GC overhead error [java.lang.OutOfMemoryError] while running snpEFF version 4.1
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20 months ago
halo22 ▴ 260

Hello All,

I am trying to run SnpEff on a multisample VCF file, the program processes variants until chr-5 and then dies with the following error. I'd really appreciate if you could help me with this. NOTE: I have added '-c snpEff.config" because I have edited the config file for the download and install of the reference database GRCh38.

The following is the command that I am running:

  Command: snpEff -c snpEff.config GRCh38.86 myInput.vcf.gz -v -stats Annotation.html  >  Annotated.ann.vcf



   java.lang.OutOfMemoryError: GC overhead limit exceeded
    at java.util.Arrays.copyOf(Arrays.java:3332)
    at java.lang.String.<init>(String.java:166)
    at org.snpeff.binseq.DnaSequence.getBases(DnaSequence.java:109)
    at org.snpeff.binseq.DnaSequence.getSequence(DnaSequence.java:134)
    at org.snpeff.binseq.DnaSequence.toString(DnaSequence.java:353)
    at org.snpeff.interval.MarkerSeq.getSequence(MarkerSeq.java:226)
    at org.snpeff.binseq.GenomicSequences.querySequence(GenomicSequences.java:348)
    at org.snpeff.snpEffect.HgvsDna.isDuplication(HgvsDna.java:142)
    at org.snpeff.snpEffect.HgvsDna.toString(HgvsDna.java:426)
    at org.snpeff.snpEffect.VariantEffect.getHgvsDna(VariantEffect.java:622)
    at org.snpeff.vcf.VcfEffect.set(VcfEffect.java:1052)
    at org.snpeff.vcf.VcfEffect.<init>(VcfEffect.java:147)
    at org.snpeff.outputFormatter.VcfOutputFormatter.addInfo(VcfOutputFormatter.java:97)
    at org.snpeff.outputFormatter.VcfOutputFormatter.toString(VcfOutputFormatter.java:285)
    at org.snpeff.outputFormatter.OutputFormatter.endSection(OutputFormatter.java:112)
    at org.snpeff.outputFormatter.VcfOutputFormatter.endSection(VcfOutputFormatter.java:229)
    at org.snpeff.outputFormatter.OutputFormatter.printSection(OutputFormatter.java:145)
    at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.annotate(SnpEffCmdEff.java:282)
    at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.annotateVcf(SnpEffCmdEff.java:465)
    at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.annotate(SnpEffCmdEff.java:142)
    at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:1026)
    at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:981)
    at org.snpeff.SnpEff.run(SnpEff.java:1041)
    at org.snpeff.SnpEff.main(SnpEff.java:159)
    Error: Error while processing VCF entry (line 4319718) :
next-gen snpeff • 502 views
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You don't have enough memory to run this.

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