search

broadinstitute / pilon

Pilon is an automated genome assembly improvement and variant detection tool
GNU General Public License v2.0
337 stars 60 forks source link

Issues running pilon #137

Open myco-bradshaw opened 2 years ago

myco-bradshaw commented 2 years ago

Hello,

I have been having issues with running pilon. I have mapped and indexed my reads, however. I have also installed it using I continuously get the same error when I attempt to run pilon:

Pilon version 1.24 Thu Jan 28 13:00:45 2021 -0500 Genome: contigs.fasta Exception in thread "main" java.nio.BufferOverflowException at java.base/java.nio.HeapByteBuffer.put(HeapByteBuffer.java:240) at htsjdk.samtools.reference.AbstractIndexedFastaSequenceFile.getSubsequenceAt(AbstractIndexedFastaSequenceFile.java:222) at htsjdk.samtools.reference.IndexedFastaSequenceFile.getSubsequenceAt(IndexedFastaSequenceFile.java:49) at htsjdk.samtools.reference.AbstractIndexedFastaSequenceFile.getSequence(AbstractIndexedFastaSequenceFile.java:162) at htsjdk.samtools.reference.IndexedFastaSequenceFile.getSequence(IndexedFastaSequenceFile.java:49) at htsjdk.samtools.reference.AbstractIndexedFastaSequenceFile.nextSequence(AbstractIndexedFastaSequenceFile.java:139) at htsjdk.samtools.reference.IndexedFastaSequenceFile.nextSequence(IndexedFastaSequenceFile.java:49) at org.broadinstitute.pilon.GenomeFile.(GenomeFile.scala:39) at org.broadinstitute.pilon.Pilon$.main(Pilon.scala:108) at org.broadinstitute.pilon.Pilon.main(Pilon.scala)

I have tried calling the jar file with java as well as using the pilon command and I haven't been able to resolve the issue. Any guidance would be greatly appreciated.