Sync runs/hostkey-2026-10-22-epyc9354 (2026-10-22 12:35 BDT)

runs/hostkey-2026-10-22-epyc9354/chain/chain-jobs.tsv

@@ -0,0 +1,7 @@
+check.16k-19oct.default	-	0	-i ../data/udance-gt-16k-fasttreemp__model_lg__gamma.tre --starting-tree inputs/mre-16k.tre --guide-tree inputs/backbone-wol1-qraft-extended.tre --write-starting-tree out/check-start16k.tre
+chain.wol1.default	-	0	-i wol1/wol1-genes.tre
+chain.wol1.extended	-	0	-i wol1/wol1-genes.tre --extended
+chain.16k.default	-	0	-i ../data/udance-gt-16k-fasttreemp__model_lg__gamma.tre --guide-tree out/runs/chain.wol1.default/out.tre --write-starting-tree out/start16k-default.tre
+chain.16k.extended	-	0	-i ../data/udance-gt-16k-fasttreemp__model_lg__gamma.tre --guide-tree out/runs/chain.wol1.extended/out.tre --extended --write-starting-tree out/start16k-extended.tre
+chain.199k.default	-	0	-i ../data/gt199k-pruned.tre --guide-tree out/runs/chain.16k.default/out.tre --write-starting-tree out/start199k-default.tre
+chain.199k.extended	-	0	-i ../data/gt199k-pruned.tre --guide-tree out/runs/chain.16k.extended/out.tre --extended --write-starting-tree out/start199k-extended.tre

runs/hostkey-2026-10-22-epyc9354/chain/chain_go.log

@@ -0,0 +1 @@
+2026-10-22T06:27:19Z start; binary dad743025d3d2087

runs/hostkey-2026-10-22-epyc9354/chain/chain_go.sh

@@ -0,0 +1,17 @@
+#!/bin/bash
+# The uDANCE chain on Hostkey (user 12:05/12:19, design A): each mode end to end with its own guides, QRAFT's own MRE,
+# --guide-tree of qraft 5380c89; one timed run at a time; then exact quartet scores (tqDist, 128-bit) of the outputs.
+set -u
+R=/workspace/hk2/chain; cd $R
+log() { echo "$(date -u +%FT%TZ) $*" >> $R/chain_go.log; }
+log "start; binary $(sha256sum qraft | cut -c1-16)"
+R=$R ./queue.sh chain-jobs.tsv
+log "queue done"
+cmp -s out/runs/check.16k-19oct.default/out.tre ref19oct/chain16k-default.tre && log "check 16k vs 19 Oct: IDENTICAL" || log "check 16k vs 19 Oct: DIFFERENT"
+cmp -s out/check-start16k.tre ref19oct/start16k-chain.tre && log "check start16k vs 19 Oct: IDENTICAL" || log "check start16k vs 19 Oct: DIFFERENT"
+Q="python3 qscore_exact.py --tqdist ./pairs_quartet_dist-int128 --procs 32 --tq-procs 32 --chunk 4"
+$Q --workdir qs-wol1 --per-gene out/qs-wol1-per-gene.csv wol1/wol1-genes.tre default=out/runs/chain.wol1.default/out.tre extended=out/runs/chain.wol1.extended/out.tre astral=wol1/astral.nwk > out/qs-wol1.out 2>&1; log "qscore wol1 done"
+$Q --workdir qs-16k --per-gene out/qs-16k-per-gene.csv ../data/udance-gt-16k-fasttreemp__model_lg__gamma.tre default=out/runs/chain.16k.default/out.tre extended=out/runs/chain.16k.extended/out.tre udance16k=../data/ref-udance-16k.tre > out/qs-16k.out 2>&1; log "qscore 16k done"
+$Q --workdir qs-199k --per-gene out/qs-199k-per-gene.csv ../data/gt199k-pruned.tre default=out/runs/chain.199k.default/out.tre extended=out/runs/chain.199k.extended/out.tre > out/qs-199k.out 2>&1; log "qscore 199k done"
+rm -rf qs-wol1 qs-16k qs-199k
+log all-done; touch ALL_DONE

runs/hostkey-2026-10-22-epyc9354/chain/out/queue.log

@@ -0,0 +1,11 @@
+2026-10-22T06:27:19Z start 1/7 check.16k-19oct.default timeout=0
+2026-10-22T06:27:36Z end check.16k-19oct.default done rc=0 time=16.41,2150620
+2026-10-22T06:27:36Z start 2/7 chain.wol1.default timeout=0
+2026-10-22T06:27:48Z end chain.wol1.default done rc=0 time=12.64,1344140
+2026-10-22T06:27:48Z start 3/7 chain.wol1.extended timeout=0
+2026-10-22T06:29:15Z end chain.wol1.extended done rc=0 time=86.83,1363680
+2026-10-22T06:29:15Z start 4/7 chain.16k.default timeout=0
+2026-10-22T06:29:36Z end chain.16k.default done rc=0 time=20.60,2114556
+2026-10-22T06:29:36Z start 5/7 chain.16k.extended timeout=0
+2026-10-22T06:33:37Z end chain.16k.extended done rc=0 time=241.26,2106096
+2026-10-22T06:33:37Z start 6/7 chain.199k.default timeout=0

