Hi,
I am struggling to debug the Invalid reference index -1 error when I run pilon to polish the long-read assembly made by wtdbg2. Below is a part of my log file.
/# fix break: ctg12:8746654-8746655 0 -0 +0 NoSolution /# fix break: ctg12:8746995-8747103 0 -0 +0 NoSolution /# fix break: ctg12:8747688-8747699 0 -0 +0 NoSolution Finished processing ctg12:1-8748469 Exception in thread "main" java.lang.IllegalArgumentException: Invalid reference index -1 at htsjdk.samtools.QueryInterval.<init>(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)
I have been googling for a long time resulting in no good resolution. The following link is a post in pilon wiki who have the same question.https://github.com/broadinstitute/pilon/issues/46
Thanks,
