Question: GC overhead error [java.lang.OutOfMemoryError] while running snpEFF version 4.1
gravatar for halo22
12 months ago by
Indianapolis, IN
halo22180 wrote:

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(
    at java.lang.String.<init>(
    at org.snpeff.binseq.DnaSequence.getBases(
    at org.snpeff.binseq.DnaSequence.getSequence(
    at org.snpeff.binseq.DnaSequence.toString(
    at org.snpeff.interval.MarkerSeq.getSequence(
    at org.snpeff.binseq.GenomicSequences.querySequence(
    at org.snpeff.snpEffect.HgvsDna.isDuplication(
    at org.snpeff.snpEffect.HgvsDna.toString(
    at org.snpeff.snpEffect.VariantEffect.getHgvsDna(
    at org.snpeff.vcf.VcfEffect.set(
    at org.snpeff.vcf.VcfEffect.<init>(
    at org.snpeff.outputFormatter.VcfOutputFormatter.addInfo(
    at org.snpeff.outputFormatter.VcfOutputFormatter.toString(
    at org.snpeff.outputFormatter.OutputFormatter.endSection(
    at org.snpeff.outputFormatter.VcfOutputFormatter.endSection(
    at org.snpeff.outputFormatter.OutputFormatter.printSection(
    at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.annotate(
    at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.annotateVcf(
    at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.annotate(
    at org.snpeff.SnpEff.main(
    Error: Error while processing VCF entry (line 4319718) :
snpeff next-gen • 324 views
ADD COMMENTlink modified 12 months ago • written 12 months ago by halo22180

You don't have enough memory to run this.

ADD REPLYlink written 12 months ago by JC12k
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