runs/hostkey-2026-10-22-epyc9354/chain/out/runs.csv

@@ -0,0 +1,6 @@
+id,group,status,exit,wall_s,maxrss_kb,tree_sha256,start_utc,end_utc
+check.16k-19oct.default,,done,0,16.41,2150620,cb7e74b71fac16aa80f3b4d3b6e2509f87b6813906a1048df0148142d4072797,2026-10-22T06:27:19Z,2026-10-22T06:27:36Z
+chain.wol1.default,,done,0,12.64,1344140,fc055c030920092cb44066ee03253ca4d82ea86f5ad1cc98b52e8128493d5f80,2026-10-22T06:27:36Z,2026-10-22T06:27:48Z
+chain.wol1.extended,,done,0,86.83,1363680,916c3738254a207693b2ac10675d017661538424dff92dbb88f40dd2b3ccd95d,2026-10-22T06:27:48Z,2026-10-22T06:29:15Z
+chain.16k.default,,done,0,20.60,2114556,20d608ee06825fd4e8d396dd0a374a58480f67bcbc7430ffe649d490a1d88a1d,2026-10-22T06:29:15Z,2026-10-22T06:29:36Z
+chain.16k.extended,,done,0,241.26,2106096,6ac9a908b63b5cae498c32ff6d0bd3feac5ccb7e3fbe5ff380fae830f251e9b4,2026-10-22T06:29:36Z,2026-10-22T06:33:37Z

runs/hostkey-2026-10-22-epyc9354/chain/out/runs/chain.16k.default/DONE

@@ -0,0 +1 @@
+done

runs/hostkey-2026-10-22-epyc9354/chain/out/runs/chain.16k.default/args

@@ -0,0 +1 @@
+-i ../data/udance-gt-16k-fasttreemp__model_lg__gamma.tre --guide-tree out/runs/chain.wol1.default/out.tre --write-starting-tree out/start16k-default.tre

runs/hostkey-2026-10-22-epyc9354/chain/out/runs/chain.16k.default/stats.json

@@ -0,0 +1,156 @@
+{
+  "genes": 380,
+  "taxa": 16631,
+  "workers": 64,
+  "progress": "off",
+  "divide": true,
+  "divide_score": "quartet",
+  "bipartition_test": true,
+  "bipartition_test_available": true,
+  "bipartition_test_complete_genes": false,
+  "bipartition_test_coefficient": 0.05,
+  "bipartition_test_crossover": 10000,
+  "bipartition_test_proposals": 1,
+  "bipartition_test_anchor_pairs": 1,
+  "bipartition_test_threshold": null,
+  "regraft_score": "raw",
+  "nni": true,
+  "nni_move_cap": true,
+  "nni_support_gate": true,
+  "nni_batch": false,
+  "spr_refine": false,
+  "spr_reads_per_pass": 128,
+  "spr_min_clade": 10,
+  "spr_candidates": 150,
+  "spr_max_rounds": 2,
+  "guide_tree": true,
+  "subproblems": 7172,
+  "completed_subproblems": 7172,
+  "max_depth": 67,
+  "max_active_taxa": 16631,
+  "taxon_registry_ns": 69236396,
+  "taxon_registry_physical_labels": 4479485,
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+  "taxon_registry_sort_items": 16631,
+  "gene_index_ns": 119471651,
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+  "mre_assembly_ns": 3377643268,
+  "starting_tree_index_builds": 1,
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+  "candidates": 224483,
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+  "bipartition_score_ns": 46875598024,
+  "bipartition_test_index_ns": 21837100,
+  "bipartition_test_ns": 6825328163,
+  "bipartition_tests": 7160,
+  "bipartition_test_accepts": 7160,
+  "bipartition_test_rejects": 0,
+  "bipartition_test_negative_accepts": 520,
+  "bipartition_test_max_negative_gap_twice_k": 0,
+  "bipartition_test_singletons": 0,
+  "bipartition_test_distance_queries": 188828840,
+  "bipartition_test_incomplete": 7160,
+  "bipartition_test_uncovered_pairs": 0,
+  "bipartition_test_untestable": 0,
+  "bipartition_test_shared_genes": 1719457,
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+  "contract_scratch_peak_bytes": 3833987,
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+  "worker_total_peak_bytes": 109052235,
+  "max_scoring_source_taxa": 16631,
+  "scoring_source_inflation_violations": 0,
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+  "child_gene_set_attempts": 7171,
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+  "child_gene_set_pair_violations": 0,
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+  "child_gene_set_max_accepted_ratio_ppm": 749862,
+  "child_gene_set_ns": 11152714105,
+  "live_child_gene_sets": 0,
+  "max_child_gene_sets": 212,
+  "live_child_gene_set_slots": 0,
+  "max_child_gene_set_slots": 68500,
+  "max_child_gene_set_bytes": 152746904,
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+  "peak_continuation_taxa": 6055,
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+  "peak_gene_set_nodes": 46642074,
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+  "peak_gene_set_entries": 239532704,
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+  "peak_gene_set_taxa": 68500,
+  "live_tree_nodes": 0,
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+  "accounting_violations": 0,
+  "nni_gain": 1767485777959321,
+  "spr_gain": 0,
+  "complexity_contract_satisfied": true
+}

runs/hostkey-2026-10-22-epyc9354/chain/out/runs/chain.16k.default/time

@@ -0,0 +1 @@
+20.60,2114556

runs/hostkey-2026-10-22-epyc9354/chain/out/runs/chain.16k.extended/DONE

@@ -0,0 +1 @@
+done

runs/hostkey-2026-10-22-epyc9354/chain/out/runs/chain.16k.extended/args

@@ -0,0 +1 @@
+-i ../data/udance-gt-16k-fasttreemp__model_lg__gamma.tre --guide-tree out/runs/chain.wol1.extended/out.tre --extended --write-starting-tree out/start16k-extended.tre

