Pilon running error

[Jung19911124]

Hi. I'm trying to run pilon on my Pacbio assembly. But everytime I run Pilon, I encountered the error below. What is the cause and how to solve this?

Any comments would be appreciated.

Best, Jung

######################################################################## Exception in thread "main" 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: htsjdk.samtools.util.RuntimeIOException: Read error; BinaryCodec in readmode; file: /media/sf_F_DRIVE/all_merged_hgap.jump.uniq.s.bam at htsjdk.samtools.util.BinaryCodec.readBytesOrFewer(BinaryCodec.java:406) at htsjdk.samtools.util.BinaryCodec.readBytes(BinaryCodec.java:380) at htsjdk.samtools.util.BinaryCodec.readByteBuffer(BinaryCodec.java:490) at htsjdk.samtools.util.BinaryCodec.readInt(BinaryCodec.java:501) at htsjdk.samtools.BAMRecordCodec.decode(BAMRecordCodec.java:177) at htsjdk.samtools.BAMFileReader$BAMFileIterator.getNextRecord(BAMFileReader.java:660) at htsjdk.samtools.BAMFileReader$BAMFileIndexIterator.getNextRecord(BAMFileReader.java:780) at htsjdk.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:634) at htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:628) at htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:598) at htsjdk.samtools.BAMFileReader$BAMQueryFilteringIterator.advance(BAMFileReader.java:831) at htsjdk.samtools.BAMFileReader$BAMQueryFilteringIterator.next(BAMFileReader.java:821) at htsjdk.samtools.BAMFileReader$BAMQueryFilteringIterator.next(BAMFileReader.java:787) at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:544) at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:518) at scala.collection.convert.Wrappers$JIteratorWrapper.next(Wrappers.scala:43) at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:462) at scala.collection.Iterator$class.foreach(Iterator.scala:893) at scala.collection.AbstractIterator.foreach(Iterator.scala:1336) at scala.collection.generic.Growable$class.$plus$plus$eq(Growable.scala:59) at scala.collection.mutable.ListBuffer.$plus$plus$eq(ListBuffer.scala:183) at scala.collection.mutable.ListBuffer.$plus$plus$eq(ListBuffer.scala:45) at scala.collection.TraversableOnce$class.to(TraversableOnce.scala:310) at scala.collection.AbstractIterator.to(Iterator.scala:1336) at scala.collection.TraversableOnce$class.toList(TraversableOnce.scala:294) at scala.collection.AbstractIterator.toList(Iterator.scala:1336) at org.broadinstitute.pilon.BamFile.readsInRegion(BamFile.scala:329) at org.broadinstitute.pilon.BamFile.recruitBadMates(BamFile.scala:357) at org.broadinstitute.pilon.GapFiller$$anonfun$recruitJumps$1.apply(GapFiller.scala:380) at org.broadinstitute.pilon.GapFiller$$anonfun$recruitJumps$1.apply(GapFiller.scala:379) at scala.collection.immutable.List.foreach(List.scala:381) at org.broadinstitute.pilon.GapFiller.recruitJumps(GapFiller.scala:379) at org.broadinstitute.pilon.GapFiller.recruitReads(GapFiller.scala:391) at org.broadinstitute.pilon.GapFiller.assembleAcrossBreak(GapFiller.scala:51) at org.broadinstitute.pilon.GapFiller.fixBreak(GapFiller.scala:45) at org.broadinstitute.pilon.GenomeRegion$$anonfun$identifyAndFixIssues$4.apply(GenomeRegion.scala:383) at org.broadinstitute.pilon.GenomeRegion$$anonfun$identifyAndFixIssues$4.apply(GenomeRegion.scala:381) at scala.collection.immutable.List.foreach(List.scala:381) at org.broadinstitute.pilon.GenomeRegion.identifyAndFixIssues(GenomeRegion.scala:381) at org.broadinstitute.pilon.GenomeFile$$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$class.internal(Tasks.scala:169) at scala.collection.parallel.AdaptiveWorkStealingForkJoinTasks$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) Caused by: java.io.IOException: Invalid argument at java.io.RandomAccessFile.readBytes(Native Method) at java.io.RandomAccessFile.read(RandomAccessFile.java:377) at htsjdk.samtools.seekablestream.SeekableFileStream.read(SeekableFileStream.java:80) at htsjdk.samtools.util.BlockCompressedInputStream.readBytes(BlockCompressedInputStream.java:421) at htsjdk.samtools.util.BlockCompressedInputStream.readBytes(BlockCompressedInputStream.java:409) at htsjdk.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:380) at htsjdk.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:127) at htsjdk.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:252) at java.io.DataInputStream.read(DataInputStream.java:149) at htsjdk.samtools.util.BinaryCodec.readBytesOrFewer(BinaryCodec.java:404) ... 57 more

[w1bw]

As far as I can tell, this is a malformed bam file, but since your report is quite old, I hope you were able to figure it out.