snpEff: annottation problem
0
0
Entering edit mode
5 weeks ago

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 annottation. Can someone give me some advice on how I can solve this error? I think it is a memory problem. Maybe adjusting some parameters ?

snpEff • 198 views
ADD COMMENT
1
Entering edit mode
ADD REPLY
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 1723 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6