runs/hostkey-2026-10-22-epyc9354/chain/out/runs/chain.16k.extended/stats.json

@@ -0,0 +1,156 @@
+{
+  "genes": 380,
+  "taxa": 16631,
+  "workers": 64,
+  "progress": "off",
+  "divide": true,
+  "divide_score": "quartet",
+  "bipartition_test": true,
+  "bipartition_test_available": true,
+  "bipartition_test_complete_genes": false,
+  "bipartition_test_coefficient": 0.05,
+  "bipartition_test_crossover": 10000,
+  "bipartition_test_proposals": 1,
+  "bipartition_test_anchor_pairs": 1,
+  "bipartition_test_threshold": null,
+  "regraft_score": "raw",
+  "nni": true,
+  "nni_move_cap": false,
+  "nni_support_gate": false,
+  "nni_batch": true,
+  "spr_refine": true,
+  "spr_reads_per_pass": 128,
+  "spr_min_clade": 10,
+  "spr_candidates": 150,
+  "spr_max_rounds": 2,
+  "guide_tree": true,
+  "subproblems": 7165,
+  "completed_subproblems": 7165,
+  "max_depth": 67,
+  "max_active_taxa": 16631,
+  "taxon_registry_ns": 52423940,
+  "taxon_registry_physical_labels": 4479485,
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+  "taxon_registry_sort_items": 16631,
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+  "mre_assembly_ns": 3628283326,
+  "starting_tree_index_builds": 1,
+  "starting_tree_index_nodes": 33168,
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+  "bipartition_score_ns": 39926623098,
+  "bipartition_test_index_ns": 22131533,
+  "bipartition_test_ns": 6067667651,
+  "bipartition_tests": 7153,
+  "bipartition_test_accepts": 7153,
+  "bipartition_test_rejects": 0,
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+  "bipartition_test_max_negative_gap_twice_k": 0,
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+  "nni_local_edges_scored": 83858,
+  "nni_moves_accepted": 4678,
+  "nni_batch_passes": 129,
+  "nni_support_stops": 0,
+  "nni_split_support_ns": 0,
+  "nni_ns": 14458871016,
+  "spr_rounds": 2,
+  "spr_reads": 256,
+  "spr_candidates_scored": 114,
+  "spr_moves": 36,
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+  "guide_contracted_edges": 1924,
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+  "active_taxa_index_entries": 13202910,
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+  "query_tree_retained_nodes": 479116,
+  "gene_set_scoring_calls": 12992,
+  "gene_set_scoring_nodes": 1239898178,
+  "hdt_builds": 4987120,
+  "hdt_build_ns": 39604576833,
+  "hdt_queries": 923132245,
+  "hdt_recolor_ops": 9681384516,
+  "hdt_nodes_recomputed": 25539771769,
+  "extract_scratch_peak_bytes": 1505368,
+  "contract_scratch_peak_bytes": 4709267,
+  "state_arena_peak_bytes": 107607140,
+  "worker_total_peak_bytes": 109176237,
+  "max_scoring_source_taxa": 16631,
+  "scoring_source_inflation_violations": 0,
+  "child_gene_set_reuses": 7476,
+  "child_gene_set_attempts": 7164,
+  "child_gene_set_accepts": 6854,
+  "child_gene_set_heavy_reuses": 310,
+  "child_gene_set_pair_violations": 0,
+  "child_gene_set_input_nodes": 232168821,
+  "child_gene_set_output_nodes": 112756857,
+  "child_gene_set_max_accepted_ratio_ppm": 749862,
+  "child_gene_set_ns": 8588453397,
+  "live_child_gene_sets": 0,
+  "max_child_gene_sets": 170,
+  "live_child_gene_set_slots": 0,
+  "max_child_gene_set_slots": 67420,
+  "max_child_gene_set_bytes": 152718872,
+  "serial_children": 7037,
+  "parallel_children": 128,
+  "parallel_child_budget_rejections": 14,
+  "parallel_child_size_rejections": 0,
+  "max_parallel_child_slots": 16631,
+  "recursion_calls": 14331,
+  "recursion_nonbase_calls": 7165,
+  "recursion_max_depth": 68,
+  "recursion_taxon_mass": 261119,
+  "recursion_split_tests": 244488,
+  "recursion_partition_moves": 244488,
+  "recursion_balanced_splits": 2014,
+  "recursion_skewed_splits": 12,
+  "recursion_tree_node_visits": 460328,
+  "recursion_radix_entries": 1955808,
+  "recursion_radix_bucket_ops": 14661632,
+  "recursion_unique_taxa": 244488,
+  "recursion_root_gene_set_nodes": 8712139,
+  "recursion_root_gene_set_entries": 49880475,
+  "live_payload": 0,
+  "peak_payload": 281506872,
+  "live_taxa": 0,
+  "peak_taxa": 16631,
+  "live_continuation_taxa": 0,
+  "peak_continuation_taxa": 11073,
+  "live_gene_set_nodes": 0,
+  "peak_gene_set_nodes": 45846593,
+  "live_gene_set_entries": 0,
+  "peak_gene_set_entries": 235555615,
+  "live_gene_set_taxa": 0,
+  "peak_gene_set_taxa": 67127,
+  "live_tree_nodes": 0,
+  "peak_tree_nodes": 58726,
+  "live_tree_adjacencies": 0,
+  "peak_tree_adjacencies": 117448,
+  "live_taxon_scratch": 0,
+  "peak_taxon_scratch": 29365,
+  "accounting_violations": 0,
+  "nni_gain": 4926947116900142,
+  "spr_gain": 437349380208142,
+  "complexity_contract_satisfied": true
+}

runs/hostkey-2026-10-22-epyc9354/chain/out/runs/chain.16k.extended/time

@@ -0,0 +1 @@
+241.26,2106096

runs/hostkey-2026-10-22-epyc9354/chain/out/runs/chain.199k.default/args

@@ -0,0 +1 @@
+-i ../data/gt199k-pruned.tre --guide-tree out/runs/chain.16k.default/out.tre --write-starting-tree out/start199k-default.tre

runs/hostkey-2026-10-22-epyc9354/chain/out/runs/chain.wol1.default/DONE

@@ -0,0 +1 @@
+done

runs/hostkey-2026-10-22-epyc9354/chain/out/runs/chain.wol1.default/args

@@ -0,0 +1 @@
+-i wol1/wol1-genes.tre

runs/hostkey-2026-10-22-epyc9354/chain/out/runs/chain.wol1.default/stats.json

@@ -0,0 +1,156 @@
+{
+  "genes": 381,
+  "taxa": 10575,
+  "workers": 64,
+  "progress": "off",
+  "divide": true,
+  "divide_score": "quartet",
+  "bipartition_test": true,
+  "bipartition_test_available": true,
+  "bipartition_test_complete_genes": false,
+  "bipartition_test_coefficient": 0.05,
+  "bipartition_test_crossover": 10000,
+  "bipartition_test_proposals": 1,
+  "bipartition_test_anchor_pairs": 1,
+  "bipartition_test_threshold": null,
+  "regraft_score": "raw",
+  "nni": true,
+  "nni_move_cap": true,
+  "nni_support_gate": true,
+  "nni_batch": false,
+  "spr_refine": false,
+  "spr_reads_per_pass": 128,
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+  "child_gene_set_max_accepted_ratio_ppm": 749795,
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+  "live_child_gene_sets": 0,
+  "max_child_gene_sets": 180,
+  "live_child_gene_set_slots": 0,
+  "max_child_gene_set_slots": 31420,
+  "max_child_gene_set_bytes": 102595716,
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+  "live_payload": 0,
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+}

runs/hostkey-2026-10-22-epyc9354/chain/out/runs/chain.wol1.default/time

@@ -0,0 +1 @@
+12.64,1344140

runs/hostkey-2026-10-22-epyc9354/chain/out/runs/chain.wol1.extended/DONE

@@ -0,0 +1 @@
+done

runs/hostkey-2026-10-22-epyc9354/chain/out/runs/chain.wol1.extended/args

@@ -0,0 +1 @@
+-i wol1/wol1-genes.tre --extended

runs/hostkey-2026-10-22-epyc9354/chain/out/runs/chain.wol1.extended/stats.json

@@ -0,0 +1,156 @@
+{
+  "genes": 381,
+  "taxa": 10575,
+  "workers": 64,
+  "progress": "off",
+  "divide": true,
+  "divide_score": "quartet",
+  "bipartition_test": true,
+  "bipartition_test_available": true,
+  "bipartition_test_complete_genes": false,
+  "bipartition_test_coefficient": 0.05,
+  "bipartition_test_crossover": 10000,
+  "bipartition_test_proposals": 1,
+  "bipartition_test_anchor_pairs": 1,
+  "bipartition_test_threshold": null,
+  "regraft_score": "raw",
+  "nni": true,
+  "nni_move_cap": false,
+  "nni_support_gate": false,
+  "nni_batch": true,
+  "spr_refine": true,
+  "spr_reads_per_pass": 128,
+  "spr_min_clade": 10,
+  "spr_candidates": 150,
+  "spr_max_rounds": 2,
+  "guide_tree": false,
+  "subproblems": 4603,
+  "completed_subproblems": 4603,
+  "max_depth": 73,
+  "max_active_taxa": 10575,
+  "taxon_registry_ns": 39753037,
+  "taxon_registry_physical_labels": 2834712,
+  "taxon_registry_unique_labels": 10575,
+  "taxon_registry_sort_items": 10575,
+  "gene_index_ns": 81089370,
+  "startup_ns": 2944930937,
+  "mre_distinct_splits": 832559,
+  "mre_accepted_splits": 10305,
+  "mre_count_ns": 786292654,
+  "mre_assembly_ns": 1979725203,
+  "starting_tree_index_builds": 1,
+  "starting_tree_index_nodes": 20881,
+  "candidate_sets": 4603,
+  "candidates": 162471,
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+  "bipartition_score_ns": 27991827877,
+  "bipartition_test_index_ns": 15379928,
+  "bipartition_test_ns": 3532683724,
+  "bipartition_tests": 4506,
+  "bipartition_test_accepts": 4506,
+  "bipartition_test_rejects": 0,
+  "bipartition_test_negative_accepts": 281,
+  "bipartition_test_max_negative_gap_twice_k": 0,
+  "bipartition_test_singletons": 0,
+  "bipartition_test_distance_queries": 138005058,
+  "bipartition_test_incomplete": 4506,
+  "bipartition_test_uncovered_pairs": 0,
+  "bipartition_test_untestable": 0,
+  "bipartition_test_shared_genes": 1079779,
+  "regraft_calls": 9258,
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+  "nni_local_edges_scored": 24140,
+  "nni_moves_accepted": 1836,
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+  "nni_split_support_ns": 0,
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+  "hdt_nodes_recomputed": 5414068952,
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+  "worker_total_peak_bytes": 67451503,
+  "max_scoring_source_taxa": 10575,
+  "scoring_source_inflation_violations": 0,
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+  "child_gene_set_attempts": 4602,
+  "child_gene_set_accepts": 4377,
+  "child_gene_set_heavy_reuses": 225,
+  "child_gene_set_pair_violations": 0,
+  "child_gene_set_input_nodes": 172410734,
+  "child_gene_set_output_nodes": 80359041,
+  "child_gene_set_max_accepted_ratio_ppm": 749795,
+  "child_gene_set_ns": 5654177983,
+  "live_child_gene_sets": 0,
+  "max_child_gene_sets": 132,
+  "live_child_gene_set_slots": 0,
+  "max_child_gene_set_slots": 31018,
+  "max_child_gene_set_bytes": 102595716,
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+  "parallel_child_budget_rejections": 0,
+  "parallel_child_size_rejections": 0,
+  "max_parallel_child_slots": 10575,
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+  "recursion_radix_bucket_ops": 9327616,
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+  "recursion_root_gene_set_nodes": 5434867,
+  "recursion_root_gene_set_entries": 31203410,
+  "live_payload": 0,
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+  "live_taxa": 0,
+  "peak_taxa": 10575,
+  "live_continuation_taxa": 0,
+  "peak_continuation_taxa": 544,
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+  "peak_gene_set_nodes": 23346739,
+  "live_gene_set_entries": 0,
+  "peak_gene_set_entries": 120763539,
+  "live_gene_set_taxa": 0,
+  "peak_gene_set_taxa": 31018,
+  "live_tree_nodes": 0,
+  "peak_tree_nodes": 36082,
+  "live_tree_adjacencies": 0,
+  "peak_tree_adjacencies": 72158,
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+  "peak_taxon_scratch": 17138,
+  "accounting_violations": 0,
+  "nni_gain": 177190318521378,
+  "spr_gain": 20019483405675,
+  "complexity_contract_satisfied": true
+}

