I made up an arbitrary ranking file with all taxa ranked 1 and continued with creating a consensus haplotype.

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[pool-1-thread-1] INFO net.maizegenetics.pangenome.api.CreateGraphUtils - referenceRangesAsMap: query statement: select reference_ranges.ref_range_id, chrom, range_start, range_end, methods.name from reference_r$
methods size: 1
[pool-1-thread-1] INFO net.maizegenetics.pangenome.api.CreateGraphUtils - referenceRangesAsMap: number of reference ranges: 94229
[pool-1-thread-1] INFO net.maizegenetics.pangenome.api.CreateGraphUtils - referenceRangesAsMap: time: 0.564907808 secs.
[pool-1-thread-1] INFO net.maizegenetics.pangenome.api.CreateGraphUtils - taxaListMap: query statement: SELECT gamete_haplotypes.gamete_grp_id, genotypes.line_name FROM gamete_haplotypes INNER JOIN gametes ON ga$
[pool-1-thread-1] INFO net.maizegenetics.pangenome.api.CreateGraphUtils - taxaListMap: number of taxa lists: 95
[pool-1-thread-1] INFO net.maizegenetics.pangenome.api.CreateGraphUtils - taxaListMap: time: 0.003135835 secs.
[pool-1-thread-1] INFO net.maizegenetics.pangenome.api.VariantUtils - variantIdsToVariantMap: query statement: SELECT variant_id, chrom, position, ref_allele_id, alt_allele_id FROM variants;
[pool-1-thread-1] INFO net.maizegenetics.pangenome.api.CreateGraphUtils - createHaplotypeNodes: haplotype method: GATK_PIPELINE range group method: null
[pool-1-thread-1] INFO net.maizegene ...



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