Wednesday 9 November 2011

snpEff crashed java.lang.Exception at ca.mcgill.mcb.pcingola.fileIterator.NeedlemanWunsch.(NeedlemanWunsch.java:23)

snpEff crashed on my system, Would you know how I can solve this?
downloaded the GRCh37.64 version of genome but it isn't in the config file (I can only see hg37.63) anyway I tried it with the subdirectory name in ./data/ just to give it a try I think it works
up to the point it crashes .

error msg as below


java -version
java version "1.6.0_26"
Java(TM) SE Runtime Environment (build 1.6.0_26-b03)
Java HotSpot(TM) 64-Bit Server VM (build 20.1-b02, mixed mode)


time java -Xmx6g -jar snpEff.jar -i vcf GRCh37.64 /data/ngsdata/RAWREADS/-exome-hiseq/cleandata/-bwa-hg19/var.flt.vcf > /data/ngsdata/RAWREADS/-exome-hiseq/cleandata/-bwa-hg19/var.flt.vcf.s_snpeff.txt
 NeedlemanWunsch.<init>(22): a.length: 101 b.length: 103
TTCTCTCTCTCTCTCTCTCTCTGTCTCTCTCTCTCTGTCTCTCTCTGTCTCTCTCTCTGTCTCTCTCTCTGTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC
TTCTCTCTCTCTCTCTCTCTCTCTGTCTCTCTCTCTCTGTCTCTCTCTGTCTCTCTCTCTGTCTCTCTCTCTGTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC
java.lang.Exception
at ca.mcgill.mcb.pcingola.fileIterator.NeedlemanWunsch.<init>(NeedlemanWunsch.java:23)
at ca.mcgill.mcb.pcingola.vcf.VcfEntry.createSeqChange(VcfEntry.java:115)
at ca.mcgill.mcb.pcingola.vcf.VcfEntry.seqChanges(VcfEntry.java:372)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.iterateVcf(SnpEffCmdEff.java:205)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.runAnalysis(SnpEffCmdEff.java:547)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:506)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:226)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:69)
NeedlemanWunsch.<init>(22): a.length: 187 b.length: 184
TCTCCTCCTCCTCCTCCTCCTCCTTCTCCTGCTCCTTCTCCTCCTCCTCCTCCTGCTCCTTCTCCTCCTCCTCCTCCTTCTCCTCCTCCTCCTCCTGCTTCTCCTCCTCCTCCTTCTCCTCCTCCTGCTTCTCCTCCTCCTCCTTCTCCTCCTCCTCCTTCTCCTCCTCCTCCTTCTCCTCCTCCTC
TCTCCTCCTCCTCCTCCTCCTTCTCCTGCTCCTTCTCCTCCTCCTCCTCCTGCTCCTTCTCCTCCTCCTCCTCCTTCTCCTCCTCCTCCTCCTGCTTCTCCTCCTCCTCCTTCTCCTCCTCCTGCTTCTCCTCCTCCTCCTTCTCCTCCTCCTCCTTCTCCTCCTCCTCCTTCTCCTCCTCCTC
java.lang.Exception
at ca.mcgill.mcb.pcingola.fileIterator.NeedlemanWunsch.<init>(NeedlemanWunsch.java:23)
at ca.mcgill.mcb.pcingola.vcf.VcfEntry.createSeqChange(VcfEntry.java:128)
at ca.mcgill.mcb.pcingola.vcf.VcfEntry.seqChanges(VcfEntry.java:372)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.iterateVcf(SnpEffCmdEff.java:205)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.runAnalysis(SnpEffCmdEff.java:547)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:506)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:226)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:69)

real 1m20.198s
user 1m56.060s
sys 0m3.230s

1 comment:

  1. Hmmm I have what I believe is truncated output so I think the commandline is correct although I will try again with this
    'java -Xmx4G -jar snpEff.jar eff -v -i vcf -o vcf GRCh37.63 1000G.exomes.vcf > snpEff_output.vcf'

    tomorrow ..

    the sequence that triggered the error also looks dubious .. hmmm hope the author replies soon ... updates to come

    ReplyDelete

Datanami, Woe be me