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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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Exception in thread "main" java.lang.reflect.InvocationTargetException #102

Open nsgarcia27 opened 5 years ago

nsgarcia27 commented 5 years ago

Hello,

I keep getting the error below whenever I run Pilon

Exception in thread "main" java.lang.reflect.InvocationTargetException at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:497) at com.simontuffs.onejar.Boot.run(Boot.java:340) at com.simontuffs.onejar.Boot.main(Boot.java:166) Caused by: java.lang.OutOfMemoryError: Java heap space at org.broadinstitute.pilon.GenomeRegion.(GenomeRegion.scala:55) at org.broadinstitute.pilon.GenomeFile$$anonfun$contigRegions$1.apply(GenomeFile.scala:72) at org.broadinstitute.pilon.GenomeFile$$anonfun$contigRegions$1.apply(GenomeFile.scala:72) at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:234) at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:234) at scala.collection.immutable.Range.foreach(Range.scala:160) at scala.collection.TraversableLike$class.map(TraversableLike.scala:234) at scala.collection.AbstractTraversable.map(Traversable.scala:104) at org.broadinstitute.pilon.GenomeFile.contigRegions(GenomeFile.scala:72) at org.broadinstitute.pilon.GenomeFile$$anonfun$2.apply(GenomeFile.scala:52) at org.broadinstitute.pilon.GenomeFile$$anonfun$2.apply(GenomeFile.scala:52) at scala.collection.immutable.List.map(List.scala:277) at org.broadinstitute.pilon.GenomeFile.(GenomeFile.scala:52) at org.broadinstitute.pilon.Pilon$.main(Pilon.scala:98) at org.broadinstitute.pilon.Pilon.main(Pilon.scala) ... 6 more

I read in one of the threads here it is due to insufficient memory. However, I already increased the memory to 512GB and I am still getting this error. My genome is 1.5 Gb

Are there any other factors that might be giving this error aside from insufficient memory?

Nelson

onkarnath89 commented 3 years ago

I had the similar error by adding -Xmx200G as a parameter the error was resolved. I am using pilon from github not the jar file