sbilobram
commented
4 years ago Yes I have been trying to get pass this error for last couple of days too. Has anybody resolved this ??
Open emmannaemeka opened 5 years ago
sbilobram
commented
4 years ago Yes I have been trying to get pass this error for last couple of days too. Has anybody resolved this ??
jade-davies
commented
1 year ago Yes I am also having this issue, but I see that this thread is old now. Did anyone have any luck?
Hi. I'm trying to run pilon on my nanopore assembly. But everytime I run Pilon, I encountered the error below.
Thanks
Exception in thread "main" java.lang.IllegalArgumentException: Invalid reference index -1 at htsjdk.samtools.QueryInterval.(QueryInterval.java:24)
at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:533)
at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.queryOverlapping(SamReader.java:395)
at org.broadinstitute.pilon.BamFile.process(BamFile.scala:118)
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.internal(Tasks.scala:156)
at scala.collection.parallel.AdaptiveWorkStealingTasks$WrappedTask.internal$(Tasks.scala:153)
at scala.collection.parallel.AdaptiveWorkStealingForkJoinTasks$WrappedTask.internal(Tasks.scala:436)
at scala.collection.parallel.AdaptiveWorkStealingTasks$WrappedTask.compute(Tasks.scala:146)
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)
Suppressed: java.lang.IllegalArgumentException: Invalid reference index -1