java.lang.reflect.InvocationTargetException

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Solutions on the web23813

  • via Terracotta by johannr, 11 months ago
    This exception has no message.
  • via Terracotta by pgovindraj, 11 months ago
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  • via Terracotta by bradleyw, 11 months ago
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  • Stack trace

    • java.lang.reflect.InvocationTargetException at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at com.simontuffs.onejar.Boot.run(Boot.java:340) at com.simontuffs.onejar.Boot.main(Boot.java:166) Caused by: java.lang.IllegalStateException: Inappropriate call if not paired read at htsjdk.samtools.SAMRecord.requireReadPaired(SAMRecord.java:648) at htsjdk.samtools.SAMRecord.getFirstOfPairFlag(SAMRecord.java:706) at org.broadinstitute.pilon.BamFile$MateMap.addRead(BamFile.scala:224) at org.broadinstitute.pilon.BamFile$MateMap$$anonfun$addReads$1.apply(BamFile.scala:220) at org.broadinstitute.pilon.BamFile$MateMap$$anonfun$addReads$1.apply(BamFile.scala:220) at scala.collection.immutable.List.foreach(List.scala:381) at org.broadinstitute.pilon.BamFile$MateMap.addReads(BamFile.scala:220) at org.broadinstitute.pilon.BamFile$MateMap.<init>(BamFile.scala:218) at org.broadinstitute.pilon.BamFile.recruitFlankReads(BamFile.scala:339) at org.broadinstitute.pilon.GapFiller$$anonfun$recruitReadsOfType$1.apply(GapFiller.scala:367) at org.broadinstitute.pilon.GapFiller$$anonfun$recruitReadsOfType$1.apply(GapFiller.scala:366) at scala.collection.immutable.List.foreach(List.scala:381) at org.broadinstitute.pilon.GapFiller.recruitReadsOfType(GapFiller.scala:366) at org.broadinstitute.pilon.GapFiller.recruitFrags(GapFiller.scala:375) at org.broadinstitute.pilon.GapFiller.recruitLocalReads(GapFiller.scala:389) at org.broadinstitute.pilon.GapFiller.recruitReads(GapFiller.scala:391) at org.broadinstitute.pilon.GapFiller.assembleAcrossBreak(GapFiller.scala:51) at org.broadinstitute.pilon.GapFiller.fixBreak(GapFiller.scala:45) at org.broadinstitute.pilon.GenomeRegion$$anonfun$identifyAndFixIssues$4.apply(GenomeRegion.scala:381) at org.broadinstitute.pilon.GenomeRegion$$anonfun$identifyAndFixIssues$4.apply(GenomeRegion.scala:379) at scala.collection.immutable.List.foreach(List.scala:381) at org.broadinstitute.pilon.GenomeRegion.identifyAndFixIssues(GenomeRegion.scala:379) at org.broadinstitute.pilon.GenomeFile$$anonfun$processRegions$4.apply(GenomeFile.scala:120) at org.broadinstitute.pilon.GenomeFile$$anonfun$processRegions$4.apply(GenomeFile.scala:109) at scala.collection.Iterator$class.foreach(Iterator.scala:893) at scala.collection.AbstractIterator.foreach(Iterator.scala:1336) at scala.collection.parallel.ParIterableLike$Foreach.leaf(ParIterableLike.scala:972) at scala.collection.parallel.Task$$anonfun$tryLeaf$1.apply$mcV$sp(Tasks.scala:49) at scala.collection.parallel.Task$$anonfun$tryLeaf$1.apply(Tasks.scala:48) at scala.collection.parallel.Task$$anonfun$tryLeaf$1.apply(Tasks.scala:48) at scala.collection.parallel.Task$class.tryLeaf(Tasks.scala:51) at scala.collection.parallel.ParIterableLike$Foreach.tryLeaf(ParIterableLike.scala:969) at scala.collection.parallel.AdaptiveWorkStealingTasks$WrappedTask$class.compute(Tasks.scala:152) at scala.collection.parallel.AdaptiveWorkStealingForkJoinTasks$WrappedTask.compute(Tasks.scala:443) at scala.concurrent.forkjoin.RecursiveAction.exec(RecursiveAction.java:160) at scala.concurrent.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260) at scala.concurrent.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339) at scala.concurrent.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979) at scala.concurrent.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)

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