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SnpEff len analysis NullPointerException Error #151

Closed suimye closed 4 years ago

suimye commented 8 years ago

Hi. When I am running SnpEff with "len" option, I get the following error messages.

java -Xmx4g -jar ~/tool/snpEff/snpEff.jar len -r 100 GRCh37.75 java.lang.NullPointerException at >ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdLen.run(SnpEffCmdLen.java:159) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:978) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:136)

To test the other conditions, I changed memory size range from 10g to 1g. At the memory range over 3g, I got the similar error code as java.lang.NullPointerException. On the other hand, at the range of 2g to 1g, I got the OutOfMemoryError.

-bash-4.1$ java -Xmx2g -jar ~/tool/snpEff/snpEff.jar len -r 100 GRCh37.75 java.lang.OutOfMemoryError: Java heap space at ca.mcgill.mcb.pcingola.interval.Intron.(Intron.java:35) at ca.mcgill.mcb.pcingola.interval.Transcript.introns(Transcript.java:1174) at >ca.mcgill.mcb.pcingola.interval.Transcript.createSpliceSites(Transcript.java:655) at ca.mcgill.mcb.pcingola.interval.Genes.createSpliceSites(Genes.java:147) at >ca.mcgill.mcb.pcingola.snpEffect.SnpEffectPredictor.createGenomicRegions(SnpEffectPredi>ctor.java:205) at >ca.mcgill.mcb.pcingola.snpEffect.SnpEffectPredictor.buildForest(SnpEffectPredictor.java>:165) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.loadDb(SnpEff.java:451) at >ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdLen.run(SnpEffCmdLen.java:156) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:978) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:136)

I wondered about 32bit condition in JAVA. I also tried -d64 option in similar command. But I could not resolve this problem. On the other hand, the other SnpEff analyses such as "annotate, -cancer" were successfully done.Thus, this problem was only occurred in "len" analysis.

If you have any suggestion for this error, please reply to me.

My software environment is..

SnpEff version SnpEff 4.2 (build 2015-12-05) java version "1.7.0_79" Java(TM) SE Runtime Environment (build 1.7.0_79-b15) Java HotSpot(TM) 64-Bit Server VM (build 24.79-b02, mixed mode)

distribution CentOS release 6.7 (Final) memory 16GB

kevin-oh commented 4 years ago

I have the same problem. Error showed up irrespective of which genome I selected.

pcingola commented 4 years ago

Closing old issues.