But when I'm using SelectVariants command to extact the filtered site:
gatk-4.1.2.0/gatk --java-options "-Djava.io.tmpdir=/tmp/" SelectVariants -R genome.fa -V snp_rmnan.raw.vcf.tmp.vcf --exclude-filtered -O snp_rmnan.raw.vcf.filter.vcf
I get this java ERROR below, even without the wrong line number and do not know how to deal with it......... o(╥﹏╥)o,Thank you very much!
11:15:52.195 INFO ProgressMeter - Chr01:15144308 19.9 541000 27161.2
11:16:04.187 INFO ProgressMeter - Chr01:15388212 20.1 547000 27189.6
11:16:12.515 INFO SelectVariants - Shutting down engine
[May 9, 2019 11:16:12 AM CST] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 20.37 minutes.
Runtime.totalMemory()=2814377984
java.lang.NumberFormatException: For input string: "1,0"
at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
at java.lang.Integer.parseInt(Integer.java:580)
at java.lang.Integer.parseInt(Integer.java:615)
at htsjdk.variant.vcf.AbstractVCFCodec.createGenotypeMap(AbstractVCFCodec.java:734)
at htsjdk.variant.vcf.AbstractVCFCodec$LazyVCFGenotypesParser.parse(AbstractVCFCodec.java:132)
at htsjdk.variant.variantcontext.LazyGenotypesContext.decode(LazyGenotypesContext.java:158)
at htsjdk.variant.variantcontext.LazyGenotypesContext.getGenotypes(LazyGenotypesContext.java:148)
at htsjdk.variant.variantcontext.GenotypesContext.iterator(GenotypesContext.java:465)
at org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants.initalizeAlleleAnyploidIndicesCache(SelectVariants.java:674)
at org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants.apply(SelectVariants.java:580)
at org.broadinstitute.hellbender.engine.VariantWalker.lambda$traverse$0(VariantWalker.java:106)
at org.broadinstitute.hellbender.engine.VariantWalker$$Lambda$73/388489274.accept(Unknown Source)
at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:183)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.Iterator.forEachRemaining(Iterator.java:116)
at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:512)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:502)
at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:150)
at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:173)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:418)
at org.broadinstitute.hellbender.engine.VariantWalker.traverse(VariantWalker.java:104)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1039)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:139)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:162)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:205)
at org.broadinstitute.hellbender.Main.main(Main.java:291)~~~
Hi,
First I filter snp.raw.vcf with
VariantFiltration
command below:gatk-4.1.2.0/gatk --java-options "-Djava.io.tmpdir=/tmp/" VariantFiltration -R genome.fa -V snp_rmnan.raw.vcf --filter-expression "QUAL < 30.0 || QD < 2.0 || FS > 60.0 || MQ < 40.0 || SOR > 4.0 || ReadPosRankSum < -8.0" --filter-name "my_snp_filter" --missing-values-evaluate-as-failing true -O snp_rmnan.raw.vcf.tmp.vcf
This command runs successfully.
But when I'm using
SelectVariants
command to extact the filtered site:gatk-4.1.2.0/gatk --java-options "-Djava.io.tmpdir=/tmp/" SelectVariants -R genome.fa -V snp_rmnan.raw.vcf.tmp.vcf --exclude-filtered -O snp_rmnan.raw.vcf.filter.vcf
I get this java ERROR below, even without the wrong line number and do not know how to deal with it......... o(╥﹏╥)o,Thank you very much!