runs/hostkey-2026-10-22-epyc9354/chain/out/runs/chain.wol1.extended/time

@@ -0,0 +1 @@
+86.83,1363680

runs/hostkey-2026-10-22-epyc9354/chain/out/runs/check.16k-19oct.default/DONE

@@ -0,0 +1 @@
+done

runs/hostkey-2026-10-22-epyc9354/chain/out/runs/check.16k-19oct.default/args

@@ -0,0 +1 @@
+-i ../data/udance-gt-16k-fasttreemp__model_lg__gamma.tre --starting-tree inputs/mre-16k.tre --guide-tree inputs/backbone-wol1-qraft-extended.tre --write-starting-tree out/check-start16k.tre

runs/hostkey-2026-10-22-epyc9354/chain/out/runs/check.16k-19oct.default/stats.json

@@ -0,0 +1,156 @@
+{
+  "genes": 380,
+  "taxa": 16631,
+  "workers": 64,
+  "progress": "off",
+  "divide": true,
+  "divide_score": "quartet",
+  "bipartition_test": true,
+  "bipartition_test_available": true,
+  "bipartition_test_complete_genes": false,
+  "bipartition_test_coefficient": 0.05,
+  "bipartition_test_crossover": 10000,
+  "bipartition_test_proposals": 1,
+  "bipartition_test_anchor_pairs": 1,
+  "bipartition_test_threshold": null,
+  "regraft_score": "raw",
+  "nni": true,
+  "nni_move_cap": true,
+  "nni_support_gate": true,
+  "nni_batch": false,
+  "spr_refine": false,
+  "spr_reads_per_pass": 128,
+  "spr_min_clade": 10,
+  "spr_candidates": 150,
+  "spr_max_rounds": 2,
+  "guide_tree": true,
+  "subproblems": 7163,
+  "completed_subproblems": 7163,
+  "max_depth": 64,
+  "max_active_taxa": 16631,
+  "taxon_registry_ns": 61447215,
+  "taxon_registry_physical_labels": 4479485,
+  "taxon_registry_unique_labels": 16631,
+  "taxon_registry_sort_items": 16631,
+  "gene_index_ns": 99125474,
+  "startup_ns": 243293766,
+  "mre_distinct_splits": 0,
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+  "mre_assembly_ns": 0,
+  "starting_tree_index_builds": 1,
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+  "bipartition_score_ns": 39065910659,
+  "bipartition_test_index_ns": 21064077,
+  "bipartition_test_ns": 6419710119,
+  "bipartition_tests": 7152,
+  "bipartition_test_accepts": 7152,
+  "bipartition_test_rejects": 0,
+  "bipartition_test_negative_accepts": 552,
+  "bipartition_test_max_negative_gap_twice_k": 0,
+  "bipartition_test_singletons": 0,
+  "bipartition_test_distance_queries": 184481640,
+  "bipartition_test_incomplete": 7152,
+  "bipartition_test_uncovered_pairs": 0,
+  "bipartition_test_untestable": 0,
+  "bipartition_test_shared_genes": 1717647,
+  "regraft_calls": 14326,
+  "regraft_vertices": 214197,
+  "regraft_edge_ties": 119,
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+  "nni_full_score_passes": 1,
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+  "nni_local_edges_scored": 1484,
+  "nni_moves_accepted": 20,
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+  "nni_support_stops": 0,
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+  "active_taxa_index_entries": 1288543,
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+  "contract_scratch_peak_bytes": 3832787,
+  "state_arena_peak_bytes": 107607140,
+  "worker_total_peak_bytes": 109175549,
+  "max_scoring_source_taxa": 16631,
+  "scoring_source_inflation_violations": 0,
+  "child_gene_set_reuses": 7473,
+  "child_gene_set_attempts": 7162,
+  "child_gene_set_accepts": 6853,
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+  "child_gene_set_pair_violations": 0,
+  "child_gene_set_input_nodes": 231157792,
+  "child_gene_set_output_nodes": 112030596,
+  "child_gene_set_max_accepted_ratio_ppm": 749862,
+  "child_gene_set_ns": 6734272267,
+  "live_child_gene_sets": 0,
+  "max_child_gene_sets": 132,
+  "live_child_gene_set_slots": 0,
+  "max_child_gene_set_slots": 67657,
+  "max_child_gene_set_bytes": 152718872,
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+  "live_continuation_taxa": 0,
+  "peak_continuation_taxa": 11301,
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+  "peak_gene_set_entries": 231549730,
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+  "peak_gene_set_taxa": 67545,
+  "live_tree_nodes": 0,
+  "peak_tree_nodes": 58726,
+  "live_tree_adjacencies": 0,
+  "peak_tree_adjacencies": 117448,
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+  "accounting_violations": 0,
+  "nni_gain": 1566933366405096,
+  "spr_gain": 0,
+  "complexity_contract_satisfied": true
+}

runs/hostkey-2026-10-22-epyc9354/chain/out/runs/check.16k-19oct.default/time

@@ -0,0 +1 @@
+16.41,2150620

runs/hostkey-2026-10-22-epyc9354/chain/qraft.sha256

@@ -0,0 +1 @@
+dad743025d3d20871ed853dccfdebff16f0f8ae9f4a902d6bc007e3c1fe3afce

runs/hostkey-2026-10-22-epyc9354/chain/qscore_exact.py

@@ -0,0 +1,231 @@
+#!/usr/bin/env python3
+"""Exact quartet score of species trees on gene trees, with tqDist, gene by gene.
+
+    python3 qscore_exact.py [--tqdist PATH] [--workdir DIR] [--procs N] [--tq-procs N] [--chunk N]
+                            [--first N] [--per-gene CSV] GENES NAME=TREE [NAME=TREE ...]
+
+Each gene tree and the species trees are restricted to the gene's taxa that the first species
+tree has (repeated labels keep their first leaf; unary nodes are suppressed, lengths and
+supports dropped), and tqDist's pairs_quartet_dist -v reports, per gene, the number of
+resolved quartets the two trees share. The gene's unresolved quartets (four leaves in four
+different arms of one polytomy) are counted from its restricted tree, so that
+
+    normalized score = sum of shared quartets / sum of quartets resolved in the genes,
+
+the quantity quartet_sample.py estimates. --per-gene writes one row per gene; the totals go to
+standard output. --first N scores only the first N gene trees (for timing).
+"""
+import argparse
+import multiprocessing as mp
+import os
+import re
+import subprocess
+import tempfile
+
+TOKEN = re.compile(r'[(),;]|[^(),;]+')
+
+
+def parse(s):
+    """kids lists and labels; node 0 is a virtual root holding the top-level children."""
+    kids, label, stack = [[]], [None], [0]
+    after_close = False
+    for tok in TOKEN.findall(s):
+        if tok == '(':
+            kids.append([]); label.append(None)
+            kids[stack[-1]].append(len(kids) - 1)
+            stack.append(len(kids) - 1)
+            after_close = False
+        elif tok == ')':
+            stack.pop(); after_close = True
+        elif tok in ',;':
+            after_close = False
+        else:
+            tok = tok.strip()
+            if after_close or not tok or tok.startswith(':'):
+                after_close = False
+                continue
+            kids.append(None); label.append(tok.split(':', 1)[0].strip("'"))
+            kids[stack[-1]].append(len(kids) - 1)
+    return kids, label
+
+
+def restrict(kids, label, keep):
+    """Newick of the tree restricted to the leaf labels in keep (first occurrence of each)."""
+    order, st = [], [0]
+    while st:
+        v = st.pop(); order.append(v)
+        if kids[v] is not None:
+            st.extend(kids[v])
+    seen = set()
+    kept = [0] * len(kids)
+    leaf_ok = [False] * len(kids)
+    for v in reversed(order):
+        if kids[v] is None:
+            lab = label[v]
+            if lab in keep and lab not in seen:
+                seen.add(lab); leaf_ok[v] = True; kept[v] = 1
+        else:
+            kept[v] = sum(kept[c] for c in kids[v])
+
+    def live(v):
+        while kids[v] is not None:
+            ch = [c for c in kids[v] if kept[c]]
+            if len(ch) != 1:
+                return v
+            v = ch[0]
+        return v
+
+    out, st = [], [('n', live(0))]
+    while st:
+        kind, v = st.pop()
+        if kind == 's':
+            out.append(v); continue
+        if kids[v] is None:
+            out.append(label[v]); continue
+        ch = [live(c) for c in kids[v] if kept[c]]
+        out.append('(')
+        st.append(('s', ')'))
+        for k, c in enumerate(reversed(ch)):
+            st.append(('n', c))
+            if k < len(ch) - 1:
+                st.append(('s', ','))
+    return ''.join(out) + ';'
+
+
+def unresolved_quartets(newick):
+    """Quartets with their four leaves in four different arms of one node (e4 of the arm sizes)."""
+    kids, label = parse(newick)
+    size = [0] * len(kids)
+    order, st = [], [0]
+    while st:
+        v = st.pop(); order.append(v)
+        if kids[v] is not None:
+            st.extend(kids[v])
+    for v in reversed(order):
+        size[v] = 1 if kids[v] is None else sum(size[c] for c in kids[v])
+    n = size[0]
+    total = 0
+    for v in order:
+        if kids[v] is None or len(kids[v]) + (v != 0) < 4:
+            continue
+        arms = [size[c] for c in kids[v]] + ([n - size[v]] if v != 0 else [])
+        e = [1, 0, 0, 0, 0]
+        for a in arms:
+            for j in (4, 3, 2, 1):
+                e[j] += e[j - 1] * a
+        total += e[4]
+    return total
+
+
+SPECIES = None
+
+
+def init(species):
+    global SPECIES
+    SPECIES = species
+
+
+def one_gene(line):
+    gk, gl = parse(line)
+    gene_taxa = {l for l in gl if l is not None}
+    keep = gene_taxa & SPECIES[2]
+    if len(keep) < 4:
+        return None
+    g = restrict(gk, gl, keep)
+    return g, [restrict(k, l, keep) for k, l, _ in SPECIES[0]], unresolved_quartets(g)
