search

broadinstitute / pilon

Pilon is an automated genome assembly improvement and variant detection tool
GNU General Public License v2.0
340 stars 60 forks source link

Exception in thread "main" java.lang.reflect.InvocationTargetException #65

Closed wenjiexiaomeng closed 5 years ago

wenjiexiaomeng commented 6 years ago

Hi, I dont know what cause this, could you give me a hand ? I tried different parameters but it seemed doen't work. and I also got all the contig name in my sam head.

####################################################################### Exception in thread "main" java.lang.reflect.InvocationTargetException at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:606) at com.simontuffs.onejar.Boot.run(Boot.java:340) at com.simontuffs.onejar.Boot.main(Boot.java:166) Caused by: java.lang.IllegalArgumentException: Invalid reference index -1 at htsjdk.samtools.QueryInterval.(QueryInterval.java:24) at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:503) at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.queryOverlapping(SamReader.java:365) at org.broadinstitute.pilon.BamFile.process(BamFile.scala:106) at org.broadinstitute.pilon.GenomeRegion.processBam(GenomeRegion.scala:279) at org.broadinstitute.pilon.GenomeFile$$anonfun$processRegions$4$$anonfun$apply$3.apply(GenomeFile.scala:111) at org.broadinstitute.pilon.GenomeFile$$anonfun$processRegions$4$$anonfun$apply$3.apply(GenomeFile.scala:111) at scala.collection.immutable.List.foreach(List.scala:381) at org.broadinstitute.pilon.GenomeFile$$anonfun$processRegions$4.apply(GenomeFile.scala:111) at org.broadinstitute.pilon.GenomeFile$$anonfun$processRegions$4.apply(GenomeFile.scala:108) at scala.collection.Iterator$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$class.internal(Tasks.scala:169) at scala.collection.parallel.AdaptiveWorkStealingForkJoinTasks$WrappedTask.internal(Tasks.scala:443) at scala.collection.parallel.AdaptiveWorkStealingTasks$WrappedTask$class.compute(Tasks.scala:149) 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)

astewart-twist commented 5 years ago

I've only seen this when running out of memory, but the cause message is buried a bit further down:

Caused by: java.lang.IllegalArgumentException: Invalid reference index -1

Maybe that helps elucidate the problem a bit further?