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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!
The text was updated successfully, but these errors were encountered:
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:
Please help me resolve this error. orz thank you!
The text was updated successfully, but these errors were encountered: