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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R1/mre+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R1/mre+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..2aaf6cbd2cf465429ade13b762e14e823d0a89dc --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R1/mre+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R1/mre+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R1/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R1/mre+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R1/mre+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R1/mre+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R1/mre+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R1/mre+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..68f8f5fd1c020eca2b19c0c4a068e909d3b2a70d --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R1/mre+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, 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/home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R1/mre_nni_div+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R1/mre_nni_div+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R1/mre_nni_div+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..a07771bd9df7ce8d195e88887e1537e4bcca98d0 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R1/mre_nni_div+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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": 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R1/no_test+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R1/no_test+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..510c9b3fe4c72ca0685b451f1d6cfda6e58d9a64 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R1/no_test+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R1/no_test+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R1/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R1/no_test+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R1/no_test+none.base.json --no-nni --no-bipartition-test diff --git 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R1/regraft_norm+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R1/regraft_norm+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..d0201bd649a05668eed21d9ad076f7940ab5920b --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R1/regraft_norm+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R1/regraft_norm+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R1/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R1/regraft_norm+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R1/regraft_norm+none.base.json --no-nni 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R1/test_4x2+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R1/test_4x2+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..d3b05d6f430e034c093182079dd42fda5031c805 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R1/test_4x2+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R1/test_4x2+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R1/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R1/test_4x2+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R1/test_4x2+none.base.json --no-nni --test-proposals 4 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R1/test_4x2+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R1/test_4x2+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..93fa1a7dbbe6a62a55fd081fa01e5dfbe99ff525 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R1/test_4x2+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R1/test_4x2+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R1/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R1/test_4x2+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R1/test_4x2+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R1/test_4x2+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R1/test_4x2+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R1/test_4x2+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..a5b62f54bee54ec7408e1a967ba680e74299fac3 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R1/test_4x2+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R10/balanced+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R10/balanced+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..dda1449ca346969044c1b3693686a2a2f13f42ed --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R10/balanced+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R10/balanced+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R10/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R10/balanced+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R10/balanced+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R10/balanced+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R10/balanced+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R10/balanced+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..047d67b409f12b7a04e506260fcda7fdb613e820 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R10/balanced+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R10/default+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R10/default+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..e94eef74146eb1abc776b6c7fccbd335694b5ca5 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R10/default+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R10/default+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R10/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R10/default+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R10/default+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R10/default+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R10/default+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R10/default+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..e0742837670d4636afa5b90508210e0f88e0aa61 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R10/default+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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/home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R10/mre+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R10/mre+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R10/mre+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..9eeb9be1adf7ccf6def110570f2d52d2fdcbcb2b --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R10/mre+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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": 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R10/mre_nni_div+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R10/mre_nni_div+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..849fe9378b0377a850e517498f44879a7f8bc3fd --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R10/mre_nni_div+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R10/mre_nni_div+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R10/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R10/mre_nni_div+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R10/mre_nni_div+none.base.json --no-nni --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R10/mre+rel.tre diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R10/mre_nni_div+none.base.json b/runs/local-2026-10-21-ablation/idcheck/1000/R10/mre_nni_div+none.base.json new file mode 100644 index 0000000000000000000000000000000000000000..6e509b3cde248151fd961e13a8c58fffca78476f --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R10/mre_nni_div+none.base.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": true, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": true, + "bipartition_test_complete_genes": true, + "bipartition_test_coefficient": 0.05, + "bipartition_test_crossover": 10000, + "bipartition_test_proposals": 1, + "bipartition_test_anchor_pairs": 1, + "bipartition_test_threshold": -1.28427, + "regraft_score": "raw", + "nni": false, + "nni_move_cap": 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R10/mre_nni_div+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R10/mre_nni_div+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..5d2447338ca7093e4018614294a0bed0ead20c0b --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R10/mre_nni_div+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R10/mre_nni_div+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R10/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R10/mre_nni_div+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R10/mre_nni_div+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R10/mre_nni_div+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R10/mre_nni_div+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R10/mre_nni_div+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..da191ed876077eeb09d2e7f045164edce4012c29 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R10/mre_nni_div+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R10/regraft_norm+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R10/regraft_norm+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..7aed890b74c9279c79947811ce6ca5717a283c8b --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R10/regraft_norm+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R10/regraft_norm+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R10/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R10/regraft_norm+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R10/regraft_norm+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R10/regraft_norm+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R10/regraft_norm+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R10/regraft_norm+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..13fd1beea7d1b064f9dcbbc9b48475cd9f230b0a --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R10/regraft_norm+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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": 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R10/test_4x2+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R10/test_4x2+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..b25810d01263008e8c6d310a9b089b4c702f8775 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R10/test_4x2+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R10/test_4x2+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R10/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R10/test_4x2+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R10/test_4x2+none.base.json --no-nni --test-proposals 4 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R10/test_4x2+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R10/test_4x2+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..0ff3705c19fa10159711a0f4e1b637d53afc8e15 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R10/test_4x2+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R10/test_4x2+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R10/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R10/test_4x2+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R10/test_4x2+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R10/test_4x2+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R10/test_4x2+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R10/test_4x2+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..a2c8df851149b960dfd7e60382f627c9d1a94c1d --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R10/test_4x2+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R11/balanced+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R11/balanced+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..adc5654ca9612396efd8433dd76cabaaed5edded --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R11/balanced+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R11/balanced+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R11/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R11/balanced+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R11/balanced+none.base.json --no-nni --divide-score balanced 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R11/balanced+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R11/balanced+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..1dd7db9cab21f03f18292173b332b368fc4408a9 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R11/balanced+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R11/balanced+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R11/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R11/balanced+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R11/balanced+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R11/balanced+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R11/balanced+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R11/balanced+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..912ac8a8e9f7344c7ddb664c9baaedcaeb9e32a4 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R11/balanced+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R11/default+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R11/default+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..9f7803b71058c31d21a3e01963633ccc9c887f66 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R11/default+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R11/default+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R11/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R11/default+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R11/default+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R11/default+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R11/default+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R11/default+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..e3faea0ff48716cfb1269ad7e7fceece6d4a15a7 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R11/default+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R11/mre+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R11/mre+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..2c14c2ee57d0862ebd970954e07116c0ad0771e2 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R11/mre+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R11/mre+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R11/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R11/mre+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R11/mre+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R11/mre+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R11/mre+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R11/mre+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..bf1212c41611afd6b240305b33a6f29d8450fe7e --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R11/mre+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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": 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R11/mre_nni_div+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R11/mre_nni_div+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..e333ccdd686bce17ffa00b8344ece12a4c80cf6c --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R11/mre_nni_div+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R11/mre_nni_div+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R11/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R11/mre_nni_div+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R11/mre_nni_div+none.base.json --no-nni --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R11/mre+rel.tre diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R11/mre_nni_div+none.base.json b/runs/local-2026-10-21-ablation/idcheck/1000/R11/mre_nni_div+none.base.json new file mode 100644 index 0000000000000000000000000000000000000000..e39aa64a7f0851ec92a6810788e0ef5ba8b8278a --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R11/mre_nni_div+none.base.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": true, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": true, + "bipartition_test_complete_genes": true, + "bipartition_test_coefficient": 0.05, + "bipartition_test_crossover": 10000, + "bipartition_test_proposals": 1, + "bipartition_test_anchor_pairs": 1, + "bipartition_test_threshold": -1.28427, + "regraft_score": "raw", + "nni": false, + "nni_move_cap": 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/home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R11/mre_nni_div+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R11/mre_nni_div+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R11/mre_nni_div+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..dac0bffc931b6601a92451111ed4397daa5659a1 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R11/mre_nni_div+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R11/no_test+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R11/no_test+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..fd4773820b9f568ad79afcd6b604f72965aba24e --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R11/no_test+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R11/no_test+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R11/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R11/no_test+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R11/no_test+none.base.json --no-nni --no-bipartition-test diff --git 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R11/no_test+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R11/no_test+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..7077f4c5e086fab435e2a10ca215218b96703204 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R11/no_test+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R11/no_test+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R11/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R11/no_test+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R11/no_test+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R11/no_test+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R11/no_test+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R11/no_test+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..a741dffba0e199b09ad1939cb8c27729cacdbfc1 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R11/no_test+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R11/regraft_norm+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R11/regraft_norm+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..56036496be4f03bba69d0613cdba032aa6726979 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R11/regraft_norm+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R11/regraft_norm+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R11/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R11/regraft_norm+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R11/regraft_norm+none.base.json --no-nni --regraft-score normalized diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R11/regraft_norm+none.base.json b/runs/local-2026-10-21-ablation/idcheck/1000/R11/regraft_norm+none.base.json new file mode 100644 index 0000000000000000000000000000000000000000..08ee84ed19a6be2631a4f7caa3d0dca494100156 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R11/regraft_norm+none.base.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": true, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": true, + "bipartition_test_complete_genes": true, + "bipartition_test_coefficient": 0.05, + "bipartition_test_crossover": 10000, + "bipartition_test_proposals": 1, + "bipartition_test_anchor_pairs": 1, + "bipartition_test_threshold": -1.28427, + "regraft_score": "normalized", + "nni": false, + "nni_move_cap": true, + "nni_support_gate": true, + "nni_batch": false, + "spr_refine": false, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R11/regraft_norm+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R11/regraft_norm+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..ff5a5a5fc8f86e0dec8ca6828296606091ff4f9e --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R11/regraft_norm+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R11/regraft_norm+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R11/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R11/regraft_norm+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R11/regraft_norm+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R11/regraft_norm+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R11/regraft_norm+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R11/regraft_norm+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..bfae4a413347b6bbeebd1cd3d30c135ffd8ada21 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R11/regraft_norm+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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": 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R11/test_4x2+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R11/test_4x2+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..bd630683020ca4ceb0842756404a667d7dee06f5 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R11/test_4x2+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R11/test_4x2+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R11/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R11/test_4x2+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R11/test_4x2+none.base.json --no-nni --test-proposals 4 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R11/test_4x2+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R11/test_4x2+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..3f2e447c793882375e82f8d7e3713c82003e06d9 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R11/test_4x2+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R11/test_4x2+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R11/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R11/test_4x2+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R11/test_4x2+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R11/test_4x2+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R11/test_4x2+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R11/test_4x2+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..d9a199888e1da4876753c995b34e163e89f29f4a --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R11/test_4x2+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R12/balanced+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R12/balanced+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..b6ab05e012dbe328439791de66f25378d9371539 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R12/balanced+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R12/balanced+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R12/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R12/balanced+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R12/balanced+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R12/balanced+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R12/balanced+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R12/balanced+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..1e845e216f8ce994dc03ed69ba616cfada2e2cf5 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R12/balanced+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R12/default+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R12/default+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..c87e54478e829f2d2771b665a0981d6c6083c655 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R12/default+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R12/default+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R12/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R12/default+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R12/default+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R12/default+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R12/default+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R12/default+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..3742533d04b372d8f3db12f07af3cf0891222ff1 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R12/default+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R12/mre+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R12/mre+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..186e013f32a5d72b67c503ff6f9491b15dec8536 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R12/mre+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R12/mre+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R12/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R12/mre+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R12/mre+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R12/mre+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R12/mre+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R12/mre+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..09dd9a9c0f76b9902c9d4ea0c9fe5b0410b32aa8 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R12/mre+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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": 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R12/mre_nni_div+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R12/mre_nni_div+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..a9f6199ff32c9003427a998f7d929140c80ac312 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R12/mre_nni_div+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R12/mre_nni_div+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R12/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R12/mre_nni_div+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R12/mre_nni_div+none.base.json --no-nni --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R12/mre+rel.tre diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R12/mre_nni_div+none.base.json b/runs/local-2026-10-21-ablation/idcheck/1000/R12/mre_nni_div+none.base.json new file mode 100644 index 0000000000000000000000000000000000000000..484e112270c561ae2bd4a4d912822103454ef702 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R12/mre_nni_div+none.base.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": true, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": true, + "bipartition_test_complete_genes": true, + "bipartition_test_coefficient": 0.05, + "bipartition_test_crossover": 10000, + "bipartition_test_proposals": 1, + "bipartition_test_anchor_pairs": 1, + "bipartition_test_threshold": -1.28427, + "regraft_score": "raw", + "nni": false, + "nni_move_cap": 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/home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R12/mre_nni_div+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R12/mre_nni_div+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R12/mre_nni_div+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..2ce5f87d7a6be5b9f5ea107b4533335eb2d8eace --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R12/mre_nni_div+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R12/no_test+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R12/no_test+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..b39c9c3df8f0524107a27088d179243d59308b4c --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R12/no_test+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R12/no_test+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R12/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R12/no_test+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R12/no_test+none.base.json --no-nni --no-bipartition-test diff --git 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R12/no_test+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R12/no_test+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..7b96b63892573cfb4fb4ba3f9ead8f300d8cf46e --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R12/no_test+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R12/no_test+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R12/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R12/no_test+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R12/no_test+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R12/no_test+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R12/no_test+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R12/no_test+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..25b8b8dda7791e197e2460671deb6da6bc56654d --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R12/no_test+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R12/regraft_norm+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R12/regraft_norm+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..3fbd304754dc6489903c7b8e9c2e1c42162cda4c --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R12/regraft_norm+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R12/regraft_norm+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R12/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R12/regraft_norm+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R12/regraft_norm+none.base.json --no-nni 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R12/regraft_norm+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R12/regraft_norm+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..8a8f2c9408734cd509f62f7f68d25ccfe9942fbb --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R12/regraft_norm+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R12/regraft_norm+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R12/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R12/regraft_norm+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R12/regraft_norm+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R12/regraft_norm+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R12/regraft_norm+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R12/regraft_norm+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..635d637a49c2b8050de9d0a30383d3ee8ca16503 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R12/regraft_norm+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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": 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R12/test_4x2+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R12/test_4x2+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..fc2dd79e8eb1d803a4916bea931d0ece2df60296 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R12/test_4x2+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R12/test_4x2+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R12/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R12/test_4x2+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R12/test_4x2+none.base.json --no-nni --test-proposals 4 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R12/test_4x2+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R12/test_4x2+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..992c390f62bbd246ac95a0ca7a4a10f64de3e868 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R12/test_4x2+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R12/test_4x2+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R12/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R12/test_4x2+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R12/test_4x2+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R12/test_4x2+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R12/test_4x2+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R12/test_4x2+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..411137763f777659f686c3441df84b1a850b600b --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R12/test_4x2+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R13/balanced+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R13/balanced+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..426ed38737b7f79dc541c29242e0d5d3f42bb4b4 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R13/balanced+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R13/balanced+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R13/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R13/balanced+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R13/balanced+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R13/balanced+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R13/balanced+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R13/balanced+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..9896d5dd6c8012526c3d5935fdbdd5bccf9696ab --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R13/balanced+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R13/default+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R13/default+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..b599e76ee8a9f9ff5b7943c09f79272f068ed3a5 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R13/default+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R13/default+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R13/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R13/default+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R13/default+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R13/default+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R13/default+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R13/default+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..861840499cc2b0e9fdf298bf85cf1f6afa391fd2 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R13/default+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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/home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R13/mre+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R13/mre+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R13/mre+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..92c43ade7ed6004310409c44742b82022a307f58 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R13/mre+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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": 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R13/mre_nni_div+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R13/mre_nni_div+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..fccd47a22672db5dafe0c100cce37da567c0176b --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R13/mre_nni_div+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R13/mre_nni_div+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R13/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R13/mre_nni_div+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R13/mre_nni_div+none.base.json --no-nni --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R13/mre+rel.tre diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R13/mre_nni_div+none.base.json b/runs/local-2026-10-21-ablation/idcheck/1000/R13/mre_nni_div+none.base.json new file mode 100644 index 0000000000000000000000000000000000000000..f1cdbae936adc77bef5160b90de288848305f3c7 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R13/mre_nni_div+none.base.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": true, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": true, + "bipartition_test_complete_genes": true, + "bipartition_test_coefficient": 0.05, + "bipartition_test_crossover": 10000, + "bipartition_test_proposals": 1, + "bipartition_test_anchor_pairs": 1, + "bipartition_test_threshold": -1.28427, + "regraft_score": "raw", + "nni": false, + "nni_move_cap": 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/home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R13/mre_nni_div+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R13/mre_nni_div+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R13/mre_nni_div+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..7cfc575f3a5c1cb05bcea956cd33a54d7355b949 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R13/mre_nni_div+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R13/no_test+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R13/no_test+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..f5201b9539baf67962e0a255848a4e2cc2c05508 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R13/no_test+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R13/no_test+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R13/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R13/no_test+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R13/no_test+none.base.json --no-nni --no-bipartition-test diff --git 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/home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R13/no_test+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R13/no_test+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R13/no_test+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..4913dce6cda84b66c4717998fecdcb585d03fa6a --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R13/no_test+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R13/regraft_norm+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R13/regraft_norm+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..c0eb726f9f7782b87bc3647209d3916e056c04dc --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R13/regraft_norm+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R13/regraft_norm+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R13/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R13/regraft_norm+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R13/regraft_norm+none.base.json --no-nni 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R13/regraft_norm+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R13/regraft_norm+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..8239bc76890b7ed3ea048d552f71d98f84e32f40 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R13/regraft_norm+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R13/regraft_norm+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R13/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R13/regraft_norm+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R13/regraft_norm+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R13/regraft_norm+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R13/regraft_norm+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R13/regraft_norm+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..b972c351c3d503577534b31b26bc7995246716e8 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R13/regraft_norm+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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": 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R13/test_4x2+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R13/test_4x2+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..e77a21964cc302968e2c9e7d59ca4b0ef0b2b91f --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R13/test_4x2+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R13/test_4x2+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R13/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R13/test_4x2+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R13/test_4x2+none.base.json --no-nni --test-proposals 4 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R13/test_4x2+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R13/test_4x2+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..12fe79fd0d3c5c3711b44860ebb63651f3970d6c --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R13/test_4x2+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R13/test_4x2+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R13/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R13/test_4x2+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R13/test_4x2+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R13/test_4x2+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R13/test_4x2+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R13/test_4x2+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..a59774eb93c8b2133fc27faf81e88c0a96fa3448 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R13/test_4x2+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R14/balanced+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R14/balanced+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..ddabd22fb60a6b54615917953f41871473379eb5 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R14/balanced+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R14/balanced+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R14/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R14/balanced+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R14/balanced+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R14/balanced+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R14/balanced+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R14/balanced+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..1491789f7c78414b6355bdd953c7252b59c912d5 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R14/balanced+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R14/default+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R14/default+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..d32d6fde2e8468d2352efcb7cda513a849737301 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R14/default+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R14/default+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R14/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R14/default+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R14/default+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R14/default+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R14/default+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R14/default+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..b616ce7f6b7b6b2f87fc9910fe4db5654f16dabd --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R14/default+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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/home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R14/mre+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R14/mre+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R14/mre+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..48130c1045697a68ca9fc9ef6c3f0a8445efe377 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R14/mre+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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": 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R14/mre_nni_div+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R14/mre_nni_div+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..9ec3c8186d2e860cce335c0e63c7c9f2a22e96a7 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R14/mre_nni_div+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R14/mre_nni_div+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R14/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R14/mre_nni_div+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R14/mre_nni_div+none.base.json --no-nni --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R14/mre+rel.tre diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R14/mre_nni_div+none.base.json b/runs/local-2026-10-21-ablation/idcheck/1000/R14/mre_nni_div+none.base.json new file mode 100644 index 0000000000000000000000000000000000000000..d9004d29ba387d3e4cc6de90f3979058b8553b8c --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R14/mre_nni_div+none.base.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": true, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": true, + "bipartition_test_complete_genes": true, + "bipartition_test_coefficient": 0.05, + "bipartition_test_crossover": 10000, + "bipartition_test_proposals": 1, + "bipartition_test_anchor_pairs": 1, + "bipartition_test_threshold": -1.28427, + "regraft_score": "raw", + "nni": false, + "nni_move_cap": 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/home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R14/mre_nni_div+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R14/mre_nni_div+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R14/mre_nni_div+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..bba7cfe80403598a59d70ac0e9e5ade276dfc5c9 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R14/mre_nni_div+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R14/no_test+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R14/no_test+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..e642ea1d37720604cd211c7909c503c62d99b38f --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R14/no_test+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R14/no_test+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R14/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R14/no_test+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R14/no_test+none.base.json --no-nni --no-bipartition-test diff --git 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R14/regraft_norm+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R14/regraft_norm+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..cc52733c81b0fab2daa39b58304bd02d3b57bb65 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R14/regraft_norm+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R14/regraft_norm+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R14/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R14/regraft_norm+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R14/regraft_norm+none.base.json --no-nni 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R14/regraft_norm+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R14/regraft_norm+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..6098e03ac19d9f13b4ce7fa1786085b5c0a438a1 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R14/regraft_norm+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R14/regraft_norm+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R14/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R14/regraft_norm+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R14/regraft_norm+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R14/regraft_norm+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R14/regraft_norm+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R14/regraft_norm+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..d765c8290394d664ebaa252efcb15f044eca32a4 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R14/regraft_norm+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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": 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R14/test_4x2+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R14/test_4x2+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..226b7d3c98a9e02046dc1c705793f7ae02f70721 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R14/test_4x2+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R14/test_4x2+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R14/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R14/test_4x2+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R14/test_4x2+none.base.json --no-nni --test-proposals 4 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R14/test_4x2+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R14/test_4x2+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..08710c1ef932bc3affadd5125b0fc28fe1284ebb --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R14/test_4x2+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R14/test_4x2+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R14/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R14/test_4x2+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R14/test_4x2+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R14/test_4x2+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R14/test_4x2+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R14/test_4x2+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..2f3afae5cdd821586df07d1f047bce346be98b52 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R14/test_4x2+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R15/balanced+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R15/balanced+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..a631f6707cc836aca828855bc671ff665dd4afa5 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R15/balanced+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R15/balanced+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R15/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R15/balanced+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R15/balanced+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R15/balanced+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R15/balanced+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R15/balanced+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..4fd7d99206987879c28cbfd4197b1d5a10b42a45 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R15/balanced+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R15/default+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R15/default+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..8c7e6e649726110dfbe9ba0ba3c72a3be77c4e85 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R15/default+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R15/default+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R15/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R15/default+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R15/default+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R15/default+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R15/default+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R15/default+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..e3228de25740f942e42d6ea97288567401cc0185 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R15/default+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R15/mre+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R15/mre+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..0645d22bbd1413555174ec53e87cc7c0afaf73b7 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R15/mre+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R15/mre+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R15/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R15/mre+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R15/mre+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R15/mre+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R15/mre+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R15/mre+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..e4b36b7f4694dc3d63becf50d1831b4168148419 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R15/mre+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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": 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R15/mre_nni_div+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R15/mre_nni_div+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..4b4fde48abd41c1e6d45d35d3303058ca25f11af --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R15/mre_nni_div+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R15/mre_nni_div+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R15/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R15/mre_nni_div+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R15/mre_nni_div+none.base.json --no-nni --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R15/mre+rel.tre diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R15/mre_nni_div+none.base.json b/runs/local-2026-10-21-ablation/idcheck/1000/R15/mre_nni_div+none.base.json new file mode 100644 index 0000000000000000000000000000000000000000..a69d44167e7b0c38288be73227e2c01b98d7c77e --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R15/mre_nni_div+none.base.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": true, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": true, + "bipartition_test_complete_genes": true, + "bipartition_test_coefficient": 0.05, + "bipartition_test_crossover": 10000, + "bipartition_test_proposals": 1, + "bipartition_test_anchor_pairs": 1, + "bipartition_test_threshold": -1.28427, + "regraft_score": "raw", + "nni": false, + "nni_move_cap": 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/home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R15/mre_nni_div+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R15/mre_nni_div+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R15/mre_nni_div+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..d6092c755b27a4e61cec686427a2a972cdaa5b2e --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R15/mre_nni_div+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R15/no_test+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R15/no_test+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..ad7dc5644ed7953bf1c913ea3d8e403d9e12ab80 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R15/no_test+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R15/no_test+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R15/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R15/no_test+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R15/no_test+none.base.json --no-nni --no-bipartition-test diff --git 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/home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R15/no_test+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R15/no_test+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R15/no_test+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..93e22ab474c2964366744508317155e7f40d126a --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R15/no_test+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R15/regraft_norm+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R15/regraft_norm+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..8c3478e27fe90faffeab3d78b4c2a219c1a97b70 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R15/regraft_norm+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R15/regraft_norm+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R15/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R15/regraft_norm+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R15/regraft_norm+none.base.json --no-nni 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R15/regraft_norm+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R15/regraft_norm+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..e2bc409a93a095c256305d3a8551c23b04d1fc71 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R15/regraft_norm+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R15/regraft_norm+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R15/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R15/regraft_norm+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R15/regraft_norm+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R15/regraft_norm+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R15/regraft_norm+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R15/regraft_norm+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..3100f36d67dd97bf65cc5364626a6d8cbfbba483 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R15/regraft_norm+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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": 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R15/test_4x2+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R15/test_4x2+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..1c3b49f4b21972e100840da6b798e08c0463209b --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R15/test_4x2+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R15/test_4x2+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R15/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R15/test_4x2+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R15/test_4x2+none.base.json --no-nni --test-proposals 4 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R15/test_4x2+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R15/test_4x2+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..a50075ffd8563e1ce81d9fb2de7dea67f708a689 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R15/test_4x2+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R15/test_4x2+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R15/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R15/test_4x2+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R15/test_4x2+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R15/test_4x2+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R15/test_4x2+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R15/test_4x2+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..b33daa18ab12675e2b4773589e152a38662cdaf0 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R15/test_4x2+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R16/balanced+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R16/balanced+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..395da3cff71b56486597f138e8d0971892645dc1 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R16/balanced+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R16/balanced+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R16/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R16/balanced+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R16/balanced+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R16/balanced+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R16/balanced+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R16/balanced+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..c956122f5e7291e0247fc5110803069531592c8a --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R16/balanced+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R16/default+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R16/default+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..daec22bf072af0f3b1b006a650ed6a880d3fb039 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R16/default+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R16/default+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R16/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R16/default+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R16/default+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R16/default+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R16/default+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R16/default+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..7cbf65acaf8dc61a5258adbe996be051004682a8 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R16/default+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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/home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R16/mre+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R16/mre+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R16/mre+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..0a24c431383992d6a06fbb22dfd17daab6cf82dc --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R16/mre+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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": 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R16/mre_nni_div+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R16/mre_nni_div+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..b6e687dd80c9a35089acc0b9ae2f871fa4d4a94b --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R16/mre_nni_div+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R16/mre_nni_div+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R16/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R16/mre_nni_div+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R16/mre_nni_div+none.base.json --no-nni --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R16/mre+rel.tre diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R16/mre_nni_div+none.base.json b/runs/local-2026-10-21-ablation/idcheck/1000/R16/mre_nni_div+none.base.json new file mode 100644 index 0000000000000000000000000000000000000000..defe7543f1cdb06dd0bcb95312164b3387ed01e7 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R16/mre_nni_div+none.base.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": true, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": true, + "bipartition_test_complete_genes": true, + "bipartition_test_coefficient": 0.05, + "bipartition_test_crossover": 10000, + "bipartition_test_proposals": 1, + "bipartition_test_anchor_pairs": 1, + "bipartition_test_threshold": -1.28427, + "regraft_score": "raw", + "nni": false, + "nni_move_cap": 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/home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R16/mre_nni_div+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R16/mre_nni_div+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R16/mre_nni_div+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..d94db485395f2930e9a7e30b39bc67e82eff9ed6 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R16/mre_nni_div+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R16/no_test+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R16/no_test+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..250caf99f03313b5ab5dff06f6119eea39149acf --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R16/no_test+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R16/no_test+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R16/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R16/no_test+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R16/no_test+none.base.json --no-nni --no-bipartition-test diff --git 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R16/no_test+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R16/no_test+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..9740a8032f38c5e66deeabc841c6103e81486532 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R16/no_test+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R16/no_test+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R16/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R16/no_test+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R16/no_test+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R16/no_test+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R16/no_test+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R16/no_test+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..2d4744c9e278ff408fb2fbb2564a25af2fcb4433 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R16/no_test+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R16/regraft_norm+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R16/regraft_norm+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..989810ead8f5e030529ec1658fd6f30d31e503da --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R16/regraft_norm+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R16/regraft_norm+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R16/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R16/regraft_norm+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R16/regraft_norm+none.base.json --no-nni 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R16/regraft_norm+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R16/regraft_norm+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..2d519355cc8171d61c1c60cddc3f77c6cf3a550a --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R16/regraft_norm+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R16/regraft_norm+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R16/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R16/regraft_norm+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R16/regraft_norm+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R16/regraft_norm+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R16/regraft_norm+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R16/regraft_norm+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..b04badbd21e7f0ecb6888bc4c7641b02ba18e4a7 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R16/regraft_norm+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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": 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R16/test_4x2+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R16/test_4x2+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..49625bf0f953f84b828227ea7c7f0db2e51efc05 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R16/test_4x2+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R16/test_4x2+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R16/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R16/test_4x2+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R16/test_4x2+none.base.json --no-nni --test-proposals 4 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R16/test_4x2+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R16/test_4x2+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..6351315efb5cc741bb6c2cd6bcc20bc95966cc82 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R16/test_4x2+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R16/test_4x2+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R16/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R16/test_4x2+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R16/test_4x2+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R16/test_4x2+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R16/test_4x2+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R16/test_4x2+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..f85baf38415036dcf6ffd7f9d42bdc0f19604f90 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R16/test_4x2+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R17/balanced+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R17/balanced+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..0432d682d05d8c8973e88e80de15283135146309 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R17/balanced+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R17/balanced+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R17/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R17/balanced+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R17/balanced+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R17/balanced+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R17/balanced+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R17/balanced+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..f0fb29e85837d50d848e5f411357d8e269340f05 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R17/balanced+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R17/default+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R17/default+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..9689592a852e5a1f02ff7a15ecb7713447b0f30c --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R17/default+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R17/default+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R17/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R17/default+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R17/default+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R17/default+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R17/default+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R17/default+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..e43642d67be5477a281055f992194403d3e55c48 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R17/default+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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/home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R17/mre+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R17/mre+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R17/mre+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..ee91445085a76c5a039e6620d8b8c6077561b875 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R17/mre+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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": 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R17/mre_nni_div+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R17/mre_nni_div+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..2bb859735f3d5d1de06c36f070e50ebb65984d90 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R17/mre_nni_div+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R17/mre_nni_div+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R17/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R17/mre_nni_div+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R17/mre_nni_div+none.base.json --no-nni --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R17/mre+rel.tre diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R17/mre_nni_div+none.base.json b/runs/local-2026-10-21-ablation/idcheck/1000/R17/mre_nni_div+none.base.json new file mode 100644 index 0000000000000000000000000000000000000000..c936f1d6f6217a770543d9a90990ce275fe85ac8 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R17/mre_nni_div+none.base.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": true, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": true, + "bipartition_test_complete_genes": true, + "bipartition_test_coefficient": 0.05, + "bipartition_test_crossover": 10000, + "bipartition_test_proposals": 1, + "bipartition_test_anchor_pairs": 1, + "bipartition_test_threshold": -1.28427, + "regraft_score": "raw", + "nni": false, + "nni_move_cap": 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/home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R17/mre_nni_div+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R17/mre_nni_div+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R17/mre_nni_div+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..0dbb7d73d8ac7aaf8f45e09aa4caabd7160d1f20 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R17/mre_nni_div+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R17/no_test+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R17/no_test+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..ef83524bd3e7544e0b323627805feff33653bed9 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R17/no_test+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R17/no_test+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R17/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R17/no_test+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R17/no_test+none.base.json --no-nni --no-bipartition-test diff --git 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R17/no_test+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R17/no_test+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..3c40df6c819ae7c208824bd91ded11e084981791 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R17/no_test+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R17/no_test+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R17/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R17/no_test+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R17/no_test+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R17/no_test+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R17/no_test+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R17/no_test+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..720b638549e8ff2d0a2f1aaaf314e2900cb19afe --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R17/no_test+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R17/regraft_norm+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R17/regraft_norm+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..f897ab7d0e2ca7c0f4b5dfd87039662374da753f --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R17/regraft_norm+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R17/regraft_norm+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R17/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R17/regraft_norm+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R17/regraft_norm+none.base.json --no-nni 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R17/regraft_norm+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R17/regraft_norm+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..0c2ffca4d06e9a8322b37eb7ca0b38df380507d1 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R17/regraft_norm+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R17/regraft_norm+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R17/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R17/regraft_norm+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R17/regraft_norm+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R17/regraft_norm+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R17/regraft_norm+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R17/regraft_norm+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..3d7a4b9f0aa64db554e1bc9ac23bf82183e08925 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R17/regraft_norm+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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": 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R17/test_4x2+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R17/test_4x2+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..82e66cb3ec7cb50373289ec26df91f1bdc6994a1 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R17/test_4x2+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R17/test_4x2+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R17/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R17/test_4x2+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R17/test_4x2+none.base.json --no-nni --test-proposals 4 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R17/test_4x2+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R17/test_4x2+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..ecf655750571fed946d6a00f626d921e2d625a3b --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R17/test_4x2+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R17/test_4x2+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R17/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R17/test_4x2+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R17/test_4x2+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R17/test_4x2+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R17/test_4x2+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R17/test_4x2+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..145a3aad1a1a5b69c07b5bfa26c6e785a977dab7 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R17/test_4x2+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R18/balanced+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R18/balanced+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..caa30571d4c57b4b3e2dce68f362ed4ba9605924 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R18/balanced+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R18/balanced+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R18/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R18/balanced+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R18/balanced+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R18/balanced+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R18/balanced+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R18/balanced+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..42972f58c539c4bb6cfb98e648fc49f309646f76 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R18/balanced+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R18/default+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R18/default+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..c9e18608706d53ba023b922363b14fa48f732c6d --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R18/default+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R18/default+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R18/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R18/default+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R18/default+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R18/default+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R18/default+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R18/default+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..8ad76582f7402c2075225efe3d4b044184550088 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R18/default+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R18/mre+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R18/mre+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..e6a6a5570fe5da39369649c0c5a5e4fa11221f37 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R18/mre+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R18/mre+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R18/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R18/mre+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R18/mre+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R18/mre+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R18/mre+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R18/mre+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..c93460e4cafc07f3086f048d25eb454f81faef4a --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R18/mre+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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": 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--starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R18/mre+rel.tre diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R18/mre_nni_div+none.base.json b/runs/local-2026-10-21-ablation/idcheck/1000/R18/mre_nni_div+none.base.json new file mode 100644 index 0000000000000000000000000000000000000000..46f3162453a6a7671afededd2aa6ec850a949c4c --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R18/mre_nni_div+none.base.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": true, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": true, + "bipartition_test_complete_genes": true, + "bipartition_test_coefficient": 0.05, + "bipartition_test_crossover": 10000, + "bipartition_test_proposals": 1, + "bipartition_test_anchor_pairs": 1, + "bipartition_test_threshold": -1.28427, + "regraft_score": "raw", + "nni": false, + "nni_move_cap": 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/home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R18/mre_nni_div+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R18/mre_nni_div+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R18/mre_nni_div+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..82a508c20352fa69f690adfd69bbdec5efb3a093 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R18/mre_nni_div+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R18/regraft_norm+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R18/regraft_norm+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..9f2a306adc61475fca34165c01abd729b06efd9e --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R18/regraft_norm+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R18/regraft_norm+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R18/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R18/regraft_norm+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R18/regraft_norm+none.base.json --no-nni 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R18/regraft_norm+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R18/regraft_norm+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..4f1e06eae75b3f7832a7be94bae19985f20adbb1 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R18/regraft_norm+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R18/regraft_norm+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R18/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R18/regraft_norm+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R18/regraft_norm+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R18/regraft_norm+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R18/regraft_norm+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R18/regraft_norm+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..0db737a6d250a766d42bea44dd5f91ef43ba34b4 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R18/regraft_norm+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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": 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R18/test_4x2+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R18/test_4x2+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..4204f002767a8ca27cc29913e05c0feeefac2981 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R18/test_4x2+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R18/test_4x2+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R18/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R18/test_4x2+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R18/test_4x2+none.base.json --no-nni --test-proposals 4 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R18/test_4x2+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R18/test_4x2+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..945d90f383ff3f902266b78521da2161655fe909 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R18/test_4x2+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R18/test_4x2+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R18/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R18/test_4x2+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R18/test_4x2+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R18/test_4x2+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R18/test_4x2+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R18/test_4x2+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..3734a0ce48f4e8c701616f221ba0d28b0b97f6c3 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R18/test_4x2+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R19/balanced+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R19/balanced+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..ff4fee737829fa0abb1cb272a7cf4f790080a5fb --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R19/balanced+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R19/balanced+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R19/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R19/balanced+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R19/balanced+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R19/balanced+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R19/balanced+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R19/balanced+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..97b6bf0262d78c042e5b781f8e4319cb9a4f6ad3 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R19/balanced+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R19/default+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R19/default+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..da0fa175ad1aaf30aa23ec23e989f70532767406 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R19/default+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R19/default+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R19/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R19/default+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R19/default+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R19/default+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R19/default+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R19/default+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..850d43afd09c2c125467e99136e306985ca87b9f --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R19/default+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R19/mre+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R19/mre+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..7ffa77bf62eccec03abebe02b620512624343e83 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R19/mre+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R19/mre+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R19/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R19/mre+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R19/mre+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R19/mre+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R19/mre+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R19/mre+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..f7b83aea4b7ccd24aff3b9a84b27390c161cf902 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R19/mre+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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": 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R19/mre_nni_div+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R19/mre_nni_div+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..ef1d11d93029fdb79a9ecfd5feed5c1bdbc8fbd7 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R19/mre_nni_div+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R19/mre_nni_div+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R19/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R19/mre_nni_div+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R19/mre_nni_div+none.base.json --no-nni --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R19/mre+rel.tre diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R19/mre_nni_div+none.base.json b/runs/local-2026-10-21-ablation/idcheck/1000/R19/mre_nni_div+none.base.json new file mode 100644 index 0000000000000000000000000000000000000000..bbf34b4855d5e829c7e3ce27e2f4110b1b924452 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R19/mre_nni_div+none.base.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": true, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": true, + "bipartition_test_complete_genes": true, + "bipartition_test_coefficient": 0.05, + "bipartition_test_crossover": 10000, + "bipartition_test_proposals": 1, + "bipartition_test_anchor_pairs": 1, + "bipartition_test_threshold": -1.28427, + "regraft_score": "raw", + "nni": false, + "nni_move_cap": 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/home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R19/mre_nni_div+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R19/mre_nni_div+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R19/mre_nni_div+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..633befb8073570eb6bfb35fc5b74044a4f5f32ec --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R19/mre_nni_div+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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/home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R19/no_test+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R19/no_test+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R19/no_test+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..a5ad5f53d34f53b488f96eb3850563c4dc54b17e --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R19/no_test+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R19/regraft_norm+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R19/regraft_norm+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..c35657c58860bc39b724fa1dd8a98b58f499c8e1 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R19/regraft_norm+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R19/regraft_norm+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R19/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R19/regraft_norm+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R19/regraft_norm+none.base.json --no-nni 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R19/regraft_norm+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R19/regraft_norm+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..1935aa6bd9f6f825ee13c6457a55802456422a6c --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R19/regraft_norm+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R19/regraft_norm+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R19/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R19/regraft_norm+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R19/regraft_norm+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R19/regraft_norm+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R19/regraft_norm+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R19/regraft_norm+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..3a3dd94b8b15fc2798107142a08e5dd9f5267c07 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R19/regraft_norm+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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": 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R19/test_4x2+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R19/test_4x2+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..f182a9ce05ae4be9cc618fd6b29ac5892424ab2e --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R19/test_4x2+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R19/test_4x2+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R19/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R19/test_4x2+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R19/test_4x2+none.base.json --no-nni --test-proposals 4 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R19/test_4x2+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R19/test_4x2+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..27018d89f416fc87bd944f6a2b5a1205e4ceacf3 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R19/test_4x2+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R19/test_4x2+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R19/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R19/test_4x2+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R19/test_4x2+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R19/test_4x2+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R19/test_4x2+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R19/test_4x2+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..561d6e24f0f263cdc6fa6faec27a757ac0971c12 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R19/test_4x2+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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/home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R2/balanced+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R2/balanced+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R2/balanced+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..816478a968fec5994fab359c163fc730daf404c1 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R2/balanced+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R2/default+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R2/default+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..c250b05fb30fb2dd8b4c9522ede7e82a11622a69 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R2/default+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R2/default+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R2/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R2/default+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R2/default+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R2/default+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R2/default+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R2/default+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..9a7c6f13229139e1235a379aa21ab2078be0f10c --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R2/default+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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/home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R2/mre+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R2/mre+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R2/mre+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..b99d200dde5c03f35fe5e54479e32fa378eef004 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R2/mre+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, 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/home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R2/mre_nni_div+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R2/mre_nni_div+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R2/mre_nni_div+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..f108e646d9cc720f60fd5b771a9e81088059cbea --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R2/mre_nni_div+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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": 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/home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R2/no_test+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R2/no_test+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R2/no_test+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..ab9cc425d0cf49ca2d40b6414062ec6ffa063bff --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R2/no_test+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R2/regraft_norm+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R2/regraft_norm+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..5ce01d34d7a479474239e9f44a8feb4ae2ff7152 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R2/regraft_norm+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R2/regraft_norm+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R2/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R2/regraft_norm+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R2/regraft_norm+none.base.json --no-nni 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/home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R2/regraft_norm+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R2/regraft_norm+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R2/regraft_norm+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..250f83c9abe1d17564d0f7408757cba0c1f56aa2 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R2/regraft_norm+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R2/test_4x2+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R2/test_4x2+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..cd1a3b613cb875e671fbda361dceb7b35a2b9f31 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R2/test_4x2+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R2/test_4x2+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R2/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R2/test_4x2+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R2/test_4x2+none.base.json --no-nni --test-proposals 4 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R2/test_4x2+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R2/test_4x2+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..8c46cd273ddadbd3f520668842f6ceb5554a0bd2 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R2/test_4x2+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R2/test_4x2+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R2/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R2/test_4x2+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R2/test_4x2+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R2/test_4x2+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R2/test_4x2+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R2/test_4x2+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..8693ac2abc76fd776bb6a6dab8b2267270d01b7f --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R2/test_4x2+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R20/balanced+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R20/balanced+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..50e46b99a53b5e68e3e42d2134b0c0ed51fa173f --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R20/balanced+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R20/balanced+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R20/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R20/balanced+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R20/balanced+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R20/balanced+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R20/balanced+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R20/balanced+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..edbcfd6d871b4580948b3c4367f709a66d5daa16 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R20/balanced+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R20/default+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R20/default+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..d16552c19ea5ea9e902cce61afa1193c614590cc --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R20/default+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R20/default+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R20/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R20/default+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R20/default+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R20/default+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R20/default+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R20/default+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..b0bbe69ca38df0ebe74f44b4a07e34e8559edde1 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R20/default+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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/home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R20/mre+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R20/mre+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R20/mre+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..5077c4db38d7c762d008de6dcfc9caa085bfee3c --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R20/mre+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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": 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R20/mre_nni_div+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R20/mre_nni_div+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..506f0e2fe8f601e4be0caec91538b90ff5d13a63 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R20/mre_nni_div+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R20/mre_nni_div+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R20/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R20/mre_nni_div+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R20/mre_nni_div+none.base.json --no-nni --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R20/mre+rel.tre diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R20/mre_nni_div+none.base.json b/runs/local-2026-10-21-ablation/idcheck/1000/R20/mre_nni_div+none.base.json new file mode 100644 index 0000000000000000000000000000000000000000..b3225119287a41149c2da0e3823b8e817b9aaae0 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R20/mre_nni_div+none.base.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": true, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": true, + "bipartition_test_complete_genes": true, + "bipartition_test_coefficient": 0.05, + "bipartition_test_crossover": 10000, + "bipartition_test_proposals": 1, + "bipartition_test_anchor_pairs": 1, + "bipartition_test_threshold": -1.28427, + "regraft_score": "raw", + "nni": false, + "nni_move_cap": 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/home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R20/mre_nni_div+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R20/mre_nni_div+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R20/mre_nni_div+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..db23654a8c9d53b0ee51fe5c82039cfe3012148a --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R20/mre_nni_div+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R20/no_test+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R20/no_test+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..2e5d8a1dd23427062863468cadfd52e710fcaf57 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R20/no_test+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R20/no_test+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R20/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R20/no_test+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R20/no_test+none.base.json --no-nni --no-bipartition-test diff --git 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R20/no_test+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R20/no_test+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..29f148f1dbcae97d712563d55686ab1d78538a57 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R20/no_test+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R20/no_test+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R20/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R20/no_test+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R20/no_test+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R20/no_test+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R20/no_test+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R20/no_test+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..4eab97a05f9ff8bc2d406b6592096a3b0636012c --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R20/no_test+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R20/regraft_norm+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R20/regraft_norm+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..57a30b1bb3f353060838aa276d69424b67863bb6 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R20/regraft_norm+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R20/regraft_norm+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R20/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R20/regraft_norm+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R20/regraft_norm+none.base.json --no-nni --regraft-score normalized diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R20/regraft_norm+none.base.json b/runs/local-2026-10-21-ablation/idcheck/1000/R20/regraft_norm+none.base.json new file mode 100644 index 0000000000000000000000000000000000000000..df0f92d6a4a6cc6e4fe454059bd7a746d87d64f7 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R20/regraft_norm+none.base.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": true, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": true, + "bipartition_test_complete_genes": true, + "bipartition_test_coefficient": 0.05, + "bipartition_test_crossover": 10000, + "bipartition_test_proposals": 1, + "bipartition_test_anchor_pairs": 1, + "bipartition_test_threshold": -1.28427, + "regraft_score": "normalized", + "nni": false, + "nni_move_cap": true, + "nni_support_gate": true, + "nni_batch": false, + "spr_refine": false, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R20/regraft_norm+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R20/regraft_norm+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..ccac627b235cb85e6011b3974971e6cfc62c20cc --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R20/regraft_norm+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R20/regraft_norm+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R20/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R20/regraft_norm+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R20/regraft_norm+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R20/regraft_norm+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R20/regraft_norm+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R20/regraft_norm+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..9cf50878bc80d20b46a45146e91eae9aae9d553c --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R20/regraft_norm+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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": 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R20/test_4x2+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R20/test_4x2+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..506f279c7280518b2f86d9e797a72ba01943f4ba --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R20/test_4x2+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R20/test_4x2+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R20/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R20/test_4x2+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R20/test_4x2+none.base.json --no-nni --test-proposals 4 --test-anchor-pairs 2 diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R20/test_4x2+none.base.json b/runs/local-2026-10-21-ablation/idcheck/1000/R20/test_4x2+none.base.json new file mode 100644 index 0000000000000000000000000000000000000000..086c1dd825d170b7b6e62672ea94abd9675c4631 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R20/test_4x2+none.base.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": true, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": true, + "bipartition_test_complete_genes": true, + "bipartition_test_coefficient": 0.05, + "bipartition_test_crossover": 10000, + "bipartition_test_proposals": 4, + "bipartition_test_anchor_pairs": 2, + "bipartition_test_threshold": -1.28427, + "regraft_score": "raw", + "nni": false, + "nni_move_cap": true, + "nni_support_gate": true, + "nni_batch": false, + "spr_refine": false, + "spr_reads_per_pass": 128, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R20/test_4x2+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R20/test_4x2+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..a8984c376c0add402316460312e599215b91a49d --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R20/test_4x2+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R20/test_4x2+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R20/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R20/test_4x2+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R20/test_4x2+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R20/test_4x2+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R20/test_4x2+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R20/test_4x2+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..e0865c59ced98b666eadf9afd8b38de963bee583 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R20/test_4x2+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R3/balanced+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R3/balanced+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..dd69d12bc3e6500f62f20f92a467cae86a3a3e7f --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R3/balanced+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R3/balanced+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R3/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R3/balanced+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R3/balanced+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R3/balanced+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R3/balanced+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R3/balanced+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..a62b0ad4f23497ed26132750aca8296d5398704a --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R3/balanced+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R3/default+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R3/default+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..60de64479c45de364bf862e50cae6227b0d88d84 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R3/default+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R3/default+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R3/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R3/default+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R3/default+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R3/default+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R3/default+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R3/default+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..3006d1a23cd609174d2ccca1632f9dda5948bfcb --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R3/default+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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/home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R3/mre+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R3/mre+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R3/mre+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..66694139b48314e1367554b859c2b1ba81d25d9f --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R3/mre+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, 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/home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R3/mre_nni_div+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R3/mre_nni_div+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R3/mre_nni_div+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..2f16f57a0c0267cc55a97825c71bd9db8284782f --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R3/mre_nni_div+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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": 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R3/no_test+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R3/no_test+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..ccaf67edbf7d8eb9216fc55069c1ebf585ddc014 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R3/no_test+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R3/no_test+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R3/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R3/no_test+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R3/no_test+none.base.json --no-nni --no-bipartition-test diff --git 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R3/regraft_norm+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R3/regraft_norm+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..085c9010a150e030ef811ec6489a55c4dc7edc1b --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R3/regraft_norm+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R3/regraft_norm+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R3/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R3/regraft_norm+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R3/regraft_norm+none.base.json --no-nni 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R3/test_4x2+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R3/test_4x2+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..b03a5cf8e541fc2b45075271338a35d6adeae8e3 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R3/test_4x2+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R3/test_4x2+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R3/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R3/test_4x2+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R3/test_4x2+none.base.json --no-nni --test-proposals 4 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R3/test_4x2+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R3/test_4x2+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..5aca9ba6d602927e98c36236a0cf7a95b62dd23c --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R3/test_4x2+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R3/test_4x2+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R3/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R3/test_4x2+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R3/test_4x2+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R3/test_4x2+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R3/test_4x2+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R3/test_4x2+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..3c2d6383a4e9327593af42f1d68efc44e3e5a714 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R3/test_4x2+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R4/balanced+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R4/balanced+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..415d5c67162b7b5ee31989b520124748a79ce5f5 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R4/balanced+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R4/balanced+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R4/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R4/balanced+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R4/balanced+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R4/balanced+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R4/balanced+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R4/balanced+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..06cb1f3a35d6b2d7e5de8197b1b7018632c30872 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R4/balanced+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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/home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R4/default+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R4/default+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R4/default+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..ae22f98540ceba78d0068fa5fea7b46994014a89 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R4/default+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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/home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R4/mre_nni_div+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R4/mre_nni_div+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R4/mre_nni_div+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..ae93fe2db4949b7ab7620dadc36be9bdc8ffef27 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R4/mre_nni_div+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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": 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R4/test_4x2+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R4/test_4x2+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..a11fc7dc48e9bf9bd133add963a49a8276674a8d --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R4/test_4x2+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R4/test_4x2+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R4/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R4/test_4x2+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R4/test_4x2+none.base.json --no-nni --test-proposals 4 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R5/balanced+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R5/balanced+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..1e1d9513f10ce238945a0b4c9b06500c2bc37b25 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R5/balanced+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R5/balanced+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R5/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R5/balanced+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R5/balanced+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R5/balanced+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R5/balanced+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R5/balanced+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..e32a47cb4382fd3bc815ed2982a9bad321544b9a --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R5/balanced+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R5/default+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R5/default+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..d7a16ce203fd74f190d25ea73780c4395b061a5f --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R5/default+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R5/default+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R5/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R5/default+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R5/default+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R5/default+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R5/default+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R5/default+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..5f35eff3ed3bfdda8ee3aad435b309af5d98b038 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R5/default+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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/home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R5/mre+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R5/mre+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R5/mre+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..92f3345dcc8243020d9e0ad4bbcca176b5f59cac --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R5/mre+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R5/mre_nni_div+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R5/mre_nni_div+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..1de6cd8ccfceb749ded941581301b37e35b9396d --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R5/mre_nni_div+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R5/mre_nni_div+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R5/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R5/mre_nni_div+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R5/mre_nni_div+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R5/mre_nni_div+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R5/mre_nni_div+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R5/mre_nni_div+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..fcbba165745e7dc0fe549811320215fe9eea5cd5 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R5/mre_nni_div+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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": 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R5/regraft_norm+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R5/regraft_norm+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..19e40dd9533a42b483a71569e9a6ec1bcdccb5a3 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R5/regraft_norm+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R5/regraft_norm+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R5/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R5/regraft_norm+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R5/regraft_norm+none.base.json --no-nni 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R5/test_4x2+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R5/test_4x2+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..b2e2ea6edbf76d09fc75fcc2b76412a0f0e97fa3 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R5/test_4x2+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R5/test_4x2+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R5/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R5/test_4x2+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R5/test_4x2+none.base.json --no-nni --test-proposals 4 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R5/test_4x2+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R5/test_4x2+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..10731e3638559c8034f4ccc8bfed53eb020e68e1 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R5/test_4x2+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R5/test_4x2+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R5/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R5/test_4x2+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R5/test_4x2+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R5/test_4x2+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R5/test_4x2+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R5/test_4x2+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..d8fd51cedab4ecf82a608067cff358fd45325228 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R5/test_4x2+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R6/balanced+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R6/balanced+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..7c995fdfb9a26d6fe669d3de9fce79b5346362e4 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R6/balanced+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R6/balanced+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R6/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R6/balanced+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R6/balanced+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R6/balanced+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R6/balanced+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R6/balanced+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..cdeb6c292ddfdb43591581e4fc2bbb5f031af3c1 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R6/balanced+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R6/default+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R6/default+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..7cecd436dddba34e824738de2e902ca5ec596935 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R6/default+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R6/default+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R6/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R6/default+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R6/default+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R6/default+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R6/default+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R6/default+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..e9525e2e153f34d7262421acf5bdad3ae8f2ccf4 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R6/default+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R6/mre+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R6/mre+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..de8af5b182c6ce4eea449540899ac7ede1dc10e3 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R6/mre+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R6/mre+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R6/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R6/mre+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R6/mre+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R6/mre+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R6/mre+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R6/mre+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..81753c87c0eba2bbb414865d442be5e655fd56ea --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R6/mre+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, 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/home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R6/mre_nni_div+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R6/mre_nni_div+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R6/mre_nni_div+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..9bbbd505758f40a2028a9b4f3bd7c0250b343113 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R6/mre_nni_div+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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": 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R6/no_test+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R6/no_test+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..8fef98c0b2a8614b56ff80711fdcbf7aa694ad43 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R6/no_test+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R6/no_test+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R6/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R6/no_test+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R6/no_test+none.base.json --no-nni --no-bipartition-test diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R6/no_test+none.base.json b/runs/local-2026-10-21-ablation/idcheck/1000/R6/no_test+none.base.json new file mode 100644 index 0000000000000000000000000000000000000000..4df31bbf520d145e016aece2f48b0589c43b6f28 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R6/no_test+none.base.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": true, + "divide_score": "quartet", + "bipartition_test": false, + "bipartition_test_available": false, + "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": false, + "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, 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R6/no_test+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R6/no_test+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..c37626b4739f8b705248af497e6688f6ac5c03e5 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R6/no_test+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R6/no_test+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R6/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R6/no_test+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R6/no_test+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R6/no_test+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R6/no_test+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R6/no_test+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..9e699c26d91c8bf2c722a8d13bbbcfcd1f3ff3e9 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R6/no_test+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R6/regraft_norm+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R6/regraft_norm+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..1ac64afc9cba9b7b6fe59234e3ea902bcbacc66a --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R6/regraft_norm+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R6/regraft_norm+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R6/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R6/regraft_norm+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R6/regraft_norm+none.base.json --no-nni 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R6/test_4x2+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R6/test_4x2+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..67361ccfd79864acd17c832e81e35d6bbaa39260 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R6/test_4x2+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R6/test_4x2+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R6/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R6/test_4x2+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R6/test_4x2+none.base.json --no-nni --test-proposals 4 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R6/test_4x2+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R6/test_4x2+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..0ed6d38db235ca1da1b1caddbbe840d8c937db17 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R6/test_4x2+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R6/test_4x2+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R6/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R6/test_4x2+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R6/test_4x2+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R6/test_4x2+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R6/test_4x2+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R6/test_4x2+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..e03cc283ce323c24ed6b031b47b0510d09f98f3a --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R6/test_4x2+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R7/balanced+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R7/balanced+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..f80674b75c0e6457865fa680950ead908dd63344 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R7/balanced+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R7/balanced+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R7/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R7/balanced+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R7/balanced+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R7/balanced+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R7/balanced+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R7/balanced+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..61b0f7e4648235fdd5b0b52fb4fe2c5873af9e42 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R7/balanced+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R7/default+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R7/default+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..771100efd7a9807099b5f7b72a36af0d1bc4a7cf --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R7/default+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R7/default+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R7/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R7/default+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R7/default+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R7/default+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R7/default+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R7/default+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..c4599726ed27c5998ca4106102a45e691ad1aed3 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R7/default+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R7/mre+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R7/mre+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..90959e1371fbf71f7cbd80c60d188f5cfea47fce --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R7/mre+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R7/mre+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R7/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R7/mre+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R7/mre+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R7/mre+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R7/mre+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R7/mre+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..7a049583c2106a77ca3dcc18d1fef5989ee3b96a --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R7/mre+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, 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/home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R7/mre_nni_div+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R7/mre_nni_div+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R7/mre_nni_div+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..9efe31e8df875c84c97efce06b39d76f263cee3d --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R7/mre_nni_div+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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": 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R7/no_test+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R7/no_test+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..67f58e1af96dd51eced735cbfd43e2e0ae9510e4 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R7/no_test+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R7/no_test+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R7/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R7/no_test+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R7/no_test+none.base.json --no-nni --no-bipartition-test diff --git 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/home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R7/no_test+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R7/no_test+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R7/no_test+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..15517501b6faa50c7064b04871242f22a7591b5a --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R7/no_test+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R7/regraft_norm+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R7/regraft_norm+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..1e8040abe16eb382a25d95d0698c77ba55753933 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R7/regraft_norm+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R7/regraft_norm+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R7/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R7/regraft_norm+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R7/regraft_norm+none.base.json --no-nni --regraft-score normalized diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R7/regraft_norm+none.base.json b/runs/local-2026-10-21-ablation/idcheck/1000/R7/regraft_norm+none.base.json new file mode 100644 index 0000000000000000000000000000000000000000..97f2d1d4ae7fbf9d964b8cf0c9662ead8de16cbf --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R7/regraft_norm+none.base.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": true, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": true, + "bipartition_test_complete_genes": true, + "bipartition_test_coefficient": 0.05, + "bipartition_test_crossover": 10000, + "bipartition_test_proposals": 1, + "bipartition_test_anchor_pairs": 1, + "bipartition_test_threshold": -1.28427, + "regraft_score": "normalized", + "nni": false, + "nni_move_cap": true, + "nni_support_gate": true, + "nni_batch": false, + "spr_refine": false, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R7/regraft_norm+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R7/regraft_norm+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..dd8767b7d394fcb539b566ddf7da2b857e3e7c2b --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R7/regraft_norm+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R7/regraft_norm+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R7/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R7/regraft_norm+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R7/regraft_norm+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R7/regraft_norm+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R7/regraft_norm+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R7/regraft_norm+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..6deb740e269f38444b354ee10f1640f76c2c079c --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R7/regraft_norm+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R7/test_4x2+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R7/test_4x2+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..e2911ffaf09bfb92770ea314b954c80d4fe57fa9 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R7/test_4x2+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R7/test_4x2+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R7/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R7/test_4x2+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R7/test_4x2+none.base.json --no-nni --test-proposals 4 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R7/test_4x2+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R7/test_4x2+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..2b75ea15c605bab7a3dd5cddd72b227d9aa1c1e0 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R7/test_4x2+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R7/test_4x2+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R7/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R7/test_4x2+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R7/test_4x2+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R7/test_4x2+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R7/test_4x2+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R7/test_4x2+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..23e4227b7f548cc20c3f7e86457d078ab9d4ff89 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R7/test_4x2+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R8/balanced+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R8/balanced+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..4770f8ea3df5c21133579afab255f60692749d1b --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R8/balanced+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R8/balanced+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R8/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R8/balanced+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R8/balanced+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R8/balanced+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R8/balanced+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R8/balanced+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..179da906e9f4bba1f59ce0c792b012d28c7b387c --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R8/balanced+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R8/default+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R8/default+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..e09c15fd56495218345c42f0e59a21124ace02c3 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R8/default+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R8/default+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R8/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R8/default+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R8/default+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R8/default+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R8/default+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R8/default+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..4b9766167502a766a4c473c41b8586375ce27d43 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R8/default+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R8/mre+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R8/mre+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..236fd1b29c5def9c184843c119afea27db51733b --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R8/mre+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R8/mre+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R8/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R8/mre+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R8/mre+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R8/mre+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R8/mre+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R8/mre+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..6e5578249158812f25cfd317455f1c67dd4d1b7a --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R8/mre+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, 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/home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R8/mre+rel.tre diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R8/mre_nni_div+none.base.json b/runs/local-2026-10-21-ablation/idcheck/1000/R8/mre_nni_div+none.base.json new file mode 100644 index 0000000000000000000000000000000000000000..c78a3572f2c676ba58191db838f454112c91c1e0 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R8/mre_nni_div+none.base.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": true, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": true, + "bipartition_test_complete_genes": true, + "bipartition_test_coefficient": 0.05, + "bipartition_test_crossover": 10000, + "bipartition_test_proposals": 1, + "bipartition_test_anchor_pairs": 1, + "bipartition_test_threshold": -1.28427, + "regraft_score": "raw", + "nni": false, + "nni_move_cap": true, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R8/mre_nni_div+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R8/mre_nni_div+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..8352ef8408b885071050609b4a7ed8d68b2e8c0a --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R8/mre_nni_div+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R8/mre_nni_div+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R8/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R8/mre_nni_div+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R8/mre_nni_div+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R8/mre_nni_div+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R8/mre_nni_div+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R8/mre_nni_div+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..97698aa84c47f5da517c64d9496f75818c80da83 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R8/mre_nni_div+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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": 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R8/regraft_norm+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R8/regraft_norm+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..43b1e4c89cfc2d089558b30eb43f0b8d88fafa16 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R8/regraft_norm+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R8/regraft_norm+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R8/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R8/regraft_norm+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R8/regraft_norm+none.base.json --no-nni 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R8/regraft_norm+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R8/regraft_norm+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..f4dbbb5407b7e1372a7f5a7a19fa52fd6f7675a2 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R8/regraft_norm+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R8/regraft_norm+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R8/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R8/regraft_norm+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R8/regraft_norm+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R8/regraft_norm+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R8/regraft_norm+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R8/regraft_norm+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..4f376f23f7649c50a413a644a6290bd5cde41824 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R8/regraft_norm+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R8/test_4x2+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R8/test_4x2+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..6830ae0724d1bc779d5b1778e6877ebd2e4f01e9 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R8/test_4x2+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R8/test_4x2+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R8/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R8/test_4x2+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R8/test_4x2+none.base.json --no-nni --test-proposals 4 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R8/test_4x2+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R8/test_4x2+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..0c3842451f2b3e3921e26c0edd3352cd557e6d75 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R8/test_4x2+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R8/test_4x2+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R8/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R8/test_4x2+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R8/test_4x2+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R8/test_4x2+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R8/test_4x2+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R8/test_4x2+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..f71e6ba6d0f7988dcc59c32294156e9099569ca7 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R8/test_4x2+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R9/balanced+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R9/balanced+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..a1f2f2fcb16f63f49d5c30c292fe19c2e9cc2f4e --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R9/balanced+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R9/balanced+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R9/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R9/balanced+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R9/balanced+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R9/balanced+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R9/balanced+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R9/balanced+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..306a4f3722adc7d09fc1eff9171c1f127c8b2c75 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R9/balanced+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R9/default+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R9/default+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..d1180f8d4c49c2503ebcab619a41896f2a7207d5 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R9/default+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R9/default+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R9/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R9/default+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R9/default+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R9/default+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R9/default+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R9/default+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..20527f9ff9a12f278af478c31638c24ed8505285 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R9/default+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R9/mre+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R9/mre+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..b73657b1a7885f03fbc2829e94498053d4f0223a --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R9/mre+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R9/mre+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R9/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R9/mre+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R9/mre+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R9/mre+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R9/mre+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R9/mre+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..fe775a4a389cfcca6cc022770c014f919b893edb --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R9/mre+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, 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/home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R9/mre_nni_div+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R9/mre_nni_div+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R9/mre_nni_div+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..5b0261585ffabea06a40bf510c8ac5a82e868192 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R9/mre_nni_div+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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": 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R9/regraft_norm+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R9/regraft_norm+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..5395c30ed15a327cb0d9de4672f285d0effd410b --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R9/regraft_norm+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R9/regraft_norm+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R9/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R9/regraft_norm+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R9/regraft_norm+none.base.json --no-nni 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R9/test_4x2+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R9/test_4x2+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..997ebde64dc63425d6f4f12cb0aca2950ef00473 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R9/test_4x2+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R9/test_4x2+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R9/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R9/test_4x2+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R9/test_4x2+none.base.json --no-nni --test-proposals 4 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R9/test_4x2+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1000/R9/test_4x2+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..e83093d62b3c5f08db9bbb63179eac09e81b8685 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R9/test_4x2+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R9/test_4x2+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/inputs/1000-taxon/R9/gt-cleaned-rooted-og-0.tre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R9/test_4x2+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1000/R9/test_4x2+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1000-taxon/R9/test_4x2+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1000/R9/test_4x2+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1000/R9/test_4x2+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..0290b83b6f87ebc5a4e129a408c9b3d6f861c8a5 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1000/R9/test_4x2+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 1001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1KP/R0/balanced+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1KP/R0/balanced+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..f626b9fc47132020cd7bbad9a4a688b68b6f086a --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1KP/R0/balanced+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1KP/R0/balanced+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/wQFM-turbo/datasets/normalized/1kp/Best.33.FAA.genes.nwk -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1KP/R0/balanced+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1KP/R0/balanced+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1kp/Best.33.FAA/balanced+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1KP/R0/balanced+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1KP/R0/balanced+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..47772c21c9836df985957422add71ad673a3afa1 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1KP/R0/balanced+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 410, + "taxa": 1178, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1KP/R0/default+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1KP/R0/default+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..d7144e4f1990194ce8d14f67018d5c9379e796a7 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1KP/R0/default+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1KP/R0/default+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/wQFM-turbo/datasets/normalized/1kp/Best.33.FAA.genes.nwk -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1KP/R0/default+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1KP/R0/default+none.base.json --no-nni diff --git 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1KP/R0/default+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1KP/R0/default+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..a12b5290e2df6c6672835edb4efe61e01fec139b --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1KP/R0/default+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1KP/R0/default+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/wQFM-turbo/datasets/normalized/1kp/Best.33.FAA.genes.nwk -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1KP/R0/default+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1KP/R0/default+rel.chain.json --starting-tree 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1KP/R0/default+rel.full.cmd b/runs/local-2026-10-21-ablation/idcheck/1KP/R0/default+rel.full.cmd new file mode 100644 index 0000000000000000000000000000000000000000..9b6b225bc12468b986c78fc1800430d755a3db6b --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1KP/R0/default+rel.full.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1KP/R0/default+rel.full.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/wQFM-turbo/datasets/normalized/1kp/Best.33.FAA.genes.nwk -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1KP/R0/default+rel.full.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1KP/R0/default+rel.full.json diff --git a/runs/local-2026-10-21-ablation/idcheck/1KP/R0/default+rel.full.json b/runs/local-2026-10-21-ablation/idcheck/1KP/R0/default+rel.full.json new file mode 100644 index 0000000000000000000000000000000000000000..8236db5d6d73f4a686d783a909115e9e2fa58a8f --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1KP/R0/default+rel.full.json @@ -0,0 +1,151 @@ +{ + "genes": 410, + "taxa": 1178, + "workers": 8, + "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, + "subproblems": 507, + "completed_subproblems": 507, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1KP/R0/mre+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1KP/R0/mre+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..a3679a515458f465d7ddf8a29d5d5cc38e997ae6 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1KP/R0/mre+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1KP/R0/mre+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/wQFM-turbo/datasets/normalized/1kp/Best.33.FAA.genes.nwk -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1KP/R0/mre+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1KP/R0/mre+none.base.json --no-nni --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1KP/R0/mre+none.base.json b/runs/local-2026-10-21-ablation/idcheck/1KP/R0/mre+none.base.json new file mode 100644 index 0000000000000000000000000000000000000000..3558688bebc7a8628c684010f6367f44ed9e482b --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1KP/R0/mre+none.base.json @@ -0,0 +1,151 @@ +{ + "genes": 410, + "taxa": 1178, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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": false, + "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, + "subproblems": 0, + "completed_subproblems": 0, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1KP/R0/mre+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1KP/R0/mre+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..2c8632d66c9e9a23572194ea5869c55990f1b477 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1KP/R0/mre+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1KP/R0/mre+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/wQFM-turbo/datasets/normalized/1kp/Best.33.FAA.genes.nwk -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1KP/R0/mre+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1KP/R0/mre+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1kp/Best.33.FAA/mre+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1KP/R0/mre+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1KP/R0/mre+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..bc400cef660a68e70dea92128b3f2d026669fa46 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1KP/R0/mre+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 410, + "taxa": 1178, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1KP/R0/mre_nni_div+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1KP/R0/mre_nni_div+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..22f3c903b44ffa345ffa106b07420e0400ee2cbd --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1KP/R0/mre_nni_div+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1KP/R0/mre_nni_div+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/wQFM-turbo/datasets/normalized/1kp/Best.33.FAA.genes.nwk -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1KP/R0/mre_nni_div+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1KP/R0/mre_nni_div+none.base.json --no-nni --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1kp/Best.33.FAA/mre+rel.tre diff --git a/runs/local-2026-10-21-ablation/idcheck/1KP/R0/mre_nni_div+none.base.json b/runs/local-2026-10-21-ablation/idcheck/1KP/R0/mre_nni_div+none.base.json new file mode 100644 index 0000000000000000000000000000000000000000..9be06f9ee89d439286d6d13e94983e2c5b18eb6a --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1KP/R0/mre_nni_div+none.base.json @@ -0,0 +1,151 @@ +{ + "genes": 410, + "taxa": 1178, + "workers": 8, + "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": false, + "nni_move_cap": true, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1KP/R0/mre_nni_div+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1KP/R0/mre_nni_div+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..cfcb05d635fbf348efa9c83dd2a82fdff059cd32 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1KP/R0/mre_nni_div+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1KP/R0/mre_nni_div+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/wQFM-turbo/datasets/normalized/1kp/Best.33.FAA.genes.nwk -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1KP/R0/mre_nni_div+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1KP/R0/mre_nni_div+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1kp/Best.33.FAA/mre_nni_div+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1KP/R0/mre_nni_div+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1KP/R0/mre_nni_div+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..b92c4bfc0c93a2f73fb8e1ba8fa4b3811e320c68 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1KP/R0/mre_nni_div+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 410, + "taxa": 1178, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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": 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1KP/R0/no_test+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1KP/R0/no_test+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..7aeadbc24082de5405382c2578131806c3ef4ae8 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1KP/R0/no_test+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1KP/R0/no_test+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/wQFM-turbo/datasets/normalized/1kp/Best.33.FAA.genes.nwk -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1KP/R0/no_test+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1KP/R0/no_test+none.base.json --no-nni --no-bipartition-test diff --git 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1KP/R0/no_test+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1KP/R0/no_test+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..1cffaa2b7ad2a0fd0f19018a23935340106edb87 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1KP/R0/no_test+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1KP/R0/no_test+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/wQFM-turbo/datasets/normalized/1kp/Best.33.FAA.genes.nwk -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1KP/R0/no_test+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1KP/R0/no_test+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1kp/Best.33.FAA/no_test+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1KP/R0/no_test+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1KP/R0/no_test+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..9555d562cda3ec351ea946bb268e73edf9920bdd --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1KP/R0/no_test+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 410, + "taxa": 1178, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1KP/R0/regraft_norm+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1KP/R0/regraft_norm+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..c1ba17f0e3428ed0db9033ebfe19ba117005866d --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1KP/R0/regraft_norm+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1KP/R0/regraft_norm+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/wQFM-turbo/datasets/normalized/1kp/Best.33.FAA.genes.nwk -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1KP/R0/regraft_norm+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1KP/R0/regraft_norm+none.base.json --no-nni --regraft-score normalized diff --git a/runs/local-2026-10-21-ablation/idcheck/1KP/R0/regraft_norm+none.base.json b/runs/local-2026-10-21-ablation/idcheck/1KP/R0/regraft_norm+none.base.json new file mode 100644 index 0000000000000000000000000000000000000000..63c32180287a20847be12e27fc86b4f5c2135e73 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1KP/R0/regraft_norm+none.base.json @@ -0,0 +1,151 @@ +{ + "genes": 410, + "taxa": 1178, + "workers": 8, + "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": "normalized", + "nni": false, + "nni_move_cap": true, + "nni_support_gate": true, + "nni_batch": false, + "spr_refine": false, + "spr_reads_per_pass": 128, + "spr_min_clade": 10, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1KP/R0/regraft_norm+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1KP/R0/regraft_norm+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..ccb4521671e4cccceceaaa5c82fd506688bcbf10 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1KP/R0/regraft_norm+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1KP/R0/regraft_norm+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/wQFM-turbo/datasets/normalized/1kp/Best.33.FAA.genes.nwk -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1KP/R0/regraft_norm+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1KP/R0/regraft_norm+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1kp/Best.33.FAA/regraft_norm+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1KP/R0/regraft_norm+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1KP/R0/regraft_norm+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..c8f895e9a2d1a4f7c58f969a7b4d6c6fbd0b6653 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1KP/R0/regraft_norm+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 410, + "taxa": 1178, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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": 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1KP/R0/test_4x2+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/1KP/R0/test_4x2+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..6aa6c6dba166dfd480d99775b6e480f01c55930c --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1KP/R0/test_4x2+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1KP/R0/test_4x2+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/wQFM-turbo/datasets/normalized/1kp/Best.33.FAA.genes.nwk -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1KP/R0/test_4x2+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1KP/R0/test_4x2+none.base.json --no-nni --test-proposals 4 --test-anchor-pairs 2 diff --git 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diff --git a/runs/local-2026-10-21-ablation/idcheck/1KP/R0/test_4x2+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/1KP/R0/test_4x2+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..3bfe7ba2958eaef1b7ca88da1b7effe484744f14 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1KP/R0/test_4x2+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1KP/R0/test_4x2+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/wQFM-turbo/datasets/normalized/1kp/Best.33.FAA.genes.nwk -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1KP/R0/test_4x2+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/1KP/R0/test_4x2+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/1kp/Best.33.FAA/test_4x2+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/1KP/R0/test_4x2+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/1KP/R0/test_4x2+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..90b01c12af57de21089de7a50e39bf6a486f73a3 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/1KP/R0/test_4x2+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 410, + "taxa": 1178, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/A-II/R46/balanced+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/A-II/R46/balanced+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..1435473b8c6dae0561b1786d15fa9b33e4ca4ce8 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-II/R46/balanced+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-II/R46/balanced+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/wQFM-turbo/datasets/sources/astral2/estimated-gene-trees/model.200.500000.0.000001/46/estimatedgenetre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-II/R46/balanced+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-II/R46/balanced+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/astral2-200.500000.0.000001/R46/balanced+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/A-II/R46/balanced+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/A-II/R46/balanced+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..7d87ec0bbd6ef3baef4e621f084568cf619bf487 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-II/R46/balanced+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 201, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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": 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diff --git a/runs/local-2026-10-21-ablation/idcheck/A-II/R47/balanced+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/A-II/R47/balanced+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..7e3ee7b130b763d042450a5d9519e1fea3da1f8a --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-II/R47/balanced+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-II/R47/balanced+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/wQFM-turbo/datasets/sources/astral2/estimated-gene-trees/model.200.500000.0.000001/47/estimatedgenetre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-II/R47/balanced+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-II/R47/balanced+rel.chain.json 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diff --git a/runs/local-2026-10-21-ablation/idcheck/A-II/R48/balanced+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/A-II/R48/balanced+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..9fac8cb7b61cb8f2c7d012f0bc488e28cc8fc163 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-II/R48/balanced+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-II/R48/balanced+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/wQFM-turbo/datasets/sources/astral2/estimated-gene-trees/model.200.500000.0.000001/48/estimatedgenetre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-II/R48/balanced+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-II/R48/balanced+rel.chain.json 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diff --git a/runs/local-2026-10-21-ablation/idcheck/A-II/R50/balanced+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/A-II/R50/balanced+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..c29fc854c1373465ac2aff5a4fe54c44341e17f2 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-II/R50/balanced+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-II/R50/balanced+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/wQFM-turbo/datasets/sources/astral2/estimated-gene-trees/model.200.500000.0.000001/50/estimatedgenetre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-II/R50/balanced+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-II/R50/balanced+none.base.json --no-nni 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diff --git a/runs/local-2026-10-21-ablation/idcheck/A-II/R50/balanced+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/A-II/R50/balanced+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..6f7a2aed23ba383680b96aeb7c31a5e23f910bc4 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-II/R50/balanced+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-II/R50/balanced+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/wQFM-turbo/datasets/sources/astral2/estimated-gene-trees/model.200.500000.0.000001/50/estimatedgenetre -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-II/R50/balanced+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-II/R50/balanced+rel.chain.json 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diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R1/balanced+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/A-III/R1/balanced+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..0459c28b39f5aaefa1eba1b08fe1a70a6976fab2 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R1/balanced+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R1/balanced+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/wQFM-turbo/datasets/normalized/astral3_2000/2k.01.full.genes.nwk -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R1/balanced+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R1/balanced+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/astral3-2000/R1/balanced+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R1/balanced+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/A-III/R1/balanced+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..5f1f0988520c83050259cfb59aa13880ee865d8c --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R1/balanced+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 2001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R1/default+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/A-III/R1/default+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..edd7eb2ea8074c9bfccda6caea094c7a2f780777 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R1/default+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R1/default+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/wQFM-turbo/datasets/normalized/astral3_2000/2k.01.full.genes.nwk -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R1/default+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R1/default+none.base.json --no-nni diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R1/default+none.base.json b/runs/local-2026-10-21-ablation/idcheck/A-III/R1/default+none.base.json new file mode 100644 index 0000000000000000000000000000000000000000..7702f6fe8250eadbb8cba1e8400af32a58a3a8fc --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R1/default+none.base.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 2001, + "workers": 8, + "progress": "off", + "divide": true, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": true, + "bipartition_test_complete_genes": true, + "bipartition_test_coefficient": 0.05, + "bipartition_test_crossover": 10000, + "bipartition_test_proposals": 1, + "bipartition_test_anchor_pairs": 1, + "bipartition_test_threshold": -2.56854, + "regraft_score": "raw", + "nni": false, + "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": 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diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R1/default+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/A-III/R1/default+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..77c1b8af157f005f545e10a53b7568c298a6217d --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R1/default+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R1/default+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/wQFM-turbo/datasets/normalized/astral3_2000/2k.01.full.genes.nwk -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R1/default+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R1/default+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/astral3-2000/R1/default+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R1/default+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/A-III/R1/default+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..9fb437ced714fdb2b857d078bc265952035ba081 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R1/default+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 2001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R1/default+rel.full.cmd b/runs/local-2026-10-21-ablation/idcheck/A-III/R1/default+rel.full.cmd new file mode 100644 index 0000000000000000000000000000000000000000..72ce9c14ec9354d13c4d6cc93dd421bb8245ae9d --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R1/default+rel.full.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R1/default+rel.full.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/wQFM-turbo/datasets/normalized/astral3_2000/2k.01.full.genes.nwk -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R1/default+rel.full.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R1/default+rel.full.json diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R1/default+rel.full.json b/runs/local-2026-10-21-ablation/idcheck/A-III/R1/default+rel.full.json new file mode 100644 index 0000000000000000000000000000000000000000..73f0cc284182f073a01ba0dc65d9e4e0a8d088d0 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R1/default+rel.full.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 2001, + "workers": 8, + "progress": "off", + "divide": true, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": true, + "bipartition_test_complete_genes": true, + "bipartition_test_coefficient": 0.05, + "bipartition_test_crossover": 10000, + "bipartition_test_proposals": 1, + "bipartition_test_anchor_pairs": 1, + "bipartition_test_threshold": -2.56854, + "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, 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diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R1/mre+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/A-III/R1/mre+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..eec65c105d5869941483240d9c860384aba8f43f --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R1/mre+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R1/mre+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/wQFM-turbo/datasets/normalized/astral3_2000/2k.01.full.genes.nwk -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R1/mre+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R1/mre+none.base.json --no-nni --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R1/mre+none.base.json b/runs/local-2026-10-21-ablation/idcheck/A-III/R1/mre+none.base.json new file mode 100644 index 0000000000000000000000000000000000000000..7c79a3a6c5a63bc340144b707930b4b1bba5e70a --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R1/mre+none.base.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 2001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R1/mre+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/A-III/R1/mre+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..8710ef8c38dec944fd2fe70f14ce567fe1e401e5 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R1/mre+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R1/mre+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/wQFM-turbo/datasets/normalized/astral3_2000/2k.01.full.genes.nwk -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R1/mre+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R1/mre+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/astral3-2000/R1/mre+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R1/mre+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/A-III/R1/mre+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..c137af2bbd051dfe6fa9140d304f8f9d1bf56e24 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R1/mre+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 2001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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": 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diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R1/mre_nni_div+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/A-III/R1/mre_nni_div+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..11bea2f1b2e9f0f3d6d5b6e34c01b921dd3aa3ca --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R1/mre_nni_div+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R1/mre_nni_div+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/wQFM-turbo/datasets/normalized/astral3_2000/2k.01.full.genes.nwk -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R1/mre_nni_div+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R1/mre_nni_div+none.base.json --no-nni --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/astral3-2000/R1/mre+rel.tre diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R1/mre_nni_div+none.base.json b/runs/local-2026-10-21-ablation/idcheck/A-III/R1/mre_nni_div+none.base.json new file mode 100644 index 0000000000000000000000000000000000000000..7f8c9c4149e04e97bd40388fd237d627c62b0d27 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R1/mre_nni_div+none.base.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 2001, + "workers": 8, + "progress": "off", + "divide": true, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": true, + "bipartition_test_complete_genes": true, + "bipartition_test_coefficient": 0.05, + "bipartition_test_crossover": 10000, + "bipartition_test_proposals": 1, + "bipartition_test_anchor_pairs": 1, + "bipartition_test_threshold": -2.56854, + "regraft_score": "raw", + "nni": false, + "nni_move_cap": true, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R1/mre_nni_div+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/A-III/R1/mre_nni_div+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..6c32364558075bb10495d5f8766f8933eef7b708 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R1/mre_nni_div+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R1/mre_nni_div+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/wQFM-turbo/datasets/normalized/astral3_2000/2k.01.full.genes.nwk -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R1/mre_nni_div+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R1/mre_nni_div+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/astral3-2000/R1/mre_nni_div+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R1/mre_nni_div+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/A-III/R1/mre_nni_div+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..ec260e8aba10fb506b57053e8c51213f19068e47 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R1/mre_nni_div+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 2001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R1/no_test+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/A-III/R1/no_test+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..349053a9c01125cf6c5a43c3f7b7f98b91db0a8f --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R1/no_test+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R1/no_test+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/wQFM-turbo/datasets/normalized/astral3_2000/2k.01.full.genes.nwk -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R1/no_test+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R1/no_test+none.base.json --no-nni --no-bipartition-test diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R1/no_test+none.base.json b/runs/local-2026-10-21-ablation/idcheck/A-III/R1/no_test+none.base.json new file mode 100644 index 0000000000000000000000000000000000000000..1695ec70c329fa7b70915fab868a95c996cf1988 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R1/no_test+none.base.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 2001, + "workers": 8, + "progress": "off", + "divide": true, + "divide_score": "quartet", + "bipartition_test": false, + "bipartition_test_available": false, + "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": false, + "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": 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diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R1/no_test+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/A-III/R1/no_test+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..7c19a5b112d911f1dca36c2ad8b04f429bec8b27 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R1/no_test+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R1/no_test+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/wQFM-turbo/datasets/normalized/astral3_2000/2k.01.full.genes.nwk -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R1/no_test+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R1/no_test+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/astral3-2000/R1/no_test+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R1/no_test+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/A-III/R1/no_test+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..f32ebb9965f32a2179853647d97926a5565cd520 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R1/no_test+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 2001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R1/regraft_norm+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/A-III/R1/regraft_norm+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..71d13c4d5896766cf87fa1f48871108a616b48c7 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R1/regraft_norm+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R1/regraft_norm+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/wQFM-turbo/datasets/normalized/astral3_2000/2k.01.full.genes.nwk -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R1/regraft_norm+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R1/regraft_norm+none.base.json --no-nni --regraft-score normalized diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R1/regraft_norm+none.base.json b/runs/local-2026-10-21-ablation/idcheck/A-III/R1/regraft_norm+none.base.json new file mode 100644 index 0000000000000000000000000000000000000000..d46c7e03bfc3e38b3524955bac8d52c3696d0925 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R1/regraft_norm+none.base.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 2001, + "workers": 8, + "progress": "off", + "divide": true, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": true, + "bipartition_test_complete_genes": true, + "bipartition_test_coefficient": 0.05, + "bipartition_test_crossover": 10000, + "bipartition_test_proposals": 1, + "bipartition_test_anchor_pairs": 1, + "bipartition_test_threshold": -2.56854, + "regraft_score": "normalized", + "nni": false, + "nni_move_cap": true, + "nni_support_gate": true, + "nni_batch": false, + "spr_refine": false, + "spr_reads_per_pass": 128, 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diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R1/regraft_norm+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/A-III/R1/regraft_norm+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..5d451f45256996c15eb1c422b96544f663151ec1 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R1/regraft_norm+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R1/regraft_norm+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/wQFM-turbo/datasets/normalized/astral3_2000/2k.01.full.genes.nwk -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R1/regraft_norm+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R1/regraft_norm+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/astral3-2000/R1/regraft_norm+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R1/regraft_norm+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/A-III/R1/regraft_norm+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..7dc67d0e1d645ca16192b622c5cc4c294389aa40 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R1/regraft_norm+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 2001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R1/test_4x2+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/A-III/R1/test_4x2+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..a365b637dfd1a64b992ac981c2b29c6f2fe514d4 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R1/test_4x2+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R1/test_4x2+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/wQFM-turbo/datasets/normalized/astral3_2000/2k.01.full.genes.nwk -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R1/test_4x2+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R1/test_4x2+none.base.json --no-nni --test-proposals 4 --test-anchor-pairs 2 diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R1/test_4x2+none.base.json b/runs/local-2026-10-21-ablation/idcheck/A-III/R1/test_4x2+none.base.json new file mode 100644 index 0000000000000000000000000000000000000000..47beea1d6028603dc78ea6cb3ce429a260fa21fd --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R1/test_4x2+none.base.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 2001, + "workers": 8, + "progress": "off", + "divide": true, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": true, + "bipartition_test_complete_genes": true, + "bipartition_test_coefficient": 0.05, + "bipartition_test_crossover": 10000, + "bipartition_test_proposals": 4, + "bipartition_test_anchor_pairs": 2, + "bipartition_test_threshold": -2.56854, + "regraft_score": "raw", + "nni": false, + "nni_move_cap": true, + "nni_support_gate": true, + "nni_batch": false, + "spr_refine": false, + "spr_reads_per_pass": 128, + "spr_min_clade": 10, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R1/test_4x2+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/A-III/R1/test_4x2+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..46a1d72d78587e6244f4906ea7b49bcb4ca2cbc8 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R1/test_4x2+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R1/test_4x2+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/wQFM-turbo/datasets/normalized/astral3_2000/2k.01.full.genes.nwk -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R1/test_4x2+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R1/test_4x2+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/astral3-2000/R1/test_4x2+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R1/test_4x2+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/A-III/R1/test_4x2+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..68e0c1f0338a689fb8cb379b3d0c0dd2e87d27ca --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R1/test_4x2+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 2001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R2/balanced+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/A-III/R2/balanced+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..99e083dc1b4e94be9e59ffe12ed9830affc709f5 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R2/balanced+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R2/balanced+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/wQFM-turbo/datasets/normalized/astral3_2000/2k.02.full.genes.nwk -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R2/balanced+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R2/balanced+none.base.json --no-nni --divide-score balanced diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R2/balanced+none.base.json b/runs/local-2026-10-21-ablation/idcheck/A-III/R2/balanced+none.base.json new file mode 100644 index 0000000000000000000000000000000000000000..7f37188e2b7ff35af4ff605d93b4eceee49b888f --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R2/balanced+none.base.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 2001, + "workers": 8, + "progress": "off", + "divide": true, + "divide_score": "balanced", + "bipartition_test": true, + "bipartition_test_available": true, + "bipartition_test_complete_genes": true, + "bipartition_test_coefficient": 0.05, + "bipartition_test_crossover": 10000, + "bipartition_test_proposals": 1, + "bipartition_test_anchor_pairs": 1, + "bipartition_test_threshold": -2.56854, + "regraft_score": "raw", + "nni": false, + "nni_move_cap": true, + "nni_support_gate": true, + "nni_batch": false, + "spr_refine": false, + "spr_reads_per_pass": 128, + "spr_min_clade": 10, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R2/balanced+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/A-III/R2/balanced+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..cb6abeac209e00a91047fc770e67bb26d4241732 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R2/balanced+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R2/balanced+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/wQFM-turbo/datasets/normalized/astral3_2000/2k.02.full.genes.nwk -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R2/balanced+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R2/balanced+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/astral3-2000/R2/balanced+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R2/balanced+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/A-III/R2/balanced+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..13c7347d0f1de356148b188f174a2788131e3241 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R2/balanced+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 2001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R2/default+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/A-III/R2/default+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..e99c73e57d3ba22b3a265974d188868dce24ea1e --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R2/default+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R2/default+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/wQFM-turbo/datasets/normalized/astral3_2000/2k.02.full.genes.nwk -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R2/default+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R2/default+none.base.json --no-nni diff --git 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diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R2/default+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/A-III/R2/default+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..f84df92048e32085ef7bebda816f29ed4e54aace --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R2/default+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R2/default+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/wQFM-turbo/datasets/normalized/astral3_2000/2k.02.full.genes.nwk -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R2/default+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R2/default+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/astral3-2000/R2/default+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R2/default+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/A-III/R2/default+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..557861ea327f2bf7ec26ae57fb453d2bc436f7d7 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R2/default+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 2001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R2/default+rel.full.cmd b/runs/local-2026-10-21-ablation/idcheck/A-III/R2/default+rel.full.cmd new file mode 100644 index 0000000000000000000000000000000000000000..8537634100954893562388c083f89886fe25d3a4 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R2/default+rel.full.