+
+
+def main():
+    ap = argparse.ArgumentParser()
+    ap.add_argument('--tqdist', default=os.path.join(os.path.dirname(os.path.abspath(__file__)), 'pairs_quartet_dist'))
+    ap.add_argument('--workdir', default=None)
+    ap.add_argument('--procs', type=int, default=os.cpu_count())
+    ap.add_argument('--chunk', type=int, default=16, help='genes per tqDist call')
+    ap.add_argument('--tq-procs', type=int, default=4, help='concurrent tqDist calls')
+    ap.add_argument('--first', type=int, default=None, help='score only the first N gene trees')
+    ap.add_argument('--per-gene', default=None, help='CSV with one row per gene')
+    ap.add_argument('genes')
+    ap.add_argument('trees', nargs='+', help='NAME=PATH')
+    a = ap.parse_args()
+    names = [t.split('=', 1)[0] for t in a.trees]
+    a.trees = [t.split('=', 1)[1] for t in a.trees]
+    # each pruning worker holds the parsed species trees (about 1 GB at 200k taxa)
+    a.procs = max(1, min(a.procs, int(os.environ.get('QSCORE_MAX_PROCS', '12'))))
+    parsed = []
+    for path in a.trees:
+        k, l = parse(open(path).read().strip())
+        parsed.append((k, l, None))
+    taxa = {x for x in parsed[0][1] if x is not None}
+    lines = [x.strip() for x in open(a.genes) if '(' in x][:a.first]
+    with mp.Pool(a.procs, initializer=init, initargs=((parsed, None, taxa),)) as pool:
+        rows = pool.map(one_gene, lines, chunksize=1)
+    kept_genes = [i for i, r in enumerate(rows) if r is not None]
+    rows = [r for r in rows if r is not None]
+    work = a.workdir or tempfile.mkdtemp(prefix='qscore-')
+    os.makedirs(work, exist_ok=True)
+    genes_path = os.path.join(work, 'genes.tre')
+    with open(genes_path, 'w') as f:
+        f.write('\n'.join(r[0] for r in rows) + '\n')
+    # pairs_quartet_dist holds every pair of its input in memory (about 80 MB per pair of
+    # 150k-leaf trees), so the genes go in chunks of --chunk, at most --tq-procs at a time
+    from concurrent.futures import ThreadPoolExecutor
+    jobs = []
+    for s, path in enumerate(a.trees):
+        for c0 in range(0, len(rows), a.chunk):
+            part = rows[c0:c0 + a.chunk]
+            sp_path = os.path.join(work, f'species{s}.{c0}.tre')
+            g_path = os.path.join(work, f'genes.{c0}.tre')
+            with open(sp_path, 'w') as f:
+                f.write('\n'.join(r[1][s] for r in part) + '\n')
+            if s == 0:
+                with open(g_path, 'w') as f:
+                    f.write('\n'.join(r[0] for r in part) + '\n')
+            jobs.append((s, sp_path, g_path, os.path.join(work, f'out{s}.{c0}.txt')))
+
+    def run(job):
+        s, sp_path, g_path, out_path = job
+        # pairs_quartet_dist -v ignores its output-file argument and prints to stdout
+        with open(out_path, 'w') as out:
+            return s, subprocess.call([a.tqdist, '-v', sp_path, g_path], stdout=out), out_path
+
+    # verbose columns: n, C(n,4), distance, normalized distance, shared resolved quartets,
+    # its normalized value, quartets unresolved in both trees, its normalized value
+    per = {}
+    failed = [False] * len(a.trees)
+    with ThreadPoolExecutor(a.tq_procs) as ex:
+        for job, (s, code, out_path) in zip(jobs, ex.map(run, jobs)):
+            c0 = int(out_path.rsplit('.', 2)[-2])
+            if code != 0:
+                failed[s] = True
+                continue
+            got = [line.split() for line in open(out_path) if len(line.split()) >= 5]
+            if len(got) != len(rows[c0:c0 + a.chunk]):
+                failed[s] = True
+                continue
+            for j, parts in enumerate(got):
+                per[(s, c0 + j)] = (int(parts[0]), int(parts[1]), int(parts[4]))
+    if any(failed):
+        for s, path in enumerate(a.trees):
+            print(f'{names[s]} {path} {"tqdist_failed" if failed[s] else "ok"}')
+        raise SystemExit(1)
+    total_q = total_res = 0
+    shared = [0] * len(a.trees)
+    table = ['gene,taxa,quartets,unresolved_in_gene,resolved_in_gene,' + ','.join('shared_' + x for x in names)]
+    for i, r in enumerate(rows):
+        n, q, _ = per[(0, i)]
+        res = q - r[2]
+        total_q += q; total_res += res
+        sh = [per[(s, i)][2] for s in range(len(a.trees))]
+        assert all(per[(s, i)][:2] == (n, q) for s in range(len(a.trees)))
+        for s in range(len(a.trees)):
+            shared[s] += sh[s]
+        table.append('%d,%d,%d,%d,%d,%s' % (kept_genes[i], n, q, r[2], res, ','.join(map(str, sh))))
+    if a.per_gene:
+        open(a.per_gene, 'w').write('\n'.join(table) + '\n')
+    print(f'genes {len(rows)} quartets {total_q} resolved_in_genes {total_res}')
+    for s, path in enumerate(a.trees):
+        print(f'{names[s]} shared {shared[s]} normalized {shared[s] / total_res:.9f} astral_scale {2 * shared[s]} tree {path}')
+
+
+if __name__ == '__main__':
+    main()

