snpEff: annottation problem - .OutOfMemoryError: Java heap space

Question

[martin.gallix]

Hi everyone.

I am using snpEff on my personal computer, and when I try to annotate a VCF file I get this error:

[[0Kjava.lang.OutOfMemoryError: Java heap space[[0KM
        at java.util.Arrays.copyOfRange(Unknown Source)[[0KM
        at java.lang.String.<init>(Unknown Source)[[0KM
        at java.lang.StringBuilder.toString(Unknown Source)[[0KM
        at java.io.BufferedReader.readLine(Unknown Source)[[0KM
        at java.io.BufferedReader.readLine(Unknown Source)[[0KM
        at org.snpeff.fileIterator.LineFileIterator.readNext(LineFileIterator.java:46)[[0KM
[[0K        at org.snpeff.fileIterator.LineFileIterator.readNext(LineFileIterator.java:13)[[0K[[1GM
        at org.snpeff.fileIterator.FileIterator.hasNext(FileIterator.java:123)[[0KM
        at org.snpeff.serializer.MarkerSerializer.load(MarkerSerializer.java:148)[[0KM
        at org.snpeff.snpEffect.SnpEffectPredictor.load(SnpEffectPredictor.java:55)[[0KM
        at org.snpeff.snpEffect.Config.loadSnpEffectPredictor(Config.java:590)[[0KM
        at org.snpeff.SnpEff.loadDb(SnpEff.java:519)[[0KM
        at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:940)[[0KM
        at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:923)[[0KM
        at org.snpeff.SnpEff.run(SnpEff.java:1188)[[0KM
        at org.snpeff.SnpEff.main(SnpEff.java:168)[[0KM
[[0K00:01:32        Logging[[0KM
[[0K00:01:34        Checking for updates...[[0KM
[[0K00:01:37        Done.[[0K[[1GM
[[0K

And I do not obtain my annotation. Can someone give me some advice on how I can solve this error? I think it is a memory problem. Maybe adjusting some parameters ?

[Arup Ghosh]

What's the command you are using and the available memory in your personal computer?

Answer 1

[Pierre Lindenbaum]

use the java modifier -Xmx to increase the memory. https://stackoverflow.com/questions/14763079/what-are-the-xms-and-xmx-parameters-when-starting-jvm