Error on run using NA12878 1000 genomes vcf #13
Description
Getting an error using NA12878 1000 genomes vcf file. Tool works using the example file provided data/Miller.vcf but throws error otherwise. Any suggestions?
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/release/20190312_biallelic_SNV_and_INDEL/ALL.chr20.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz
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Inferences
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Inferring ancestors...
Checking Treatment coherency
Incoherencies : 0
Inferring descendants...
Checking Treatment coherency
Incoherencies : 0
Inferring Conceptual Leaves...
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Engine initialized
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Feb 10, 2020 7:45:52 PM sa.edu.kaust.Main runTool
INFO: Computing similarities
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computing IC ResnikIC
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Class name slib.sml.sm.core.metrics.ic.annot.IC_annot_resnik_1995_Normalized
Checking null or infinite in the ICs computed
ic ResnikIC computed ---------------------------------------------------------------
Feb 10, 2020 7:46:17 PM sa.edu.kaust.Main runTool
INFO: Getting top level phenotypes
Feb 10, 2020 7:46:17 PM sa.edu.kaust.Main runTool
INFO: Starting annotation
java.lang.NumberFormatException: For input string: "NA"
at sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:2043)
at sun.misc.FloatingDecimal.parseDouble(FloatingDecimal.java:110)
at java.lang.Double.parseDouble(Double.java:538)
at sa.edu.kaust.Annotations$1.apply(Annotations.java:206)
at sa.edu.kaust.Annotations$1.apply(Annotations.java:121)
at java.util.Arrays.lambda$parallelSetAll$0(Arrays.java:4718)
at java.util.stream.ForEachOps$ForEachOp$OfInt.accept(ForEachOps.java:204)
at java.util.stream.Streams$RangeIntSpliterator.forEachRemaining(Streams.java:110)
at java.util.Spliterator$OfInt.forEachRemaining(Spliterator.java:693)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:482)
at java.util.stream.ForEachOps$ForEachTask.compute(ForEachOps.java:290)
at java.util.concurrent.CountedCompleter.exec(CountedCompleter.java:731)
at java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:289)
at java.util.concurrent.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1056)
at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1692)
at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:157)