runs/hostkey-2026-10-22-epyc9354/chain/queue.sh

@@ -0,0 +1,43 @@
+#!/bin/bash
+# Runs the jobs of JOBS (tab-separated: id, group or "-", timeout_s, args) one after the other, each with the whole
+# machine (64 threads on all CPUs), under GNU time. Resumable: a job with out/runs/<id>/DONE is skipped.
+# A job that hits its timeout is recorded as censored; if it was a default run, the rest of its group (the same
+# size and replicate) is skipped and logged, as PLAN.md's backstop rule says.
+set -u
+R=${R:-/workspace/hk2}; cd "$R"
+Q=$R/qraft; TH=${THREADS:-64}; CPUS=0-$(( $(nproc) - 1 )); J=${1:-jobs.tsv}
+OUT=$R/out; mkdir -p "$OUT/runs"; CSV=$OUT/runs.csv
+[ -s "$CSV" ] || echo "id,group,status,exit,wall_s,maxrss_kb,tree_sha256,start_utc,end_utc" > "$CSV"
+log() { echo "$(date -u +%FT%TZ) $*" >> "$OUT/queue.log"; }
+n=$(grep -cv '^#' "$J"); i=0
+while IFS=$'\t' read -r id grp to args; do
+  [ -z "${id:-}" ] && continue; case "$id" in \#*) continue;; esac
+  [ "$grp" = "-" ] && grp=""
+  i=$((i + 1)); d=$OUT/runs/$id
+  [ -e "$d/DONE" ] && continue
+  if [ -n "$grp" ] && [ -e "$OUT/skip/$grp" ]; then
+    mkdir -p "$d"; echo skipped > "$d/DONE"
+    echo "$id,$grp,skipped,,,,,," >> "$CSV"; log "skip $id ($grp: $(cat "$OUT/skip/$grp"))"; continue
+  fi
+  mkdir -p "$d"; s=$(date -u +%FT%TZ); log "start $i/$n $id timeout=$to"
+  echo "$args" > "$d/args"
+  # shellcheck disable=SC2086
+  if [ "$to" -gt 0 ]; then
+    /usr/bin/time -o "$d/time" -f "%e,%M" timeout --signal=TERM --kill-after=60 "$to" \
+      taskset -c "$CPUS" "$Q" $args -o "$d/out.tre" -t "$TH" --no-progress --stats-json "$d/stats.json" > "$d/log" 2>&1
+  else
+    /usr/bin/time -o "$d/time" -f "%e,%M" \
+      taskset -c "$CPUS" "$Q" $args -o "$d/out.tre" -t "$TH" --no-progress --stats-json "$d/stats.json" > "$d/log" 2>&1
+  fi
+  rc=$?; e=$(date -u +%FT%TZ)
+  t=$(tail -n 1 "$d/time" 2>/dev/null | grep -E '^[0-9.]+,[0-9]+$' || echo ",")
+  if [ $rc -eq 0 ] && [ -s "$d/out.tre" ]; then st=done; h=$(sha256sum "$d/out.tre" | cut -d' ' -f1)
+  elif [ $rc -eq 124 ] || [ $rc -eq 137 ]; then st=censored; h=""
+  else st=failed; h=""; fi
+  echo "$id,$grp,$st,$rc,$t,$h,$s,$e" >> "$CSV"; echo "$st" > "$d/DONE"
+  log "end $id $st rc=$rc time=$t"
+  if [ "$st" = censored ] && [ -n "$grp" ] && [ "${id##*.}" = default ]; then
+    mkdir -p "$OUT/skip"; echo "default run $id passed its deadline ${to}s" > "$OUT/skip/$grp"; log "backstop: skip rest of $grp"
+  fi
+done < "$J"
+log "queue $J finished"

runs/hostkey-2026-10-22-epyc9354/out/discordance-100k.csv

@@ -1,3 +1,5 @@
 t100000_g1000,R1,100000,1000,500,22.59,2000,32.26
 t100000_g1000,R2,100000,1000,500,20.65,2000,29.65
 t100000_g1000,R3,100000,1000,500,23.22,2000,33.07
+t100000_g1000,R4,100000,1000,500,39.01,2000,51.71
+t100000_g1000,R5,100000,1000,500,15.64,2000,22.74