Error on run using NA12878 1000 genomes vcf

[j2moreno]

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                                                                                                                                                                                                 
================================================================                                                                                                                                                   
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)