Pilon polishing crashes in beginning of second batch

Question

[anitajnorman]

Hello,

I've been trying to run Pilon several times with different parameters and it seems to always fail when it tries to process the second batch of scaffold_1:

Finished processing scaffold_1:1-9688624
Processing scaffold_1:9688625-19377248

Is this something to do with my data? Is it a software issue? I do know it is not a memory issue. I've allocated a lot of memory and though it does use a lot since it is a large genome, it is not using the maximum before it crashes. Any help will be much appreciated.

Thanks in advance.

Anita

Call:

java -Xmx700G -jar ~/software/pilon/pilon-1.24.jar \ --genome $REF \ --fix all \ --changes \ --bam $FRAGS \ --output $OUTFILE \ --verbose --vcf --diploid --tracks

Full error msg:

Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: Index -1 out of bounds for length 9688624 at org.broadinstitute.pilon.PileUpRegion.$anonfun$addRead$5(PileUpRegion.scala:161) at org.broadinstitute.pilon.PileUpRegion.$anonfun$addRead$5$adapted(PileUpRegion.scala:145) at scala.collection.IterableOnceOps.foreach(IterableOnce.scala:563) at scala.collection.IterableOnceOps.foreach$(IterableOnce.scala:561) at scala.collection.AbstractIterable.foreach(Iterable.scala:919) at org.broadinstitute.pilon.PileUpRegion.addRead(PileUpRegion.scala:145) at org.broadinstitute.pilon.BamFile.$anonfun$process$1(BamFile.scala:133) at org.broadinstitute.pilon.BamFile.$anonfun$process$1$adapted(BamFile.scala:126) at scala.collection.IterableOnceOps.foreach(IterableOnce.scala:563) at scala.collection.IterableOnceOps.foreach$(IterableOnce.scala:561) at scala.collection.AbstractIterator.foreach(Iterator.scala:1279) at org.broadinstitute.pilon.BamFile.process(BamFile.scala:126) at org.broadinstitute.pilon.GenomeRegion.processBam(GenomeRegion.scala:294) at org.broadinstitute.pilon.GenomeFile.$anonfun$processRegions$5(GenomeFile.scala:105) at org.broadinstitute.pilon.GenomeFile.$anonfun$processRegions$5$adapted(GenomeFile.scala:105) at scala.collection.immutable.List.foreach(List.scala:333) at org.broadinstitute.pilon.GenomeFile.$anonfun$processRegions$4(GenomeFile.scala:105) at org.broadinstitute.pilon.GenomeFile.$anonfun$processRegions$4$adapted(GenomeFile.scala:102) at scala.collection.immutable.List.foreach(List.scala:333) at org.broadinstitute.pilon.GenomeFile.processRegions(GenomeFile.scala:102) at org.broadinstitute.pilon.Pilon$.main(Pilon.scala:111) at org.broadinstitute.pilon.Pilon.main(Pilon.scala)

[Pierre Lindenbaum]

check your scaffold intervals are stricly with the size of the chromosomes defined in REF.

[lieven.sterck]

Hello anitajnorman ,

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.

Thank you!

[anitajnorman]

Thank you. I will do that.