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R2/default+rel.full.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/wQFM-turbo/datasets/normalized/astral3_2000/2k.02.full.genes.nwk -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R2/default+rel.full.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R2/default+rel.full.json diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R2/default+rel.full.json b/runs/local-2026-10-21-ablation/idcheck/A-III/R2/default+rel.full.json new file mode 100644 index 0000000000000000000000000000000000000000..bc7c75089dc1e4d4e531cd4514ffcf38621522ae --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R2/default+rel.full.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 2001, + "workers": 8, + "progress": "off", + "divide": true, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": true, + "bipartition_test_complete_genes": true, + "bipartition_test_coefficient": 0.05, + "bipartition_test_crossover": 10000, + "bipartition_test_proposals": 1, + "bipartition_test_anchor_pairs": 1, + "bipartition_test_threshold": -2.56854, + "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, 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diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R2/mre+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/A-III/R2/mre+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..9e367b52177c444c41045a6bf4e74d7b04054976 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R2/mre+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R2/mre+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/wQFM-turbo/datasets/normalized/astral3_2000/2k.02.full.genes.nwk -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R2/mre+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R2/mre+none.base.json --no-nni --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R2/mre+none.base.json b/runs/local-2026-10-21-ablation/idcheck/A-III/R2/mre+none.base.json new file mode 100644 index 0000000000000000000000000000000000000000..b483bf1c46d9a8a0e3dce4aa698094cade61ad31 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R2/mre+none.base.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 2001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R2/mre+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/A-III/R2/mre+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..0831a1ee9002bc891ae3f4123961e8081007cd75 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R2/mre+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R2/mre+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/wQFM-turbo/datasets/normalized/astral3_2000/2k.02.full.genes.nwk -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R2/mre+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R2/mre+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/astral3-2000/R2/mre+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R2/mre+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/A-III/R2/mre+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..68f4ed2435d1cdfdf125af8a41c436d300116155 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R2/mre+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 2001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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": 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diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R2/mre_nni_div+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/A-III/R2/mre_nni_div+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..46941103270c7204a46ccee8ef9ea8fd95db5c41 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R2/mre_nni_div+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R2/mre_nni_div+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/wQFM-turbo/datasets/normalized/astral3_2000/2k.02.full.genes.nwk -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R2/mre_nni_div+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R2/mre_nni_div+none.base.json --no-nni --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/astral3-2000/R2/mre+rel.tre diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R2/mre_nni_div+none.base.json b/runs/local-2026-10-21-ablation/idcheck/A-III/R2/mre_nni_div+none.base.json new file mode 100644 index 0000000000000000000000000000000000000000..9f0d7e028388a89e0e7c5619915b0e1cfe3e9782 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R2/mre_nni_div+none.base.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 2001, + "workers": 8, + "progress": "off", + "divide": true, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": true, + "bipartition_test_complete_genes": true, + "bipartition_test_coefficient": 0.05, + "bipartition_test_crossover": 10000, + "bipartition_test_proposals": 1, + "bipartition_test_anchor_pairs": 1, + "bipartition_test_threshold": -2.56854, + "regraft_score": "raw", + "nni": false, + "nni_move_cap": true, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R2/mre_nni_div+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/A-III/R2/mre_nni_div+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..406b76a5f8794ce6112444615f2abdb3fceced15 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R2/mre_nni_div+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R2/mre_nni_div+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/wQFM-turbo/datasets/normalized/astral3_2000/2k.02.full.genes.nwk -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R2/mre_nni_div+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R2/mre_nni_div+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/astral3-2000/R2/mre_nni_div+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R2/mre_nni_div+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/A-III/R2/mre_nni_div+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..d96b76dfbd5061ba2de7b09d432110bd397034fa --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R2/mre_nni_div+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 2001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R2/no_test+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/A-III/R2/no_test+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..74d0342f5697167f0b3c92852eac674f0d1cb672 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R2/no_test+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R2/no_test+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/wQFM-turbo/datasets/normalized/astral3_2000/2k.02.full.genes.nwk -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R2/no_test+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R2/no_test+none.base.json --no-nni --no-bipartition-test diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R2/no_test+none.base.json b/runs/local-2026-10-21-ablation/idcheck/A-III/R2/no_test+none.base.json new file mode 100644 index 0000000000000000000000000000000000000000..7af067eae10b6424f03ce3bd1e5284162338ed31 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R2/no_test+none.base.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 2001, + "workers": 8, + "progress": "off", + "divide": true, + "divide_score": "quartet", + "bipartition_test": false, + "bipartition_test_available": false, + "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": false, + "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": 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diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R2/no_test+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/A-III/R2/no_test+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..26d72adfe55102a12d23d4cc119d9b81942bbe53 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R2/no_test+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R2/no_test+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/wQFM-turbo/datasets/normalized/astral3_2000/2k.02.full.genes.nwk -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R2/no_test+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R2/no_test+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/astral3-2000/R2/no_test+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R2/no_test+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/A-III/R2/no_test+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..2e18998710f02412f0c4d7fc67c66d91ee0ccb5d --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R2/no_test+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 2001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R2/regraft_norm+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/A-III/R2/regraft_norm+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..ef1d7860f6c3a5122ecd20b7ec9064a293cdf712 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R2/regraft_norm+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R2/regraft_norm+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/wQFM-turbo/datasets/normalized/astral3_2000/2k.02.full.genes.nwk -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R2/regraft_norm+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R2/regraft_norm+none.base.json --no-nni --regraft-score normalized diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R2/regraft_norm+none.base.json b/runs/local-2026-10-21-ablation/idcheck/A-III/R2/regraft_norm+none.base.json new file mode 100644 index 0000000000000000000000000000000000000000..1c50629c8afa7351c60e2dfcb45f689c3e45842d --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R2/regraft_norm+none.base.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 2001, + "workers": 8, + "progress": "off", + "divide": true, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": true, + "bipartition_test_complete_genes": true, + "bipartition_test_coefficient": 0.05, + "bipartition_test_crossover": 10000, + "bipartition_test_proposals": 1, + "bipartition_test_anchor_pairs": 1, + "bipartition_test_threshold": -2.56854, + "regraft_score": "normalized", + "nni": false, + "nni_move_cap": true, + "nni_support_gate": true, + "nni_batch": false, + "spr_refine": false, + "spr_reads_per_pass": 128, 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diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R2/regraft_norm+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/A-III/R2/regraft_norm+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..c1cf37da74b01ce2b8267c5238cac8f3269acb54 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R2/regraft_norm+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R2/regraft_norm+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/wQFM-turbo/datasets/normalized/astral3_2000/2k.02.full.genes.nwk -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R2/regraft_norm+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R2/regraft_norm+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/astral3-2000/R2/regraft_norm+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R2/regraft_norm+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/A-III/R2/regraft_norm+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..4ad074840fd08c14f27b7543f86feca522d2cdac --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R2/regraft_norm+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 2001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R2/test_4x2+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/A-III/R2/test_4x2+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..6c52eab4bcd7c6fdcae9cb7a38b5e522660509f0 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R2/test_4x2+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R2/test_4x2+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/wQFM-turbo/datasets/normalized/astral3_2000/2k.02.full.genes.nwk -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R2/test_4x2+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R2/test_4x2+none.base.json --no-nni --test-proposals 4 --test-anchor-pairs 2 diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R2/test_4x2+none.base.json b/runs/local-2026-10-21-ablation/idcheck/A-III/R2/test_4x2+none.base.json new file mode 100644 index 0000000000000000000000000000000000000000..e2cc786d2a6ce57df2c4becedc05399da2087c7f --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R2/test_4x2+none.base.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 2001, + "workers": 8, + "progress": "off", + "divide": true, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": true, + "bipartition_test_complete_genes": true, + "bipartition_test_coefficient": 0.05, + "bipartition_test_crossover": 10000, + "bipartition_test_proposals": 4, + "bipartition_test_anchor_pairs": 2, + "bipartition_test_threshold": -2.56854, + "regraft_score": "raw", + "nni": false, + "nni_move_cap": true, + "nni_support_gate": true, + "nni_batch": false, + "spr_refine": false, + "spr_reads_per_pass": 128, + "spr_min_clade": 10, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R2/test_4x2+rel.chain.cmd b/runs/local-2026-10-21-ablation/idcheck/A-III/R2/test_4x2+rel.chain.cmd new file mode 100644 index 0000000000000000000000000000000000000000..3e5d54518eb855cd81504c30f247b0c1233b0c16 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R2/test_4x2+rel.chain.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R2/test_4x2+rel.chain.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/wQFM-turbo/datasets/normalized/astral3_2000/2k.02.full.genes.nwk -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R2/test_4x2+rel.chain.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R2/test_4x2+rel.chain.json --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/astral3-2000/R2/test_4x2+none.tre --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R2/test_4x2+rel.chain.json b/runs/local-2026-10-21-ablation/idcheck/A-III/R2/test_4x2+rel.chain.json new file mode 100644 index 0000000000000000000000000000000000000000..b4b332676031db27a7004673b6beab929200d9dd --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R2/test_4x2+rel.chain.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 2001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R3/mre+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/A-III/R3/mre+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..e11f9ab4dc0920dd32a2ecaa715baeba55613172 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R3/mre+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R3/mre+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/wQFM-turbo/datasets/normalized/astral3_2000/2k.03.full.genes.nwk -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R3/mre+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R3/mre+none.base.json --no-nni --no-divide diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R3/mre+none.base.json b/runs/local-2026-10-21-ablation/idcheck/A-III/R3/mre+none.base.json new file mode 100644 index 0000000000000000000000000000000000000000..7ab2ea369f557d21cadb81ff0909e85e1964bf35 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R3/mre+none.base.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 2001, + "workers": 8, + "progress": "off", + "divide": false, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": false, + "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": false, + "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, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R3/mre_nni_div+none.base.cmd b/runs/local-2026-10-21-ablation/idcheck/A-III/R3/mre_nni_div+none.base.cmd new file mode 100644 index 0000000000000000000000000000000000000000..87882ed6071170d189380b93a66b5da83abc65e0 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R3/mre_nni_div+none.base.cmd @@ -0,0 +1 @@ +/usr/bin/time -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R3/mre_nni_div+none.base.time -f %e,%M nice -n 10 /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/bin/qraft -i /home/risenfromashes/Documents/code/wQFM-turbo/datasets/normalized/astral3_2000/2k.03.full.genes.nwk -o /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R3/mre_nni_div+none.base.tre -t 8 --no-progress --stats-json /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/idcheck/A-III/R3/mre_nni_div+none.base.json --no-nni --starting-tree /home/risenfromashes/Documents/code/qraft-results-update/phase2/e1/stored-texas-full/astral3-2000/R3/mre+rel.tre diff --git a/runs/local-2026-10-21-ablation/idcheck/A-III/R3/mre_nni_div+none.base.json b/runs/local-2026-10-21-ablation/idcheck/A-III/R3/mre_nni_div+none.base.json new file mode 100644 index 0000000000000000000000000000000000000000..f4586bb95bf57bb8c4d52a5fb34ae25732570728 --- /dev/null +++ b/runs/local-2026-10-21-ablation/idcheck/A-III/R3/mre_nni_div+none.base.json @@ -0,0 +1,151 @@ +{ + "genes": 1000, + "taxa": 2001, + "workers": 8, + "progress": "off", + "divide": true, + "divide_score": "quartet", + "bipartition_test": true, + "bipartition_test_available": true, + "bipartition_test_complete_genes": true, + "bipartition_test_coefficient": 0.05, + "bipartition_test_crossover": 10000, + "bipartition_test_proposals": 1, + "bipartition_test_anchor_pairs": 1, + "bipartition_test_threshold": -2.56854, + "regraft_score": "raw", + "nni": false, + "nni_move_cap": true, + 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diff --git a/runs/local-2026-10-21-ablation/idcheck/idcheck.csv b/runs/local-2026-10-21-ablation/idcheck/idcheck.csv index 7afd0e4f80abaded9f82117c7982653ae7f26a8b..b14527a64c01d2fce51ac9a220db24ef17ae3774 100644 --- a/runs/local-2026-10-21-ablation/idcheck/idcheck.csv +++ b/runs/local-2026-10-21-ablation/idcheck/idcheck.csv @@ -651,3 +651,405 @@ A-II,46,astral2/model.200.500000.0.000001/estimated/R46,balanced+none,base,0,1.3 A-II,46,astral2/model.200.500000.0.000001/estimated/R46,no_test+none,base,0,3.34,94180,1c026a321438d3581cb205ea6865da46e3a3378dd6b4b8a06b8649218c343439,1c026a321438d3581cb205ea6865da46e3a3378dd6b4b8a06b8649218c343439,1,,,,0,8 A-II,46,astral2/model.200.500000.0.000001/estimated/R46,regraft_norm+none,base,0,2.75,97608,32e1463af49b19a36c4a84866590f146b7755d57e7bb5c76f3e59cc3d9516c7d,32e1463af49b19a36c4a84866590f146b7755d57e7bb5c76f3e59cc3d9516c7d,1,,,,0,8 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+A-II,50,astral2/model.200.500000.0.000001/estimated/R50,regraft_norm+rel,chain,0,0.22,86756,4ffbd193f16d1052e3d70fe81278d71f87fdefe5f3d27f9ec452d9dc6a8e4a70,4ffbd193f16d1052e3d70fe81278d71f87fdefe5f3d27f9ec452d9dc6a8e4a70,1,,,,6,8 +A-II,50,astral2/model.200.500000.0.000001/estimated/R50,test_4x2+rel,chain,0,0.22,90180,4ffbd193f16d1052e3d70fe81278d71f87fdefe5f3d27f9ec452d9dc6a8e4a70,4ffbd193f16d1052e3d70fe81278d71f87fdefe5f3d27f9ec452d9dc6a8e4a70,1,,,,6,8 +1KP,0,1kp/Best.33.FAA,default+none,base,0,2.37,123096,cf535aaf0d69c763ecd458c0eccdc12101902c3e3f0c3eb5d3fec8b4343c5fda,cf535aaf0d69c763ecd458c0eccdc12101902c3e3f0c3eb5d3fec8b4343c5fda,1,cf535aaf0d69c763ecd458c0eccdc12101902c3e3f0c3eb5d3fec8b4343c5fda,1,,0,8 +1KP,0,1kp/Best.33.FAA,mre+none,base,0,0.18,125620,6f37af8d540f6354679ead53b8cfc78be73da4a031dba6559892ccd7b2888e6c,6f37af8d540f6354679ead53b8cfc78be73da4a031dba6559892ccd7b2888e6c,1,6f37af8d540f6354679ead53b8cfc78be73da4a031dba6559892ccd7b2888e6c,1,,0,8 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+1KP,0,1kp/Best.33.FAA,regraft_norm+none,base,0,2.37,123236,6ed11cdb720a7c2819e06262dc4014609b32182da7150ce016e8bdd39b21d8b6,6ed11cdb720a7c2819e06262dc4014609b32182da7150ce016e8bdd39b21d8b6,1,6ed11cdb720a7c2819e06262dc4014609b32182da7150ce016e8bdd39b21d8b6,1,,0,8 +1KP,0,1kp/Best.33.FAA,test_4x2+none,base,0,2.42,124520,cf535aaf0d69c763ecd458c0eccdc12101902c3e3f0c3eb5d3fec8b4343c5fda,cf535aaf0d69c763ecd458c0eccdc12101902c3e3f0c3eb5d3fec8b4343c5fda,1,cf535aaf0d69c763ecd458c0eccdc12101902c3e3f0c3eb5d3fec8b4343c5fda,1,,0,8 +1KP,0,1kp/Best.33.FAA,default+rel,full,0,2.70,127436,1eeacbf05c53f10e1d2f1d65d4d85285aa69d7d2d407a9c93b89df5b1da1dc01,1eeacbf05c53f10e1d2f1d65d4d85285aa69d7d2d407a9c93b89df5b1da1dc01,1,1eeacbf05c53f10e1d2f1d65d4d85285aa69d7d2d407a9c93b89df5b1da1dc01,1,,12,8 +1KP,0,1kp/Best.33.FAA,default+rel,chain,0,0.36,96140,1eeacbf05c53f10e1d2f1d65d4d85285aa69d7d2d407a9c93b89df5b1da1dc01,1eeacbf05c53f10e1d2f1d65d4d85285aa69d7d2d407a9c93b89df5b1da1dc01,1,1eeacbf05c53f10e1d2f1d65d4d85285aa69d7d2d407a9c93b89df5b1da1dc01,1,,12,8 +1KP,0,1kp/Best.33.FAA,mre+rel,chain,0,0.38,97216,dceb2b319f12f82e53f871653c62634c0f27627ac14ef13a2c8230b3ae3c0dde,dceb2b319f12f82e53f871653c62634c0f27627ac14ef13a2c8230b3ae3c0dde,1,dceb2b319f12f82e53f871653c62634c0f27627ac14ef13a2c8230b3ae3c0dde,1,,14,8 +1KP,0,1kp/Best.33.FAA,mre_nni_div+rel,chain,0,0.39,99792,da5fe6b63952f6366990c6ca84b80990c88e4459a195205c382e78bd17ad7482,da5fe6b63952f6366990c6ca84b80990c88e4459a195205c382e78bd17ad7482,1,da5fe6b63952f6366990c6ca84b80990c88e4459a195205c382e78bd17ad7482,1,,20,8 +1KP,0,1kp/Best.33.FAA,balanced+rel,chain,0,0.41,96188,6ec1cb12f5066a10849568377a57b544463e3ace8431f22a9d18ac4db9166b81,6ec1cb12f5066a10849568377a57b544463e3ace8431f22a9d18ac4db9166b81,1,6ec1cb12f5066a10849568377a57b544463e3ace8431f22a9d18ac4db9166b81,1,,20,8 +1KP,0,1kp/Best.33.FAA,no_test+rel,chain,0,0.37,102340,1eeacbf05c53f10e1d2f1d65d4d85285aa69d7d2d407a9c93b89df5b1da1dc01,1eeacbf05c53f10e1d2f1d65d4d85285aa69d7d2d407a9c93b89df5b1da1dc01,1,1eeacbf05c53f10e1d2f1d65d4d85285aa69d7d2d407a9c93b89df5b1da1dc01,1,,12,8 +1KP,0,1kp/Best.33.FAA,regraft_norm+rel,chain,0,0.36,99468,6bf8b0679b40e05f3e0d963d58bf8b6a1119e747d2efcf94e4f1feb8e9f2528b,6bf8b0679b40e05f3e0d963d58bf8b6a1119e747d2efcf94e4f1feb8e9f2528b,1,6bf8b0679b40e05f3e0d963d58bf8b6a1119e747d2efcf94e4f1feb8e9f2528b,1,,13,8 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+1000,1,1000-taxon/estimated/R1,balanced+none,base,0,4.37,239668,f67e61edc941bf82bdb1a57842b3c7b792f1b00adcdd16c98ad74c2db3e94895,f67e61edc941bf82bdb1a57842b3c7b792f1b00adcdd16c98ad74c2db3e94895,1,,,,0,8 +1000,1,1000-taxon/estimated/R1,no_test+none,base,0,8.49,237932,ba76e77ea4b287f79ff80a06519ed13bf3dcda70533023f1a097bea347975d40,ba76e77ea4b287f79ff80a06519ed13bf3dcda70533023f1a097bea347975d40,1,,,,0,8 +1000,1,1000-taxon/estimated/R1,regraft_norm+none,base,0,6.92,247876,0a9b225d202a1625beaba8f6e1aaee18d88f9a1759efd5de712103016d3021f9,0a9b225d202a1625beaba8f6e1aaee18d88f9a1759efd5de712103016d3021f9,1,,,,0,8 +1000,1,1000-taxon/estimated/R1,test_4x2+none,base,0,6.99,251436,ba76e77ea4b287f79ff80a06519ed13bf3dcda70533023f1a097bea347975d40,ba76e77ea4b287f79ff80a06519ed13bf3dcda70533023f1a097bea347975d40,1,,,,0,8 +1000,1,1000-taxon/estimated/R1,default+rel,full,0,7.59,246316,26b61779361599ec9c3a3db98308b18840350de0a6c3c31e82046e2144d9a7f0,26b61779361599ec9c3a3db98308b18840350de0a6c3c31e82046e2144d9a7f0,1,,,,1,8 +1000,1,1000-taxon/estimated/R1,default+rel,chain,0,0.79,215408,26b61779361599ec9c3a3db98308b18840350de0a6c3c31e82046e2144d9a7f0,26b61779361599ec9c3a3db98308b18840350de0a6c3c31e82046e2144d9a7f0,1,,,,1,8 +1000,1,1000-taxon/estimated/R1,mre+rel,chain,0,0.87,210744,65c2fd425e4d95252902503b4ca0ea58e297e0b12f6f5b23b1bb38d5ab5c3858,65c2fd425e4d95252902503b4ca0ea58e297e0b12f6f5b23b1bb38d5ab5c3858,1,,,,5,8 +1000,1,1000-taxon/estimated/R1,mre_nni_div+rel,chain,0,0.78,211224,26b61779361599ec9c3a3db98308b18840350de0a6c3c31e82046e2144d9a7f0,26b61779361599ec9c3a3db98308b18840350de0a6c3c31e82046e2144d9a7f0,1,,,,1,8 +1000,1,1000-taxon/estimated/R1,balanced+rel,chain,0,1.02,225488,5dc970a7abaa241c94c71f0d40ccf8e449f69c1baa093fb7f822006db76e9a7a,5dc970a7abaa241c94c71f0d40ccf8e449f69c1baa093fb7f822006db76e9a7a,1,,,,11,8 +1000,1,1000-taxon/estimated/R1,no_test+rel,chain,0,0.79,221564,26b61779361599ec9c3a3db98308b18840350de0a6c3c31e82046e2144d9a7f0,26b61779361599ec9c3a3db98308b18840350de0a6c3c31e82046e2144d9a7f0,1,,,,1,8 +1000,1,1000-taxon/estimated/R1,regraft_norm+rel,chain,0,0.77,221932,0a9b225d202a1625beaba8f6e1aaee18d88f9a1759efd5de712103016d3021f9,0a9b225d202a1625beaba8f6e1aaee18d88f9a1759efd5de712103016d3021f9,1,,,,0,8 +1000,1,1000-taxon/estimated/R1,test_4x2+rel,chain,0,0.82,223024,26b61779361599ec9c3a3db98308b18840350de0a6c3c31e82046e2144d9a7f0,26b61779361599ec9c3a3db98308b18840350de0a6c3c31e82046e2144d9a7f0,1,,,,1,8 +1000,2,1000-taxon/estimated/R2,default+none,base,0,10.88,263768,00a513c3b082cf5ccb8f153de441f313844f03405158df638130475d9e7fe62b,00a513c3b082cf5ccb8f153de441f313844f03405158df638130475d9e7fe62b,1,,,,0,8 +1000,2,1000-taxon/estimated/R2,mre+none,base,0,0.70,257340,2fff4a820519423f0be0157e3c7d1374dce0a9a38535d0e037a36df6e6d552b8,2fff4a820519423f0be0157e3c7d1374dce0a9a38535d0e037a36df6e6d552b8,1,,,,0,8 +1000,2,1000-taxon/estimated/R2,mre_nni_div+none,base,0,10.21,269784,00a513c3b082cf5ccb8f153de441f313844f03405158df638130475d9e7fe62b,00a513c3b082cf5ccb8f153de441f313844f03405158df638130475d9e7fe62b,1,,,,0,8 +1000,2,1000-taxon/estimated/R2,balanced+none,base,0,7.79,271524,5140a0030b4d271cea9397aacf4a48a3da278d707aaec5a564d77f2fb35721d8,5140a0030b4d271cea9397aacf4a48a3da278d707aaec5a564d77f2fb35721d8,1,,,,0,8 +1000,2,1000-taxon/estimated/R2,no_test+none,base,0,13.94,255592,00a513c3b082cf5ccb8f153de441f313844f03405158df638130475d9e7fe62b,00a513c3b082cf5ccb8f153de441f313844f03405158df638130475d9e7fe62b,1,,,,0,8 +1000,2,1000-taxon/estimated/R2,regraft_norm+none,base,0,11.02,260664,00a513c3b082cf5ccb8f153de441f313844f03405158df638130475d9e7fe62b,00a513c3b082cf5ccb8f153de441f313844f03405158df638130475d9e7fe62b,1,,,,0,8 +1000,2,1000-taxon/estimated/R2,test_4x2+none,base,0,10.89,260120,00a513c3b082cf5ccb8f153de441f313844f03405158df638130475d9e7fe62b,00a513c3b082cf5ccb8f153de441f313844f03405158df638130475d9e7fe62b,1,,,,0,8 +1000,2,1000-taxon/estimated/R2,default+rel,full,0,12.04,259404,f9d23b3c9a275cc475fd8073b296eee19f1d2f0d7cd13283052ec426a89549b4,f9d23b3c9a275cc475fd8073b296eee19f1d2f0d7cd13283052ec426a89549b4,1,,,,10,8 +1000,2,1000-taxon/estimated/R2,default+rel,chain,0,1.22,219312,f9d23b3c9a275cc475fd8073b296eee19f1d2f0d7cd13283052ec426a89549b4,f9d23b3c9a275cc475fd8073b296eee19f1d2f0d7cd13283052ec426a89549b4,1,,,,10,8 +1000,2,1000-taxon/estimated/R2,mre+rel,chain,0,0.94,224632,3e37d1408a61022dd7c21bfe32145e719b421abbf7615df230fe7cac80071c8f,3e37d1408a61022dd7c21bfe32145e719b421abbf7615df230fe7cac80071c8f,1,,,,2,8 +1000,2,1000-taxon/estimated/R2,mre_nni_div+rel,chain,0,1.26,214724,f9d23b3c9a275cc475fd8073b296eee19f1d2f0d7cd13283052ec426a89549b4,f9d23b3c9a275cc475fd8073b296eee19f1d2f0d7cd13283052ec426a89549b4,1,,,,10,8 +1000,2,1000-taxon/estimated/R2,balanced+rel,chain,0,1.59,210112,f9537756e3a16b51cc28c4bb891f76e95dbe74ae83aecd358aa4db539c79c92c,f9537756e3a16b51cc28c4bb891f76e95dbe74ae83aecd358aa4db539c79c92c,1,,,,20,8 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