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broadinstitute / pilon

Pilon is an automated genome assembly improvement and variant detection tool
GNU General Public License v2.0
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java.lang.ArrayIndexOutOfBoundsException: -5 ERROR #120

Open francicco opened 4 years ago

francicco commented 4 years ago

Hi,

I'm getting this error using pilon1.23 I dont understand why. Any idea?

Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: -5
    at org.broadinstitute.pilon.PileUpRegion.$anonfun$addRead$5(PileUpRegion.scala:161)
    at org.broadinstitute.pilon.PileUpRegion.$anonfun$addRead$5$adapted(PileUpRegion.scala:145)
    at scala.collection.Iterator.foreach(Iterator.scala:937)
    at scala.collection.Iterator.foreach$(Iterator.scala:937)
    at scala.collection.AbstractIterator.foreach(Iterator.scala:1425)
    at scala.collection.IterableLike.foreach(IterableLike.scala:70)
    at scala.collection.IterableLike.foreach$(IterableLike.scala:69)
    at scala.collection.AbstractIterable.foreach(Iterable.scala:54)
    at org.broadinstitute.pilon.PileUpRegion.addRead(PileUpRegion.scala:145)
    at org.broadinstitute.pilon.BamFile.$anonfun$process$1(BamFile.scala:132)
    at org.broadinstitute.pilon.BamFile.$anonfun$process$1$adapted(BamFile.scala:125)
    at scala.collection.Iterator.foreach(Iterator.scala:937)
    at scala.collection.Iterator.foreach$(Iterator.scala:937)
    at scala.collection.AbstractIterator.foreach(Iterator.scala:1425)
    at org.broadinstitute.pilon.BamFile.process(BamFile.scala:125)
    at org.broadinstitute.pilon.GenomeRegion.processBam(GenomeRegion.scala:292)
    at org.broadinstitute.pilon.GenomeFile.$anonfun$processRegions$5(GenomeFile.scala:112)
    at org.broadinstitute.pilon.GenomeFile.$anonfun$processRegions$5$adapted(GenomeFile.scala:112)
    at scala.collection.immutable.List.foreach(List.scala:388)
    at org.broadinstitute.pilon.GenomeFile.$anonfun$processRegions$4(GenomeFile.scala:112)
    at org.broadinstitute.pilon.GenomeFile.$anonfun$processRegions$4$adapted(GenomeFile.scala:109)
    at scala.collection.Iterator.foreach(Iterator.scala:937)
    at scala.collection.Iterator.foreach$(Iterator.scala:937)
    at scala.collection.AbstractIterator.foreach(Iterator.scala:1425)
    at scala.collection.parallel.ParIterableLike$Foreach.leaf(ParIterableLike.scala:970)
    at scala.collection.parallel.Task.$anonfun$tryLeaf$1(Tasks.scala:49)
    at scala.runtime.java8.JFunction0$mcV$sp.apply(JFunction0$mcV$sp.java:12)
    at scala.util.control.Breaks$$anon$1.catchBreak(Breaks.scala:63)
    at scala.collection.parallel.Task.tryLeaf(Tasks.scala:52)
    at scala.collection.parallel.Task.tryLeaf$(Tasks.scala:46)
    at scala.collection.parallel.ParIterableLike$Foreach.tryLeaf(ParIterableLike.scala:967)
    at scala.collection.parallel.AdaptiveWorkStealingTasks$WrappedTask.compute(Tasks.scala:149)
    at scala.collection.parallel.AdaptiveWorkStealingTasks$WrappedTask.compute$(Tasks.scala:145)
    at scala.collection.parallel.AdaptiveWorkStealingForkJoinTasks$WrappedTask.compute(Tasks.scala:436)
    at java.util.concurrent.RecursiveAction.exec(RecursiveAction.java:189)
    at java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:289)
    at java.util.concurrent.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1056)
    at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1692)
    at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:157)

Thanks F

onkarnath89 commented 3 years ago

I had the similar error by adding -Xmx200G as a parameter the error was resolved