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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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Index -1 out of bounds for length X #150

Open anitajnorman opened 2 years ago

anitajnorman commented 2 years ago

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

Can anyone tell me why this might be the case?

Thanks in advance.

Anita

Call:

java -Xmx700G -jar /proj/nobackup/snic2021-6-72/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)

tamsinlh commented 2 years ago

Anita,

Did you have any luck resolving this? I am receiving a similar error and am stuck.