DAY-EC activated.
DAY-EC activated.
## read_haps files
0 /fsx/analysis_results/ubuntu/ccv20260529r26_illumina_hg002_kitchensink_multiqc/daylily-omics-analysis/results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/contam_identity/read_haps/logs/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.read_haps.log
## read_haps output
## read_haps log
## haplocheck files
2080 /fsx/analysis_results/ubuntu/ccv20260529r26_illumina_hg002_kitchensink_multiqc/daylily-omics-analysis/results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/contam_identity/haplocheck/vcf/logs/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.haplocheck.vcf.log
## haplocheck log

haplocheck 1.3.3
https://github.com/genepi/haplocheck
(c) 2020 Sebastian Schoenherr, Hansi Weissensteiner, Lukas Forer

Check for Contamination..
RUN Load file...
RUN Split Profile into Major/Minor Profile...
RUN Classify Haplogroups...
RUN Detect Contamination...
RUN Write Contamination Report...
Text report written to results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/contam_identity/haplocheck/vcf/.haplocheck_vcf_output.Y12Mdv/contamination.txt.
Raw report written to results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/contam_identity/haplocheck/vcf/.haplocheck_vcf_output.Y12Mdv/contamination.raw.txt.
java.lang.IllegalArgumentException: Cannot calculate quantiles of an empty dataset
	at com.google.common.base.Preconditions.checkArgument(Preconditions.java:142)
	at com.google.common.math.Quantiles$ScaleAndIndex.computeInPlace(Quantiles.java:280)
	at com.google.common.math.Quantiles$ScaleAndIndex.compute(Quantiles.java:235)
	at genepi.haplocheck.steps.report.ReportGenerator.getSummary(ReportGenerator.java:67)
	at genepi.haplocheck.steps.report.ReportGenerator.generate(ReportGenerator.java:36)
	at genepi.haplocheck.steps.ContaminationStep.detectContamination(ContaminationStep.java:94)
	at genepi.haplocheck.steps.ContaminationStep.run(ContaminationStep.java:36)
	at genepi.haplocheck.commands.ContaminationCommand.call(ContaminationCommand.java:55)
	at genepi.haplocheck.commands.ContaminationCommand.call(ContaminationCommand.java:1)
	at picocli.CommandLine.executeUserObject(CommandLine.java:1933)
	at picocli.CommandLine.access$1100(CommandLine.java:145)
	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2332)
	at picocli.CommandLine$RunLast.handle(CommandLine.java:2326)
	at picocli.CommandLine$RunLast.handle(CommandLine.java:2291)
	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2159)
	at picocli.CommandLine.execute(CommandLine.java:2058)
	at genepi.haplocheck.App.main(App.java:32)
ERROR Contamination failed
