstitute.cga.rnaseq.ReadCountMetrics.runRegionCounting(
at org.broadinstitute.cga.rnaseq.ReadCountMetrics.runReadCountMetrics(
at org.broadinstitute.cga.rnaseq.RNASeqMetrics.runMetrics(
at org.broadinstitute.cga.rnaseq.RNASeqMetrics.execute(
at org.broadinstitute.cga.rnaseq.RNASeqMetrics.main(
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(
at org.reflections.Reflections.(
at org.broadinstitute.sting.utils.classloader.PluginManager.(
... 9 more
Caused by: java.util.concurrent.ExecutionException: java.lang.RuntimeException: could not create class file from NativeString.class
at java.util.concurrent.FutureTask.get(
at org.reflections.Reflections.scan(
... 11 more
Caused by: java.lang.RuntimeException: could not create class file from NativeString.class
at org.reflections.scanners.AbstractScanner.scan(
at org.reflections.Reflections$
at java.util.concurrent.Executors$
at java.util.concurrent.ThreadPoolExecutor.runWorker(
at java.util.concurrent.ThreadPoolExecutor$
Caused by: invalid constant type: 15
at javassist.bytecode.ConstPool.readOne(
at javassist.bytecode.ConstPool.(
at javassist.bytecode.ClassFile.(
at org.reflections.adapters.JavassistAdapter.createClassObject(
at org.reflections.adapters.JavassistAdapter.createClassObject(
at org.reflections.scanners.AbstractScanner.scan(
... 6 more``


Issue · Github
by Sheila

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