Haplogrep classify error
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Entering edit mode
9 months ago
jdru • 0

I am having a strange issue with haplogrep v2.4.0

When I ask it to classify the haplogroup of NCBI Nucleotide record EU558518.1 (https://www.ncbi.nlm.nih.gov/nuccore/EU558518.1?report=fasta)

$haplogrep_path classify --in EU558518.fa --out EU558518 --format fasta

It throws the following error:

Start Classification...
[M::bwa_idx_load_from_disk] read 0 ALT contigs
java.lang.NullPointerException
    at core.Polymorphism.compareTo(Polymorphism.java:526)
    at core.Polymorphism.compareTo(Polymorphism.java:19)
    at java.base/java.util.ComparableTimSort.binarySort(ComparableTimSort.java:262)
    at java.base/java.util.ComparableTimSort.sort(ComparableTimSort.java:207)
    at java.base/java.util.Arrays.sort(Arrays.java:1316)
    at java.base/java.util.Arrays.sort(Arrays.java:1510)
    at java.base/java.util.ArrayList.sort(ArrayList.java:1718)
    at java.base/java.util.Collections.sort(Collections.java:145)
    at qualityAssurance.rules.FixNomenclature.evaluate(FixNomenclature.java:88)
    at qualityAssurance.QualityAssistent.reevaluateRules(QualityAssistent.java:50)
    at core.SampleFile.applyNomenclatureRules(SampleFile.java:333)
    at genepi.haplogrep.util.HgClassifier.run(HgClassifier.java:49)
    at genepi.commands.HaplogrepCommand.call(HaplogrepCommand.java:178)
    at genepi.commands.HaplogrepCommand.call(HaplogrepCommand.java:20)
    at picocli.CommandLine.executeUserObject(CommandLine.java:1953)
    at picocli.CommandLine.access$1300(CommandLine.java:145)
    at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352)
    at picocli.CommandLine$RunLast.handle(CommandLine.java:2346)
    at picocli.CommandLine$RunLast.handle(CommandLine.java:2311)
    at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)
    at picocli.CommandLine.execute(CommandLine.java:2078)
    at genepi.App.main(App.java:59)

I find this particularly strange because I have used haplogrep in parallel to classify thousands of other records without a problem. However there seems to be nothing different about this fasta file compared to the other records so I am at a loss. I tried manually running this command on other fasta records from NCBI and I get no issue, so it seems to be isolated to this record in particular for some reason.

haplogroup mitochondria haplogrep • 252 views
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