Closed visze closed 9 years ago
Another error. I will lookup for the exact call on Monday.
Exception in thread "main" java.lang.IllegalStateException: Duplicate key chr=3 pos=107294505 ref=- alt=T qual=1275.41 FIVE_PRIME_UTR_VARIANT score=0.0 PASSED failedFilters=[] passedFilters=[Quality, Target, Frequency, Pathogenicity] compatibleWith=[]
at java.util.stream.Collectors.lambda$throwingMerger$154(Collectors.java:133)
at java.util.HashMap.merge(HashMap.java:1245)
at java.util.stream.Collectors.lambda$toMap$212(Collectors.java:1320)
at java.util.stream.ReduceOps$3ReducingSink.accept(ReduceOps.java:169)
at java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1374)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
at java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:499)
at de.charite.compbio.exomiser.core.AbstractAnalysisRunner.checkInheritanceCompatibilityOfVariants(AbstractAnalysisRunner.java:294)
at de.charite.compbio.exomiser.core.AbstractAnalysisRunner.lambda$analyseGeneInheritanceMode$17(AbstractAnalysisRunner.java:282)
at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184)
at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175)
at java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1374)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:151)
at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:418)
at de.charite.compbio.exomiser.core.AbstractAnalysisRunner.analyseGeneInheritanceMode(AbstractAnalysisRunner.java:281)
at de.charite.compbio.exomiser.core.AbstractAnalysisRunner.runSteps(AbstractAnalysisRunner.java:244)
at de.charite.compbio.exomiser.core.AbstractAnalysisRunner.runAnalysis(AbstractAnalysisRunner.java:81)
at de.charite.compbio.exomiser.cli.Main.runAnalysis(Main.java:199)
at de.charite.compbio.exomiser.cli.Main.runAnalysisFromScript(Main.java:184)
at de.charite.compbio.exomiser.cli.Main.runAnalyses(Main.java:151)
at de.charite.compbio.exomiser.cli.Main.run(Main.java:74)
at de.charite.compbio.exomiser.cli.Main.main(Main.java:66)
commit: 19ed22c8fbd9634771e95ef8973483f1b57f0a2a commit: e7474c6946034c28ff3951faeae12a65913a3c29
I found a problem with a variant using the actual version of the genomiser. I have no idear about the error...
Error:
VCF: