Hi everyone,
I am working with snpeff using a Galaxy docker. However lately I am encountering the problem, that the following error is reported "java.lang.OutOfMemoryError: Java heap space“. I read the snpeff documentation closely and found that you suggest to add -Xmx4G to the command. However, I do not exactly find where to change this memory option.
I annotate variants from Targeted sequencing (using two different panels) after Variant calling with Illumina Annotation Engine and smcounter2 with SnpEff and keep having the following error “java.lang.OutOfMemoryError: Java heap space”. In order to do so, I launched a Galaxy docker (Galaxy Docker Build Galaxy Version 19.05 (https://github.com/bgruening/docker-galaxy-stable, Cite: https://zenodo.org/record/3474211#.XcLGedF7k1I) on an Ubuntu V-Server. I installed SnpEff eff: annotate variants (Galaxy Version 4.3+T.galaxy1) repository 22 (https://toolshed.g2.bx.psu.edu/view/iuc/snpeff/268d162b9c49).
Thanks a lo for the help!
Rose
Here is an example of the the stderr:
java.lang.OutOfMemoryError: Java heap space
at java.base/java.lang.StringLatin1.toChars(StringLatin1.java:73)
at java.base/java.lang.String.toCharArray(String.java:2855)
at org.snpeff.util.GprSeq.isAmbiguous(GprSeq.java:280)
at org.snpeff.interval.MarkerSeq.setSequence(MarkerSeq.java:293)
at org.snpeff.interval.MarkerSeq.serializeParse(MarkerSeq.java:256)
at org.snpeff.serializer.MarkerSerializer.load(MarkerSerializer.java:239)
at org.snpeff.interval.Markers.load(Markers.java:219)
at org.snpeff.interval.tree.IntervalTree.load(IntervalTree.java:106)
at org.snpeff.binseq.GenomicSequences.load(GenomicSequences.java:285)
at org.snpeff.binseq.GenomicSequences.loadOrCreateFromGenome(GenomicSequences.java:298)
at org.snpeff.binseq.GenomicSequences.queryMarkerSequence(GenomicSequences.java:317)
at org.snpeff.align.VariantRealign.basesToAdd(VariantRealign.java:57)
at org.snpeff.align.VariantRealign.realign(VariantRealign.java:184)
at org.snpeff.interval.Variant.realignLeft(Variant.java:451)
at org.snpeff.interval.Gene.variantEffect(Gene.java:573)
at org.snpeff.snpEffect.SnpEffectPredictor.variantEffect(SnpEffectPredictor.java:709)
at org.snpeff.snpEffect.SnpEffectPredictor.variantEffect(SnpEffectPredictor.java:693)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.annotate(SnpEffCmdEff.java:217)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.annotateVcf(SnpEffCmdEff.java:468)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.annotate(SnpEffCmdEff.java:142)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:1029)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:984)
at org.snpeff.SnpEff.run(SnpEff.java:1183)
at org.snpeff.SnpEff.main(SnpEff.java:162)
Error: Error while processing VCF entry (line 139) :
chr15 63986202 COSM1373990;COSM1373991 CT C 7.83 HP TYPE=INDEL;RepRegion=NA;DP=511;UMT=244;VMT=8;VMF=0.0327869 GT:AD:VF 0/1:236,8:0.0327869
java.lang.OutOfMemoryError: Java heap space
Error: Error while processing VCF entry (line 149) :
chr17 7578484 COSM1324767;COSM1324768;COSM1324769;COSM1324770;COSM1324771 G GA 172.35 PASS TYPE=INDEL;RepRegion=HP;DP=650;UMT=356;VMT=102;VMF=0.2865169 GT:AD:VF 0/1:254,102:0.2865169
java.lang.OutOfMemoryError: Java heap space
java.lang.OutOfMemoryError: Java heap space
Error: Error while processing VCF entry (line 300) :
chr5 131944381 COSM1433049;COSM1433050 CA C 7.4 HP TYPE=INDEL;RepRegion=NA;DP=397;UMT=109;VMT=6;VMF=0.0550459 GT:AD:VF 0/1:103,6:0.0550459
java.lang.OutOfMemoryError: Java heap space
java.lang.OutOfMemoryError: Java heap space
Error: Error while processing VCF entry (line 375) :
chr8 128750604 . CCAG C 15.21 PASS TYPE=INDEL;RepRegion=NA;DP=2154;UMT=1261;VMT=24;VMF=0.0190325 GT:AD:VF 0/1:1237,24:0.0190325
java.lang.OutOfMemoryError: Java heap space
Error: Error while processing VCF entry (line 379) :
chrX 70360647 . ACAG A 6.97 RepT;RepS TYPE=INDEL;RepRegion=RepT,RepS;DP=620;UMT=316;VMT=8;VMF=0.0253165 GT:AD:VF 0/1:308,8:0.0253165
java.lang.OutOfMemoryError: Java heap space
5 errors.