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?
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