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pilon error:Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded #163

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smoothyly opened this issue Oct 24, 2023 · 0 comments

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@smoothyly
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Hello @bwlang
I ran the following command :
pilon --genome 08lh.fasta --fix all --changes --frags assembly_illumina.sorted.bam --output pilon --outdir pilon_result --vcf
error:

Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded
	at scala.collection.mutable.ArraySeq$ofLong.iterator(ArraySeq.scala:270)
	at scala.collection.IterableOnceOps.reduceLeft(IterableOnce.scala:725)
	at scala.collection.IterableOnceOps.reduceLeft$(IterableOnce.scala:724)
	at scala.collection.AbstractIterable.reduceLeft(Iterable.scala:919)
	at scala.collection.IterableOnceOps.reduce(IterableOnce.scala:698)
	at scala.collection.IterableOnceOps.reduce$(IterableOnce.scala:698)
	at scala.collection.AbstractIterable.reduce(Iterable.scala:919)
	at scala.collection.IterableOnceOps.sum(IterableOnce.scala:889)
	at scala.collection.IterableOnceOps.sum$(IterableOnce.scala:889)
	at scala.collection.AbstractIterable.sum(Iterable.scala:919)
	at org.broadinstitute.pilon.BaseSum.sum(BaseSum.scala:30)
	at org.broadinstitute.pilon.PileUp$BaseCall.<init>(PileUp.scala:143)
	at org.broadinstitute.pilon.PileUp.baseCall(PileUp.scala:257)
	at org.broadinstitute.pilon.GenomeRegion.$anonfun$postProcess$1(GenomeRegion.scala:240)
	at org.broadinstitute.pilon.GenomeRegion.$anonfun$postProcess$1$adapted(GenomeRegion.scala:237)
	at org.broadinstitute.pilon.GenomeRegion$$Lambda$56/1413246829.apply(Unknown Source)
	at scala.collection.immutable.Range.foreach(Range.scala:190)
	at org.broadinstitute.pilon.GenomeRegion.postProcess(GenomeRegion.scala:237)
	at org.broadinstitute.pilon.GenomeFile.$anonfun$processRegions$4(GenomeFile.scala:106)
	at org.broadinstitute.pilon.GenomeFile.$anonfun$processRegions$4$adapted(GenomeFile.scala:102)
	at org.broadinstitute.pilon.GenomeFile$$Lambda$43/1263877414.apply(Unknown Source)
	at scala.collection.immutable.List.foreach(List.scala:333)
	at org.broadinstitute.pilon.GenomeFile.processRegions(GenomeFile.scala:102)
	at org.broadinstitute.pilon.Pilon$.main(Pilon.scala:111)
	at org.broadinstitute.pilon.Pilon.main(Pilon.scala)

Please help me resolve this error. orz thank you!

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