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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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Exception in thread "main" java.nio.BufferUnderflowException #124

Open francescodc87 opened 4 years ago

francescodc87 commented 4 years ago

Hi all, I am getting this error and I hope somebody can help. After using this command: pilon --genome fastafile.fasta --bam bamfile.bam --output oneP_ --outdir onePfolder

I am getting this error after using this command:

unpaired bamfile.bam: Exception in thread "main" java.nio.BufferUnderflowException at java.base/java.nio.ByteBuffer.get(ByteBuffer.java:735) at java.base/java.nio.DirectByteBuffer.get(DirectByteBuffer.java:319) at java.base/java.nio.ByteBuffer.get(ByteBuffer.java:762) at htsjdk.samtools.AbstractBAMFileIndex$MemoryMappedFileBuffer.readBytes(AbstractBAMFileIndex.java:493) at htsjdk.samtools.AbstractBAMFileIndex.readBytes(AbstractBAMFileIndex.java:438) at htsjdk.samtools.AbstractBAMFileIndex.verifyBAMMagicNumber(AbstractBAMFileIndex.java:404) at htsjdk.samtools.AbstractBAMFileIndex.(AbstractBAMFileIndex.java:82) at htsjdk.samtools.DiskBasedBAMFileIndex.(DiskBasedBAMFileIndex.java:46) at htsjdk.samtools.BAMFileReader.getIndex(BAMFileReader.java:403) at htsjdk.samtools.BAMFileReader.createIndexIterator(BAMFileReader.java:915) at htsjdk.samtools.BAMFileReader.query(BAMFileReader.java:575) at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:528) 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.compute(Tasks.scala:149) at scala.collection.parallel.AdaptiveWorkStealingTasks$WrappedTask.compute$(Tasks.scala:145) at scala.collection.parallel.AdaptiveWorkStealingForkJoinTasks$WrappedTask.compute(Tasks.scala:436) at java.base/java.util.concurrent.RecursiveAction.exec(RecursiveAction.java:189) at java.base/java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:290) at java.base/java.util.concurrent.ForkJoinPool$WorkQueue.topLevelExec(ForkJoinPool.java:1020) at java.base/java.util.concurrent.ForkJoinPool.scan(ForkJoinPool.java:1656) at java.base/java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1594) at java.base/java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:177)

francescodc87 commented 4 years ago

Nobody else having this problem?

onkarnath89 commented 3 years ago

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